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Directed assembly of discrete gold nanoparticle groupings usingbranched DNA scaffolds
The concept of self-assembled dendrimers is explored for the creation of discrete nanoparticle assemblies. Hybridization of branched DNA trimers and nanoparticle-DNA conjugates results in the synthesis of nanoparticle trimer and tetramer complexes. Multiple tetramer architectures are investigated, utilizing Au-DNA conjugates with varying secondary structural motifs. Hybridization products are analyzed by gel electrophoresis, and discrete bands are observed corresponding to structures with increasing numbers of hybridization events. Samples extracted from each band are analyzed by transmission electron microscopy, and statistics compiled from micrographs are used to compare assembly characteristics for each architecture. Asymmetric structures are also produced in which both 5 and 10 nm Au particles are assembled on branched scaffolds.
Claridge, Shelley A.; Goh, Sarah L.; Frechet, Jean M.J.; Williams, Shara C.; Micheel, Christine M.; Alivisatos, A. Paul
DNA and Natural Algorithms Group
NSDL National Science Digital Library
This research group at the California Institute of Technology is studying the capability of DNA and other biomolecules to process information and implement algorithms. A general overview of the group's purpose and motivation is provided, as well as a number of publications.
Polycomb Group Repression Reduces DNA Accessibility
The Polycomb group proteins are responsible for long-term repression of a number of genes in Drosophila melanogaster, including the homeotic genes of the bithorax complex. The Polycomb protein is thought to alter the chromatin structure of its target genes, but there has been little direct evidence for this model. In this study, the chromatin structure of the bithorax complex was probed with three separate assays for DNA accessibility: (i) activation of polymerase II (Pol II) transcription by Gal4, (ii) transcription by the bacteriophage T7 RNA polymerase (T7RNAP), and (iii) FLP-mediated site-specific recombination. All three processes are restricted or blocked in Polycomb-repressed segments. In contrast, control test sites outside of the bithorax complex permitted Gal4, T7RNAP, and FLP activities throughout the embryo. Several P insertions in the bithorax complex were tested, providing evidence that the Polycomb-induced effect is widespread over target genes. This accessibility effect is similar to that seen for SIR silencing in Saccharomyces cerevisiae. In contrast to SIR silencing, however, episomes excised from Polycomb-repressed chromosomal sites do not show an altered superhelix density. PMID:11533246
Fitzgerald, Daniel P.; Bender, Welcome
Pyrophosphate Groups in Liquid Crystalline Phases of the DNA
We study electrostatic interaction between molecules of the DNA in which a number of phosphate groups of the sugar-phosphate backbone are exchanged for the pyrophosphate ones. We employ a model in which the DNA is considered as a one-dimensional lattice of dipoles and charges corresponding to base pairs and (pyro)phosphate groups, respectively. The interaction between molecules of the DNA is described by a pair potential $U$ of electrostatic forces between the two sets of dipoles and charges belonging to respective lattices describing the molecules. Minima of potential $U$ indicate orientational ordering of the molecules and thus liquid crystalline phases of the DNA. We use numerical methods for finding the set of minima in conjunction with symmetries verified by potential $U$. The symmetries form a noncommutative group of 8-th order, ${\\cal S}$. Using the group ${\\cal S}$ we suggest a classification of liquid crystalline phases of the DNA, which allows of several cholesteric phases, that is polymorphism. Pyrophosphate forms of the DNA could clarify the part played by charges in its liquid crystalline phases, and make for experimental research, important for nano-technological and bio-medical applications.
V. L. Golo; E. I. Kats; S. A. Kuznetsova; Yu. S. Volkov
Finding human promoter groups based on DNA physical properties
NASA Astrophysics Data System (ADS)
DNA rigidity is an important physical property originating from the DNA three-dimensional structure. Although the general DNA rigidity patterns in human promoters have been investigated, their distinct roles in transcription are largely unknown. In this paper, we discover four highly distinct human promoter groups based on similarity of their rigidity profiles. First, we find that all promoter groups conserve relatively rigid DNAs at the canonical TATA box [a consensus TATA(A/T)A(A/T) sequence] position, which are important physical signals in binding transcription factors. Second, we find that the genes activated by each group of promoters share significant biological functions based on their gene ontology annotations. Finally, we find that these human promoter groups correlate with the tissue-specific gene expression.
Zeng, Jia; Cao, Xiao-Qin; Zhao, Hongya; Yan, Hong
Renormalization Group Limit Cycle for Three-Stranded DNA
We show that there exists an Efimov-like three strand DNA bound state at the duplex melting point and it is described by a renormalization group limit cycle. A nonperturbative RG is used to obtain this result in a model involving short range pairing only. Our results suggest that Efimov physics can be tested in polymeric systems.
Tanmoy Pal; Poulomi Sadhukhan; Somendra M. Bhattacharjee
Indirect Readout of DNA Sequence by P22 Repressor: Roles of DNA and Protein Functional Groups in
Indirect Readout of DNA Sequence by P22 Repressor: Roles of DNA and Protein Functional Groups site. The "indirect readout" of these non- contacted bases is apparently based on DNA's sequence of P22R to impose structural changes on DNA and to recognize non-contacted base sequence
Williams, Loren
Mitochondrial DNA evolution in the Anaxyrus boreas species group.
The Anaxyrus boreas species group currently comprises four species in western North America including the broadly distributed A. boreas, and three localized species, Anaxyrus nelsoni, Anaxyrusexsul and Anaxyrus canorus. Phylogenetic analyses of the mtDNA 12S rDNA, cytochrome oxidase I, control region, and restriction sites data, identified three major haplotype clades. The Northwest clade (NW) includes both subspecies of A. boreas and divergent minor clades in the middle Rocky Mountains, coastal, and central regions of the west and Pacific Northwest. The Southwest (SW) clade includes A. exsul, A. nelsoni, and minor clades in southern California. Anaxyrus canorus, previously identified as paraphyletic, has populations in both the NW and SW major clades. The Eastern major clade (E) includes three divergent lineages from southern Utah, the southern Rocky Mountains, and north of the Great Basin at the border of Utah and Nevada. These results identify new genetic variation in the eastern portion of the toad's range and are consistent with previous regional studies from the west coast. Low levels of control region sequence divergence between major clades (2.2-4.7% uncorrected pair-wise distances) are consistent with Pleistocene divergence and suggest that the phylogeographic history of the group was heavily influenced by dynamic Pleistocene glacial and climatic changes, and especially pluvial changes, in western North America. Results reported here may impact conservation plans in that the current taxonomy does not reflect the diversity in the group. PMID:18662792
Goebel, Anna M; Ranker, Tom A; Corn, Paul Stephen; Olmstead, Richard G
Mitochondrial DNA evolution in the Anaxyrus boreas species group
The Anaxyrus boreas species group currently comprises four species in western North America including the broadly distributed A. boreas, and three localized species, Anaxyrus nelsoni, Anaxyrus exsul and Anaxyrus canorus. Phylogenetic analyses of the mtDNA 12S rDNA, cytochrome oxidase I, control region, and restriction sites data, identified three major haplotype clades. The Northwest clade (NW) includes both subspecies of A. boreas and divergent minor clades in the middle Rocky Mountains, coastal, and central regions of the west and Pacific Northwest. The Southwest (SW) clade includes A. exsul, A. nelsoni, and minor clades in southern California. Anaxyrus canorus, previously identified as paraphyletic, has populations in both the NW and SW major clades. The Eastern major clade (E) includes three divergent lineages from southern Utah, the southern Rocky Mountains, and north of the Great Basin at the border of Utah and Nevada. These results identify new genetic variation in the eastern portion of the toad's range and are consistent with previous regional studies from the west coast. Low levels of control region sequence divergence between major clades (2.2-4.7% uncorrected pair-wise distances) are consistent with Pleistocene divergence and suggest that the phylogeographic history of the group was heavily influenced by dynamic Pleistocene glacial and climatic changes, and especially pluvial changes, in western North America. Results reported here may impact conservation plans in that the current taxonomy does not reflect the diversity in the group. ?? 2008 Elsevier Inc.
Goebel, A.M.; Ranker, T.A.; Corn, P.S.; Olmstead, R.G.
A Fuzzy Classifier to Taxonomically Group DNA Fragments within a Metagenome
for isolation and lab cultivation of individual species [4]. The whole genome(DNA) or metagenome population canA Fuzzy Classifier to Taxonomically Group DNA Fragments within a Metagenome Sara Nasser, Adrienne classifier is used to group shotgun sequence fragments as small as 500 base pairs according to their DNA
Nicolescu, Monica
Mitochondrial DNA variation and Haldane's rule in the Papilio glaucus and P. troilus species groups
Variation in mitochondrial DNA (mtDNA) was surveyed, using restriction endonucleases, in all species of the Papilio glaucus and P. troilus groups (Lepidoptera: Papilionidae). Phylogenetic and distance relationships of mtDNA generally confirmed traditional species limits in the two species groups and compared favourably with a prior survey of their allozymes. The most notable exceptions were P. rutulus and P. eurymedon, which
Genetic Kinship Investigation from Blood Groups to DNA Markers
The forensic application of hereditary characteristics became possible after the discovery of human blood groups by Karl Landsteiner in 1901. The foundation for their use in kinship investigation was laid by Emil von Dungern and Ludwig Hirschfeld in 1910 by clarification of the inheritance of the ABO groups. Up to the middle of the 20th century further red cell membrane systems were discovered. From the 1920s Fritz Schiff and Georg Strassmann fought for the introduction of blood groups into forensic kinship investigation. A new era of hemogenetics was opened from 1955 as genetic polymorphisms were described in serum proteins. Starting in 1958 there followed the complex HLA system of white blood cells, which from 1963 was joined by polymophisms in erythrocyte enzymes. Therefore, from the 1980s, it was possible to clarify the majority of kinship cases with a combination of conventional markers. From 1990 to 2000 the conventional markers were gradually replaced by the more effective DNA markers. Simultaneously typing shifted from the phenotype level to the genotype level. The genomic structure of conventional genetic markers could also now be explained. As a reflection of scientific progress the legal situation also changed, particularly in the form of the official guidelines for kinship investigation. PMID:22851931
Geserick, Gunther; Wirth, Ingo
Genetic Kinship Investigation from Blood Groups to DNA Markers.
The forensic application of hereditary characteristics became possible after the discovery of human blood groups by Karl Landsteiner in 1901. The foundation for their use in kinship investigation was laid by Emil von Dungern and Ludwig Hirschfeld in 1910 by clarification of the inheritance of the ABO groups. Up to the middle of the 20th century further red cell membrane systems were discovered. From the 1920s Fritz Schiff and Georg Strassmann fought for the introduction of blood groups into forensic kinship investigation. A new era of hemogenetics was opened from 1955 as genetic polymorphisms were described in serum proteins. Starting in 1958 there followed the complex HLA system of white blood cells, which from 1963 was joined by polymophisms in erythrocyte enzymes. Therefore, from the 1980s, it was possible to clarify the majority of kinship cases with a combination of conventional markers. From 1990 to 2000 the conventional markers were gradually replaced by the more effective DNA markers. Simultaneously typing shifted from the phenotype level to the genotype level. The genomic structure of conventional genetic markers could also now be explained. As a reflection of scientific progress the legal situation also changed, particularly in the form of the official guidelines for kinship investigation. PMID:22851931
Geserick, Gunther; Wirth, Ingo
2006 Nature Publishing Group The information content in a given length of DNA is
axis of DNA: rotation about the axis, translation along the axis, translation lateral to the axis© 2006 Nature Publishing Group The information content in a given length of DNA is limited organism is vastly greater in length than the organism itself. The DNA-packaging problem has been well
Nollmann, Marcelo
A Reduced Number of mtSNPs Saturates Mitochondrial DNA Haplotype Diversity of Worldwide Population Groups
BackgroundThe high levels of variation characterising the mitochondrial DNA (mtDNA) molecule are due ultimately to its high average mutation rate; moreover, mtDNA variation is deeply structured in different populations and ethnic groups. There is growing interest in selecting a reduced number of mtDNA single nucleotide polymorphisms (mtSNPs) that account for the maximum level of discrimination power in a given population.
Antonio Salas; Jorge Amigo; Vincent Macaulay
Three different group I introns in the nuclear large subunit ribosomal DNA of the amoeboflagellate Naegleria.
We have amplified the large subunit ribosomal DNA (LSUrDNA) of the 12 described Naegleria spp. and of 34 other Naegleria lineages that might be distinct species. Two strains yielded a product that is longer than 3 kb, which is the length of the LSUrDNA of all described Naegleria spp. Sequencing data revealed that the insert in one of these strains is a group I intron without an open reading frame (ORF), while the other strain contains two different group I introns, of which the second intron has an ORF of 175 amino acids. In the latter ORF there is a conserved His-Cys box, as in the homing endonucleases present in group I introns in the small subunit ribosomal DNA (SSUrDNA) of Naegleria spp. Although the group I introns in the LSUrDNA differ in sequence, they are more related to each other than they are to the group I introns in the SSUrDNA of Naegleria spp. The three group I introns in the LSUrDNA in Naegleria are at different locations and are probably acquired by horizontal transfer, contrary to the SSUrDNA group I introns in this genus which are of ancestral origin and are transmitted vertically. PMID:9421500
De Jonckheere, J F; Brown, S
The Leaving Group Strongly Affects H2O2-Induced DNA Cross-Linking by Arylboronates
We evaluated the effects of the benzylic leaving group and core structure of arylboronates on H2O2-induced formation of bisquinone methides for DNA interstrand cross-linking. The mechanism of DNA cross-linking induced by these arylboronates involves generation of phenol intermediates followed by departure of benzylic leaving group leading to QMs which directly cross-link DNA via alkylation. The QM formation is the rate-determining step for DNA cross-linking. A better leaving group (Br) and stepwise bisquinone methide formation increased interstrand cross-linking efficiency. These findings provide essential guidelines for designing novel anticancer prodrugs. PMID:24378073
Cao, Sheng; Wang, Yibin; Peng, Xiaohua
Hands on Group Work Paper Model for Teaching DNA Structure, Central Dogma and Recombinant DNA
ERIC Educational Resources Information Center
Understanding life on a molecular level is greatly enhanced when students are given the opportunity to visualize the molecules. Especially understanding DNA structure and function is essential for understanding key concepts of molecular biology such as DNA, central dogma and the manipulation of DNA. Researches have shown that undergraduate�
Altiparmak, Melek; Nakiboglu Tezer, Mahmure
Hands on group work paper model for teaching DNA structure, central dogma and recombinant DNA
Understanding life on a molecular level is greatly enhanced when students are given the opportunity to visualize the molecules. Especially understanding DNA structure and function is essential for understanding key concepts of molecular biology such as DNA, central dogma and the manipulation of DNA. Researches have shown that undergraduate students typically lack a coherent view of concepts and their relationships
Melek ALTIPARMAK; Mahmure NAKIBOGLU TEZER
Mitochondrial DNA Haplogroup A may confer a genetic susceptibility to AIDS group from Southwest China.
Abstract The acquired immunodeficiency syndrome (AIDS) in humans was one of the chronic infections caused by human immunodeficiency virus (HIV), and the interactions between viral infection and mitochondrial energetic implicated that mitochondrial DNA (mtDNA) variation(s) may effect genetic susceptibility to AIDS. Thus, to illustrate the maternal genetic structure and further identify whether mtDNA variation(s) can effect HIV infection among southwest Chinese AIDS group, the whole mtDNA control region sequences of 70 AIDS patients and 480 health individuals from southwest China were analyzed here. Our results indicated the plausible recent genetic admixture results of AIDS group; comparison of matrilineal components between AIDS and matched Han groups showed that mtDNA haplogroup A (p?=?0.048, OR?=?3.006, 95% CI?=?1.109-8.145) has a significant higher difference between the two groups; further comparison illustrated that mtDNA mutations 16,209 (p?=?0.046, OR?=?2.607, 95% CI?=?0.988-6.876) and 16,319 (p?=?0.009, OR?=?2.965, 95% CI?=?1.278-6.876) have significant differences between AIDS and matched control groups, and both of which were the defining variations of mtDNA haplogroup A, they further confirmed that mtDNA haplogroup A may confer genetic susceptibility to AIDS. Our results suggested that haplogroup A may confer a genetic susceptibility to AIDS group from Southwest China. PMID:25431816
Wang, Hua-Wei; Xu, Yu; Miao, Ying-Lei; Luo, Hua-You; Wang, Kun-Hua
A DNA barcode for land plants CBOL Plant Working Group1
A DNA barcode for land plants CBOL Plant Working Group1 Communicated by Daniel H. Janzen, University of Pennsylvania, Philadelphia, PA, May 27, 2009 (received for review March 18, 2009) DNA barcoding no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation
Barrett, C.H.
Synthesis of branched DNA using oxidatively cleavable tritylsulfenyl as a hydroxy protecting group.
The application of oxidatively cleavable tritylsulfenyl (TrS) group to the synthesis of branched DNA is described. The TrS protecting group can be removed by treatment with 1�M aqueous iodine, while it is stable toward an oxaziridine-type oxidant. At the same time, the sulfur-oxygen linkage showed sufficient stability under the acidic and basic conditions used in oligonucleotide synthesis. These properties of the TrS group enabled the synthesis of branched DNA using a branched phosphoramidite in which the two hydroxy groups are protected by a 4,4'-dimethoxytrityl (DMTr) group or a TrS group. In this unit, we describe an example of the synthesis of a three-way branched DNA using a branched phosphoramidite. Curr. Protoc. Nucleic Acid Chem. 58:2.18.1-2.18.19. � 2014 by John Wiley & Sons, Inc. PMID:25199636
Seio, Kohji; Kanamori, Takashi; Sekine, Mitsuo
Mitochondrial DNA sequence diversity in two groups of Italian Veneto speakers from Veneto.
Although frequencies of mitochondrial DNA (mtDNA) haplogroups in the different European populations are rather homogenous, there are a few European populations or linguistic isolates that show different mtDNA haplogroup distributions; examples are the Saami and Ladin speakers from the eastern Italian Alps. MtDNA sequence diversity was analysed from subjects from two villages in Veneto. The first, Posina, is situated in the Venetian Alps near Vicenza. The second, Barco di Pravisdomini is a village on the plains near Venice. In spite of their common Veneto dialect, the two group populations have not preserved a genetic homogeneity; particularly, they show differences in T and J haplogroups frequencies. MtDNA diversity in these two groups seems to depend more on their geographic situation. PMID:11427175
Mogentale-Profizi, N; Chollet, L; St�vanovitch, A; Dubut, V; Poggi, C; Pradi�, M P; Spadoni, J L; Gilles, A; B�raud-Colomb, E
Preferential Inhibition of Herpes-Group Viruses by Phosphonoacetic Acid: Effect on Virus DNA Synthesis and Virus-Induced DNA Polymerase Activity
In tissue culture phosphonoacetic acid (PAA) specifically inhibited DNA synthesis of human cytomegalovirus (CMV), murine CMV, simian CMV, Epstein-Barr virus, and Herpesvirus saimiri. Fifty to one hundred micrograms per milliliter PAA completely inhibited viral DNA synthesis with no significant damage to host cell DNA synthesis. In vitro DNA polymerization assays showed that 10 ?g/ml of PAA specifically inhibited partially purified human CMV-induced DNA polymerase, while little inhibition of host-cell DNA polymerase activity was found. The specific inhibition of herpes-group virus DNA synthesis with little toxicity to host cells suggests that PAA has great potential as an antiherpesvirus therapeutic agent. PMID:960726
Huang, Eng-Shang; Huang, Chien-Hui; Huong, Shu-Mei; Selgrade, Maryjane
Efimov like phase of a three stranded DNA (Efimov-DNA) and the renormalization group limit cycle
A three-stranded DNA with short range base pairings only is known to exhibit a classical analog of the quantum Efimov effect, viz., a three chain bound state at the two chain melting point where no two are bound. By using a non-perturbative renormalization group method for a rigid duplex DNA and a flexible third strand, with base pairings and strand exchange, we show that the Efimov-DNA is associated with a limit cycle type behavior of the flow of an effective three chain interaction. The analysis also shows that thermally generated bubbles play an essential role in producing the effect. A toy model for the flow equations shows the limit cycle in an extended three dimensional parameter space of the two-chain coupling and a complex three chain interaction.
Tanmoy Pal; Poulomi Sadhukhan; Somendra M. Bhattacharjee
Efimov like phase of a three stranded DNA (Efimov-DNA) and the renormalization group limit cycle
A three-stranded DNA with short range base pairings only is known to exhibit a classical analog of the quantum Efimov effect, viz., a three chain bound state at the two chain melting point where no two are bound. By using a non-perturbative renormalization group method for a rigid duplex DNA and a flexible third strand, with base pairings and strand exchange, we show that the Efimov-DNA is associated with a limit cycle type behavior of the flow of an effective three chain interaction. The analysis also shows that thermally generated bubbles play an essential role in producing the effect. A toy model for the flow equations shows the limit cycle in an extended three dimensional parameter space of the two-chain coupling and a complex three chain interaction.
Tanmoy Pal; Poulomi Sadhukhan; Somendra M. Bhattacharjee
Xeroderma Pigmentosum Group F Caused by a Defect in a Structure-Specific DNA Repair Endonuclease
Nucleotide excision repair, which is defective in xeroderma pigmentosum (XP), involves incision of a DNA strand on each side of a lesion. We isolated a human gene homologous to yeast Rad1 and found that it corrects the repair defects of XP group F as well as rodent groups 4 and 11. Causative mutations and strongly reduced levels of encoded protein
Anneke M Sijbers; Wouter L de Laat; Rafael R Ariza; Maureen Biggerstaff; Ying-Fei Wei; Jonathan G Moggs; Kenneth C Carter; Brenda K Shell; Elizabeth Evans; Mariska C de Jong; Suzanne Rademakers; Johan de Rooij; Nicolaas G. J Jaspers; Jan H. J Hoeijmakers; Richard D Wood
The DNA helicase BRIP1 is defective in Fanconi anemia complementation group J.
The protein predicted to be defective in individuals with Fanconi anemia complementation group J (FA-J), FANCJ, is a missing component in the Fanconi anemia pathway of genome maintenance. Here we identify pathogenic mutations in eight individuals with FA-J in the gene encoding the DEAH-box DNA helicase BRIP1, also called FANCJ. This finding is compelling evidence that the Fanconi anemia pathway functions through a direct physical interaction with DNA. PMID:16116423
Levitus, Marieke; Waisfisz, Quinten; Godthelp, Barbara C; de Vries, Yne; Hussain, Shobbir; Wiegant, Wouter W; Elghalbzouri-Maghrani, Elhaam; Steltenpool, J�rgen; Rooimans, Martin A; Pals, Gerard; Arwert, Fr�; Mathew, Christopher G; Zdzienicka, Ma?gorzata Z; Hiom, Kevin; De Winter, Johan P; Joenje, Hans
Control of DNA minor groove width and Fis protein binding by the purine 2-amino group.
The width of the DNA minor groove varies with sequence and can be a major determinant of DNA shape recognition by proteins. For example, the minor groove within the center of the Fis-DNA complex narrows to about half the mean minor groove width of canonical B-form DNA to fit onto the protein surface. G/C base pairs within this segment, which is not contacted by the Fis protein, reduce binding affinities up to 2000-fold over A/T-rich sequences. We show here through multiple X-ray structures and binding properties of Fis-DNA complexes containing base analogs that the 2-amino group on guanine is the primary molecular determinant controlling minor groove widths. Molecular dynamics simulations of free-DNA targets with canonical and modified bases further demonstrate that sequence-dependent narrowing of minor groove widths is modulated almost entirely by the presence of purine 2-amino groups. We also provide evidence that protein-mediated phosphate neutralization facilitates minor groove compression and is particularly important for binding to non-optimally shaped DNA duplexes. PMID:23661683
Hancock, Stephen P; Ghane, Tahereh; Cascio, Duilio; Rohs, Remo; Di Felice, Rosa; Johnson, Reid C
�Protected DNA Probes� capable of strong hybridization without removal of base protecting groups
We propose a new strategy called the �Protected DNA Probes (PDP) method� in which appropriately protected bases selectively bind to the complementary bases without the removal of their base protecting groups. Previously, we reported that 4-N-acetylcytosine oligonucleotides (ac4C) exhibited a higher hybridization affinity for ssDNA than the unmodified oligonucleotides. For the PDP strategy, we created a modified adenine base and synthesized an N-acylated deoxyadenosine mimic having 6-N-acetyl-8-aza-7-deazaadenine (ac6az8c7A). It was found that PDP containing ac4C and ac6az8c7A exhibited higher affinity for the complementary ssDNA than the corresponding unmodified DNA probes and showed similar base recognition ability. Moreover, it should be noted that this PDP strategy could guarantee highly efficient synthesis of DNA probes on controlled pore glass (CPG) with high purity and thereby could eliminate the time-consuming procedures for isolating DNA probes. This strategy could also avoid undesired base-mediated elimination of DNA probes from CPG under basic conditions such as concentrated ammonia solution prescribed for removal of base protecting groups in the previous standard approach. Here, several successful applications of this strategy to single nucleotide polymorphism detection are also described in detail using PDPs immobilized on glass plates and those prepared on CPG plates, suggesting its potential usefulness. PMID:18272535
Ohkubo, Akihiro; Kasuya, Rintaro; Sakamoto, Kazushi; Miyata, Kenichi; Taguchi, Haruhiko; Nagasawa, Hiroshi; Tsukahara, Toshifumi; Watanobe, Takuma; Maki, Yoshiyuki; Seio, Kohji; Sekine, Mitsuo
Atomic Force Microscopy of Group II Intron Ribonucleoprotein Particle Integration into Double-Stranded DNA�
The mobile Lactococcus lactis Ll.LtrB group II intron integrates into DNA target sites by a mechanism in which the intron RNA reverse splices into one DNA strand, while the intron-encoded protein uses a C-terminal DNA endonuclease domain to cleave the opposite strand and then uses the cleaved 3� end to prime reverse transcription of the inserted intron RNA. These reactions are mediated by an RNP particle that contains the intron-encoded protein and the excised intron lariat RNA, with both the protein and base pairing of the intron RNA used to recognize DNA target sequences. Here, computational analysis indicates that Escherichia coli DNA target sequences that support Ll.LtrB integration have greater predicted bendability than do random Escherichia coli genomic sequences, and atomic force microscopy shows that target DNA is bent during the reaction with Ll.LtrB RNPs. Time-course and mutational analyses show that DNA bending occurs after reverse splicing and requires subsequent interactions between the intron-encoded protein and the 3�-exon, which lead to two progressively larger bend angles. Our results suggest a model in which RNPs bend the target DNA by maintaining initial contacts with the 5� exon, while engaging in subsequent 3�-exon interactions that successively position the scissile phosphate for bottom-strand cleavage at the DNA endonuclease active site and then reposition the 3� end of the cleaved bottom strand at the reverse transcriptase active site for initiation of cDNA synthesis. Our findings indicate that bendability of the DNA target site is a significant factor for Ll.LtrB RNP integration. PMID:17029398
Noah, James W.; Park, Soyeun; Whitt, Jacob T.; Perutka, Jiri; Frey, Wolfgang; Lambowitz, Alan M.
Self-splicing group I and group II introns encode homologous (putative) DNA endonucleases of a new family.
A new family of protein domains consisting of 50-80 amino acid residues is described. It is composed of nearly 40 members, including domains encoded by plastid and phage group I introns; mitochondrial, plastid, and bacterial group II introns; eubacterial genomes and plasmids; and phages. The name "EX1HH-HX3H" was coined for both domain and family. It is based on 2 most prominent amino acid sequence motifs, each encompassing a pair of highly conserved histidine residues in a specific arrangement: EX1HH and HX3H. The "His" motifs often alternate with amino- and carboxy-terminal motifs of a new type of Zn-finger-like structure CX2,4CX29-54[CH]X2,3[CH]. The EX1HH-HX3H domain in eubacterial E2-type bacteriocins and in phage RB3 (wild variant of phage T4) product of the nrdB group I intron was reported to be essential for DNA endonuclease activity of these proteins. In other proteins, the EX1HH-HX3H domain is hypothesized to possess DNase activity as well. Presumably, this activity promotes movement (rearrangement) of group I and group II introns encoding the EX1HH-HX3H domain and other gene targets. In the case of Escherichia coli restrictase McrA and possibly several related proteins, it appears to mediate the restriction of alien DNA molecules. PMID:7920259
Gorbalenya, A. E.
DNA DNA DNA DNA DNA DNA DNA DNA [ 2008] (d)DNA DNA DNA DNA 2 3 DNA DNA DNA DNA DNA DNA DNA (a) (c) (b) (d) #12;DNA DNA DNA DNA DNA DNA DNA DNA (b) DNA [Tanaka et al.2008] DNA DNA DNA DNA DNA DNA DNA #12;iGEM MIT MIT
Hagiya, Masami
Spy: A New Group of Eukaryotic DNA Transposons without Target Site Duplications
Class 2 or DNA transposons populate the genomes of most eukaryotes and like other mobile genetic elements have a profound impact on genome evolution. Most DNA transposons belong to the cut-and-paste types, which are relatively simple elements characterized by terminal-inverted repeats (TIRs) flanking a single gene encoding a transposase. All eukaryotic cut-and-paste transposons so far described are also characterized by target site duplications (TSDs) of host DNA generated upon chromosomal insertion. Here, we report a new group of evolutionarily related DNA transposons called Spy, which also include TIRs and DDE motif-containing transposase but surprisingly do not create TSDs upon insertion. Instead, Spy transposons appear to transpose precisely between 5?-AAA and TTT-3? host nucleotides, without duplication or modification of the AAATTT target sites. Spy transposons were identified in the genomes of diverse invertebrate species based on transposase homology searches and structure-based approaches. Phylogenetic analyses indicate that Spy transposases are distantly related to IS5, ISL2EU, and PIF/Harbinger transposases. However, Spy transposons are distinct from these and other DNA transposon superfamilies by their lack of TSD and their target site preference. Our findings expand the known diversity of DNA transposons and reveal a new group of eukaryotic DDE transposases with unusual catalytic properties. PMID:24966181
Han, Min-Jin; Xu, Hong-En; Zhang, Hua-Hao; Feschotte, C�dric; Zhang, Ze
Spy: a new group of eukaryotic DNA transposons without target site duplications.
Class 2 or DNA transposons populate the genomes of most eukaryotes and like other mobile genetic elements have a profound impact on genome evolution. Most DNA transposons belong to the cut-and-paste types, which are relatively simple elements characterized by terminal-inverted repeats (TIRs) flanking a single gene encoding a transposase. All eukaryotic cut-and-paste transposons so far described are also characterized by target site duplications (TSDs) of host DNA generated upon chromosomal insertion. Here, we report a new group of evolutionarily related DNA transposons called Spy, which also include TIRs and DDE motif-containing transposase but surprisingly do not create TSDs upon insertion. Instead, Spy transposons appear to transpose precisely between 5'-AAA and TTT-3' host nucleotides, without duplication or modification of the AAATTT target sites. Spy transposons were identified in the genomes of diverse invertebrate species based on transposase homology searches and structure-based approaches. Phylogenetic analyses indicate that Spy transposases are distantly related to IS5, ISL2EU, and PIF/Harbinger transposases. However, Spy transposons are distinct from these and other DNA transposon superfamilies by their lack of TSD and their target site preference. Our findings expand the known diversity of DNA transposons and reveal a new group of eukaryotic DDE transposases with unusual catalytic properties. PMID:24966181
Han, Min-Jin; Xu, Hong-En; Zhang, Hua-Hao; Feschotte, C�dric; Zhang, Ze
Effects of Trehalose Polycation End-group Functionalization on Plasmid DNA Uptake and Transfection
In this study, we have synthesized six analogs of a trehalose-pentaethylenehexamine glycopolymer (Tr4) that contain (1A) adamantane, (1B) carboxy, (1C) alkynyl-oligoethyleneamine, (1D) azido trehalose, (1E) octyl, or (1F) oligoethyleneamine end groups and evaluated the effects of polymer end group chemistry on the ability of these systems to bind, compact, and deliver pDNA in cultured HeLa cells. The polymers were synthesized in one-pot azide-alkyne cycloaddition reactions with an adaptation of the Carothers equation for step-growth polymerization to produce a series of polymers with similar degrees of polymerization. An excess of end-capping monomer was added at the end of the polymerizations to maximize functionalization efficiency, which was evaluated with GPC, NMR and MALDI-TOF. The polymers were all found to bind and compact pDNA at similarly low N/P ratios and form polyplexes with plasmid DNA. The effects of the different end group structures were most evident in the polyplex internalization and transfection assays completed in the presence of serum, as determined by flow cytometry and luciferase gene expression respectively. The Tr4 polymers end-capped with carboxyl groups (1B) (N/P = 7), octyne (1E) (N/P = 7), and oligoethyleneamine (1F) (N/P = 7), were taken into cells as polyplex and exhibited the highest levels of fluorescence, resulting from labeled reporter plasmid. Similarly, the polymers end-functionalized with the carboxyl groups (1E at N/P = 7), octyl groups (1E at N/P = 15) and, in particular, the oligoethyleneamine groups (F at N/P = 15) yielded dramatically higher reporter gene expression in the presence of serum. This study yields insight into how very subtle structural changes in the polymer chemistry such as end groups can yield very significant differences in the biological delivery efficiency and transgene expression of polymers used for pDNA delivery. PMID:22616977
Anderson, Kevin; Sizovs, Antons; Cortez, Mallory; Waldron, Chris; Haddleton, D.M.; Reineke, Theresa M.
The Polycomb group protein Enhancer of Zeste 2: its links to DNA repair and breast cancer
The Polycomb group protein EZH2 is a transcriptional repressor involved in controlling cellular memory and has been linked to tumorigenesis in multiple organs. In this review we summarize the current knowledge on the function of EZH2 in cancer, with special focus on breast cancer, and propose a link between EZH2, the homologous recombination pathway of DNA repair, and breast tumorigenesis.
Michael Zeidler; Celina G. Kleer
Genetic Variation Among Vegetative Compatibility Groups of Fusarium oxysporum f. sp. cubense Analyzed by DNA Fingerprinting
Bentley, S., Pegg, K. G., Moore, N. Y., Davis, R. D., and Buddenhagen, I. W. 1998. Genetic variation among vegetative compatibility groups of Fusarium oxysporum f. sp. cubense analyzed by DNA fingerprinting. Phytopathology 88:1283-1293. Genetic variation within a worldwide collection of 208 isolates of Fu- sarium oxysporum f. sp. cubense, representing physiological r aces 1, 2, 3, and 4 and
S. Bentley; K. G. Pegg; N. Y. Moore; R. D. Davis; I. W. Buddenhagen
Are the Platyhelminthes a Monophyletic Primitive Group? An Assessment Using 18s rDNA Sequences
Are the Platyhelminthes a Monophyletic Primitive Group? An Assessment Using 18s rDNA Sequences. Universitat de Barcelona, Spain In most zoological textbooks, Platyhelminthes are depicted as an early "Turbellaria," 3 species of parasitic Platyhelminthes, and several diploblastic and deuterostome and protostome
Carranza, Salvador
New reagents for the introduction of reactive functional groups into chemically synthesized DNA probes.
An efficient and versatile preparative approach is described, allowing for the preparation of DNA probes modified with an aldehyde group at the 3'- or 5'-end. The developed synthetic strategy allows for the preparation of a new family of phosphoramidites and solid supports compatible with the automated synthesis of modified oligonucleotide probes. These new reagents were prepared from intermediates 3 and 3a, obtained from the commercially available aleuritic acid 1. It was demonstrated that the new phosphoramidite reagents also could be used as new types of cleavable linkers. A new and efficient method for the production of 5' aldehyde-labeled DNA probes was developed. PMID:12757390
Skrzypczynski, Zbigniew; Wayland, Sarah
Mitochondrial DNA evolution in the Anaxyrus boreas species group Anna M. Goebel a,b,*, Tom A. Ranker c,1
Mitochondrial DNA evolution in the Anaxyrus boreas species group Anna M. Goebel a,b,*, Tom A June 2008 Available online 8 July 2008 Keywords: Amphibia Anura Bufonidae Anaxyrus boreas Bufo boreasDNA Phylogeography Conservation a b s t r a c t The Anaxyrus boreas species group currently comprises four species
Olmstead, Richard
Distinct Structural Features of the Peroxide Response Regulator from Group A Streptococcus Drive DNA Binding
Group A streptococcus (GAS, Streptococcus pyogenes) is a strict human pathogen that causes severe, invasive diseases. GAS does not produce catalase, but has an ability to resist killing by reactive oxygen species (ROS) through novel mechanisms. The peroxide response regulator (PerR), a member of ferric uptake regulator (Fur) family, plays a key role for GAS to cope with oxidative stress by regulating the expression of multiple genes. Our previous studies have found that expression of an iron-binding protein, Dpr, is under the direct control of PerR. To elucidate the molecular interactions of PerR with its cognate promoter, we have carried out structural studies on PerR and PerR-DNA complex. By combining crystallography and small-angle X-ray scattering (SAXS), we confirmed that the determined PerR crystal structure reflects its conformation in solution. Through mutagenesis and biochemical analysis, we have identified DNA-binding residues suggesting that PerR binds to the dpr promoter at the per box through a winged-helix motif. Furthermore, we have performed SAXS analysis and resolved the molecular architecture of PerR-DNA complex, in which two 30 bp DNA fragments wrap around two PerR homodimers by interacting with the adjacent positively-charged winged-helix motifs. Overall, we provide structural insights into molecular recognition of DNA by PerR and define the hollow structural arrangement of PerR-30bpDNA complex, which displays a unique topology distinct from currently proposed DNA-binding models for Fur family regulators. PMID:24586487
Hammel, Michal; Nix, Jay C.; Tseng, Hsiao-Ling; Tsou, Chih-Cheng; Fei, Chun-Hsien; Chiou, Huo-Sheng; Jeng, U-Ser; Lin, Yee-Shin; Chuang, Woei-Jer; Wu, Jiunn-Jong; Wang, Shuying
DNA content in nine species of Nematocera with special reference to the sibling species of the Anopheles maculipennis group and the Culex pipiens group
DNA values were determined for the nine species: Telmatoscopus meridionalis (family Psychodidae), Dixa obscura (family Dixidae), and Culiseta litorea, Culex pipiens, Aedes caspius, Anopheles labranchiae, Anopheles atroparvus, Anopheles stephensi, and Anopheles freeborni (family Culicidae). The DNA content indicated that the species could be divided into three categories: The Culex group with Culex pipiens, Culiseta litorea and Aedes caspius containing 1.02,
Erich Jost; Marco Mameli
Mitochondrial DNA control region analysis of three ethnic groups in the Republic of Macedonia
A total of 444 individuals representing three ethnic groups (Albanians, Turks and Romanies) in the Republic of Macedonia were sequenced in the mitochondrial control region. The mtDNA haplogroup composition differed between the three groups. Our results showed relatively high frequencies of haplogroup H12 in Albanians (8.8%) and less in Turks (3.3%), while haplogroups M5a1 and H7a1a were dominant in Romanies (13.7% and 10.3%, respectively) but rare in the former two. This highlights the importance of regional sampling for forensic mtDNA databasing purposes. These population data will be available on EMPOP under accession numbers EMP00644 (Albanians), EMP00645 (Romanies) and EMP00646 (Turks). PMID:25051224
Jankova-Ajanovska, Renata; Zimmermann, Bettina; Huber, Gabriela; R�ck, Alexander W.; Bodner, Martin; Jakovski, Zlatko; Janeska, Biljana; Duma, Aleksej; Parson, Walther
Mitochondrial DNA control region analysis of three ethnic groups in the Republic of Macedonia.
A total of 444 individuals representing three ethnic groups (Albanians, Turks and Romanies) in the Republic of Macedonia were sequenced in the mitochondrial control region. The mtDNA haplogroup composition differed between the three groups. Our results showed relatively high frequencies of haplogroup H12 in Albanians (8.8%) and less in Turks (3.3%), while haplogroups M5a1 and H7a1a were dominant in Romanies (13.7% and 10.3%, respectively) but rare in the former two. This highlights the importance of regional sampling for forensic mtDNA databasing purposes. These population data will be available on EMPOP under accession numbers EMP00644 (Albanians), EMP00645 (Romanies) and EMP00646 (Turks). PMID:25051224
Jankova-Ajanovska, Renata; Zimmermann, Bettina; Huber, Gabriela; R�ck, Alexander W; Bodner, Martin; Jakovski, Zlatko; Janeska, Biljana; Duma, Aleksej; Parson, Walther
Targeting radiosensitizers to DNA by attachment of an intercalating group: Nitroimidazole-linked phenanthridines
The nitroimidazole-linked phenanthridine series of compounds (NLP-1, 2, and 3) were synthesized under the assumption that it should be possible to enhance the molar efficiency of 2-nitroimidazoles as hypoxic cell radiosensitizers and cytotoxins by targeting them to their likely site of action, DNA. The targeting group chosen was the phenanthridine moiety, the major component of the classical DNA intercalating compound, ethidium bromide. The sole difference between the compounds is the length of the hydrocarbon chain linking the nitroimidazole to the phenanthridine. The phenanthridine group with a three-carbon side chain, P-1, was also synthesized to allow studies on the effect of the targeting group by itself. The ability of the compounds to bind to DNA is inversely proportional to their linker chain length with binding constant values ranging from approximately 1 {times} 10(5) mol-1 for NLP-2 to 6 {times} 10(5) mol-1 for NLP-3. The NLP compounds show selective toxicity to hypoxic cells at 37 degrees C at external drug concentrations 10-40 times lower than would be required for untargeted 2-nitroimidazoles such as misonidazole in vitro. Toxicity to both hypoxic and aerobic cells is dependent on the linker chain: the shorter the chain, the greater the toxicity. In addition, the NLP compounds radiosensitize hypoxic cells at external drug concentrations as low as 0.05 mM with almost the full oxygen effect being observed at a concentration of 0.5 mM. These concentrations are 10-100 times lower than would be required for similar radiosensitization using misonidazole. Radiosensitizing ability is independent of linker chain length. The present compounds represent prototypes for further studies of the efficacy and mechanism of action of 2-nitroimidazoles targeted to DNA by linkage to an intercalating group.
Cowan, D.S.; Panicucci, R.; McClelland, R.A.; Rauth, A.M. (Experimental Therapeutics Division, Ontario Cancer Institute, University of Toronto (Canada))
Single step plasmid DNA purification using methacrylate monolith bearing combination of ion-exchange and hydrophobic groups.
Purification of high quantities of human grade plasmid DNA is one of the most intensive production steps. Because of that several methods have been proposed, among them also chromatographic purification using methacrylate monoliths. Recently, a process comprising the combination of hydrophobic interaction (HIC) monolith and ion-exchange monolith was developed. In this work both chemistries were tried to be introduced on a single monolith. Methacrylate monoliths bearing octylamine groups, combination of butyl (C4) grafted methacrylate groups and diethylaminoethyl (DEAE) groups as well as grafted chains bearing both C4 and DEAE groups were prepared. All monoliths were investigated for their ionic and protein capacity and compared to conventional epoxy, C4, and DEAE methacrylate monoliths. Octylamine monolith and monolith bearing combination of C4 grafted methacrylate groups and DEAE groups were found to be the most promising candidates and were further tested for plasmid DNA (pDNA) dynamic binding capacity under ion-exchange (IEX) and HIC binding conditions and ability to separate open circular (OC) from supercoiled (SC) pDNA forms and RNA from pDNA. Since monolith bearing combination of grafted C4 methacrylate groups and DEAE groups was superior in all three tested features, exhibiting pDNA dynamic binding capacity of 4.7 mg/ml under IEX conditions and 2.1mg/ml under HIC conditions, it was used for the development of a single step purification method and tested with pure pDNA as well as with cell lysate. Developed method removed over 99% of RNA, host cell proteins (HCP) and genomic DNA (gDNA) demonstrating capacity to purify around 1.5mg of pDNA/ml of monolith from cell lysate. PMID:23305854
Smrekar, Vida; Smrekar, Franc; Strancar, Ale�; Podgornik, Ale�
Specialization of the DNA-Cleaving Activity of a Group I Ribozyme Through In Vitro Evolution
NASA Technical Reports Server (NTRS)
In an earlier study, an in vitro evolution procedure was applied to a large population of variants of the Tetrahymena group 1 ribozyme to obtain individuals with a 10(exp 5)-fold improved ability to cleave a target single-stranded DNA substrate under simulated physiological conditions. The evolved ribozymes also showed a twofold improvement, compared to the wild-type, in their ability to cleave a single-stranded RNA substrate. Here, we report continuation of the in vitro evolution process using a new selection strategy to achieve both enhanced DNA and diminished RNA-cleavage activity. Our strategy combines a positive selection for DNA cleavage with a negative selection against RNA binding. After 36 "generations" of in vitro evolution, the evolved population showed an approx. 100-fold increase in the ratio of DNA to RNA-cleavage activity. Site-directed mutagenesis experiment confirmed the selective advantage of two covarying mutations within the catalytic core of ribozyme that are largely responsible for this modified behavior. The population of ribozymes has now undergone a total of 63 successive generations of evolution, resulting in an average 28 mutations relative to the wild-type that are responsible for the altered phenotype.
Tsang, Joyce; Joyce, Gerald F.
Discovery of a group I intron in the SSU rDNA of Ploeotia costata (Euglenozoa).
The gene coding for the small ribosomal subunit RNA of Ploeotia costata contains an actively splicing group I intron (Pco.S516) which is unique among euglenozoans. Secondary structure predictions indicate that paired segments P1-P10 as well as several conserved elements typical of group I introns and of subclass IC1 in particular are present. Phylogenetic analyses of SSU rDNA sequences demonstrate a well-supported placement of Ploeotia costata within the Euglenozoa; whereas, analyses of intron data sets uncover a close phylogenetic relation of Pco.S516 to S-516 introns from Acanthamoeba, Aureoumbra lagunensis (Stramenopila) and red algae of the order Bangiales. Discrepancies between SSU rDNA and intron phylogenies suggest horizontal spread of the group I intron. Monophyly of IC1 516 introns from Ploeotia costata, A. lagunensis and rhodophytes is supported by a unique secondary structure element: helix P5b possesses an insertion of 19 nt length with a highly conserved tetraloop which is supposed to take part in tertiary interactions. Neither functional nor degenerated ORFs coding for homing endonucleases can be identified in Pco.S516. Nevertheless, degenerated ORFs with His-Cys box motifs in closely related intron sequences indicate that homing may have occurred during evolution of the investigated intron group. PMID:12812370
Busse, Ingo; Preisfeld, Angelika
Identification of group I introns within the SSU rDNA gene in species of Ceratocystiopsis and related taxa.
During a recent phylogenetic study, group I introns were noted that interrupt the nuclear small subunit ribosomal RNA (SSU rDNA) gene in species of Ceratocystiopsis. Group I introns were found to be inserted at the following rDNA positions: S943, S989, and S1199. The introns have been characterized and phylogenetic analysis of the host gene and the corresponding intron data suggest that for S943 vertical transfer and frequent loss appear to be the most parsimonious explanation for the distribution of nuclear SSU rDNA introns among species of Ceratocystiopsis. The SSU rDNA data do suggest that a recent proposal of segregating the genus Ophiostoma sensu lato into Ophiostoma sensu stricto, Grosmannia, and Ceratocystiopsis has some merit but may need further amendments, as the SSU rDNA suggests that Ophiostoma s. str. may now represent a paraphyletic grouping. PMID:22208605
Hafez, Mohamed; Iranpour, Mahmood; Mullineux, Sahra-Taylor; Sethuraman, Jyothi; Wosnitza, Kari M; Lehn, Paeta; Kroeker, Jennifer; Loewen, Peter C; Reid, James; Hausner, Georg
A dynamic combinatorial approach for identifying side groups that stabilize DNA-templated supramolecular self-assemblies.
DNA-templated self-assembly is an emerging strategy for generating functional supramolecular systems, which requires the identification of potent multi-point binding ligands. In this line, we recently showed that bis-functionalized guanidinium compounds can interact with ssDNA and generate a supramolecular complex through the recognition of the phosphodiester backbone of DNA. In order to probe the importance of secondary interactions and to identify side groups that stabilize these DNA-templated self-assemblies, we report herein the implementation of a dynamic combinatorial approach. We used an in situ fragment assembly process based on reductive amination and tested various side groups, including amino acids. The results reveal that aromatic and cationic side groups participate in secondary supramolecular interactions that stabilize the complexes formed with ssDNA. PMID:25667976
Paolantoni, Delphine; Cantel, Sonia; Dumy, Pascal; Ulrich, S�bastien
A Dynamic Combinatorial Approach for Identifying Side Groups that Stabilize DNA-Templated Supramolecular Self-Assemblies
DNA-templated self-assembly is an emerging strategy for generating functional supramolecular systems, which requires the identification of potent multi-point binding ligands. In this line, we recently showed that bis-functionalized guanidinium compounds can interact with ssDNA and generate a supramolecular complex through the recognition of the phosphodiester backbone of DNA. In order to probe the importance of secondary interactions and to identify side groups that stabilize these DNA-templated self-assemblies, we report herein the implementation of a dynamic combinatorial approach. We used an in situ fragment assembly process based on reductive amination and tested various side groups, including amino acids. The results reveal that aromatic and cationic side groups participate in secondary supramolecular interactions that stabilize the complexes formed with ssDNA. PMID:25667976
Paolantoni, Delphine; Cantel, Sonia; Dumy, Pascal; Ulrich, S�bastien
Conformational influence of the ribose 2'-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes
NASA Technical Reports Server (NTRS)
We have crystallized three double-helical DNA-RNA chimeric duplexes and determined their structures by X-ray crystallography at resolutions between 2 and 2.25 A. The two self-complementary duplexes [r(G)d(CGTATACGC)]2 and [d(GCGT)r(A)d(TACGC)]2, as well as the Okazaki fragment d(GGGTATACGC).r(GCG)d(TATACCC), were found to adopt A-type conformations. The crystal structures are non-isomorphous, and the crystallographic environments for the three chimeras are different. A number of intramolecular interactions of the ribose 2'-hydroxyl groups contribute to the stabilization of the A-conformation. Hydrogen bonds between 2'-hydroxyls and 5'-oxygens or phosphate oxygens, in addition to the previously observed hydrogen bonds to 1'-oxygens of adjacent riboses and deoxyriboses, are observed in the DNA-RNA chimeric duplexes. The crystalline chimeric duplexes do not show a transition between the DNA A- and B-conformations. CD spectra suggest that the Okazaki fragment assumes an A-conformation in solution as well. In this molecule the three RNA residues may therefore lock the complete decamer in the A-conformation. Crystals of an all-DNA strand with the same sequence as the self-complementary chimeras show a morphology which is different from those of the chimera crystals. Moreover, the oligonucleotide does not match any of the sequence characteristics of DNAs usually adopting the A-conformation in the crystalline state (e.g., octamers with short alternating stretches of purines and pyrimidines). In DNA-RNA chimeric duplexes, it is therefore possible that a single RNA residue can drive the conformational equilibrium toward the A-conformation.
Egli, M.; Usman, N.; Rich, A.
Microsatellite DNA Suggests that Group Size Affects Sex-biased Dispersal Patterns in Red Colobus Monkeys
Dispersal is a major life history trait of social organisms influencing the behavioral and genetic structure of their groups. Unfortunately, primate dispersal is difficult to quantify, because of the rarity of these events and our inability to ascertain if individuals dispersed or died when they disappear. Socioecological models have been partially developed to understand the ecological causes of different dispersal systems and their social consequences. However, these models have yielded confusing results when applied to folivores. The folivorous red colobus monkey (Procolobus rufomitratus) in Kibale National Park, Uganda is thought to exhibit female-biased dispersal, although both sexes have been observed to disperse and there remains considerable debate over the selective pressures favoring the transfers of males and females and the causes of variation in the proportion of each sex to leave the natal group. We circumvent this problem by using microsatellite DNA data to investigate the prediction that female dispersal will be more frequent in larger groups as compared to smaller ones. The rationale for this prediction is that red colobus exhibit increased within-group competition in bigger groups, which should favor higher female dispersal rates and ultimately lower female relatedness. Genetic data from two unequally sized neighboring groups of red colobus demonstrate increased female relatedness within the smaller group, suggesting females are less likely to disperse when there is less within-group competition. We suggest that the dispersal system is mediated to some degree by scramble competition and group size. Since red colobus group sizes have increased throughout Kibale by over 50% in the last decade, these changes may have major implications for the genetic structure and ultimately the population viability of this endangered primate. PMID:23307485
Miyamoto, Michael M.; Allen, Julie M.; Gogarten, Jan F.; Chapman, Colin A.
The Polycomb Group Protein EZH2 Impairs DNA Repair in Breast Epithelial Cells1
The Polycomb group protein EZH2 is a transcriptional repressor involved in controlling cellular memory and has been linked to aggressive and metastatic breast cancer. Here we report that EZH2 decreased the ex- pression of five RAD51 paralog proteins involved in homologous recombination (HR) repair of DNA double- strand breaks (RAD51B\\/RAD51L1, RAD51C\\/RAD51L2, RAD51D\\/RAD51L3, XRCC2, and XRCC3), but did not affect the
Michael Zeidler; Sooryanarayana Varambally; Qi Cao; Arul M. Chinnaiyan; David O. Ferguson; Sofia D. Merajver; Celina G. Kleer
Role of Polycomb Group Proteins in the DNA Damage Response � A Reassessment
A growing body of evidence suggests that Polycomb group (PcG) proteins, key regulators of lineage specific gene expression, also participate in the repair of DNA double-strand breaks (DSBs) but evidence for direct recruitment of PcG proteins at specific breaks remains limited. Here we explore the association of Polycomb repressive complex 1 (PRC1) components with DSBs generated by inducible expression of the AsiSI restriction enzyme in normal human fibroblasts. Based on immunofluorescent staining, the co-localization of PRC1 proteins with components of the DNA damage response (DDR) in these primary cells is unconvincing. Moreover, using chromatin immunoprecipitation and deep sequencing (ChIP-seq), which detects PRC1 proteins at common sites throughout the genome, we did not find evidence for recruitment of PRC1 components to AsiSI-induced DSBs. In contrast, the S2056 phosphorylated form of DNA-PKcs and other DDR proteins were detected at a subset of AsiSI sites that are predominantly at the 5? ends of transcriptionally active genes. Our data question the idea that PcG protein recruitment provides a link between DSB repairs and transcriptional repression. PMID:25057768
Chandler, Hollie; Patel, Harshil; Palermo, Richard; Brookes, Sharon; Matthews, Nik; Peters, Gordon
Conducting polymer based DNA biosensor for the detection of the Bacillus cereus group species
NASA Astrophysics Data System (ADS)
Biosensor designs are emerging at a significant rate and play an increasingly important role in foodborne pathogen detection. Conducting polymers are excellent tools for the fabrication of biosensors and polypyrrole has been used in the detection of biomolecules due to its unique properties. The prime intention of this paper was to pioneer the design and fabrication of a single-strand (ss) DNA biosensor for the detection of the Bacillus cereus (B.cereus) group species. Growth of B. cereus, results in production of several highly active toxins. Therefore, consumption of food containing >106 bacteria/gm may results in emetic and diarrhoeal syndromes. The most common source of this bacterium is found in liquid food products, milk powder, mixed food products and is of particular concern in the baby formula industry. The electrochemical deposition technique, such as cyclic voltammetry, was used to develop and test a model DNA-based biosensor on a gold electrode electropolymerized with polypyrrole. The electrically conducting polymer, polypyrrole is used as a platform for immobilizing DNA (1?g) on the gold electrode surface, since it can be more easily deposited from neutral pH aqueous solutions of pyrrolemonomers. The average current peak during the electrodeposition event is 288?A. There is a clear change in the current after hybridization of the complementary oligonucleotide (6.35?A) and for the noncomplementary oligonucleotide (5.77?A). The drop in current after each event was clearly noticeable and it proved to be effective.
Velusamy, Vijayalakshmi; Arshak, Khalil; Korostynska, Olga; Oliwa, Kamila; Adley, Catherine
Preparation of DNA Containing 5-Hydroxymethyl-2?-Deoxycytidine Modification Through Phosphoramidites with TBDMS as 5-Hydroxymethyl Protecting Group
This unit describes procedures for preparation of two phosphoramidite building blocks III and IV, both containing a TBDMS as 5-CH2OH-protecting group. Phosphoramidites III and IV allow efficient incorporation of 5-hmC into DNA and a �one-step� deprotection procedure to cleanly remove all the protecting groups. A �two-step� deprotection strategy is compatible with ultramild DNA synthesis, which enables the synthesis of 5hmC-containing DNA with additional modifications. Methods are also presented for their incorporation into oligonucleotides by solid-phase synthesis, subsequent deprotection, and HPLC analysis. PMID:22147420
Dai, Qing; He, Chuan
Identification of a group-I intron within the 25S rDNA from the yeast Arxula adeninivorans.
The 25S rDNA of the yeast Arxula adeninivorans LS3 has been closed from a genomic library and sequenced. This DNA could be localized on chromosome 1 from A. adeninivorans and comprised 3790 bp. The DNA sequence from this rDNA of the strain LS3 is very similar to the 25S rDNA of Candida albicans (91.7%), Saccharomyces cerevisiae (90.5%), Schizosaccharomyces pombe (83.8%) and Mucor racemosus (79.2%). Additionally a 411 bp insertion could be localized within the 25S rDNA. This intervening sequence, which is devoid of any long open reading frame, is a group-IC intron as revealed from its site of insertion, predicted secondary structure, and its self-splicing capability. The Arxula intron is intermediate in structure and sequence between the ribosomal introns of Tetrahymena thermophila and C. albicans. PMID:8905924
R�sel, H; Kunze, G
Phylogenetic analysis by 16S ribosomal DNA sequence comparison reveals two unrelated groups of species within the genus Ruminococcus
Phylogenetic analysis of the genus Ruminococcus based on 16S rDNA sequence data showed the genus to be phylogenetically heterogenous. Ruminococcus species fall within the radiation of the Bacillus \\/ Clostridium subphylum of the Gram-positive line of descent. Two distinct and unrelated clusters are recovered. One group contains R. flavefaciens, R. albus, R. bromii, and R. callidus. The second group constitutes
Frederick A. Rainey; Peter H. Janssen
The Drosophila Polycomb group gene pleiohomeotic encodes a DNA binding protein with homology to the transcription factor YY1.
Genes of the Polycomb group (PcG) of Drosophila encode proteins necessary for the maintenance of transcriptional repression of homeotic genes. PcG proteins are thought to act by binding as multiprotein complexes to DNA through Polycomb group response elements (PREs); however, specific DNA binding has not been demonstrated for any of the PcG proteins. We have identified a sequence-specific DNA binding protein that interacts with a PRE from the Drosophila engrailed gene. This protein (PHO) is a homolog of the ubiquitous mammalian transcription factor Yin Yang-1 and is encoded by pleiohomeotic, a known member of the PcG. We propose that PHO acts to anchor PcG protein complexes to DNA. PMID:9651589
Brown, J L; Mucci, D; Whiteley, M; Dirksen, M L; Kassis, J A
Thermodynamic Characterization of DNA with 3-Deazaadenine and 3-Methyl-3-Deazaadenine Substitutions: The Effect of Placing a Hydrophobic Group in the Minor Groove of DNA
In many high-resolution structures of DNA there are ordered waters associated with the floor of the minor groove and extending outward in several layers. It is thought that this hydration structure, along with cations, reduces the Coulombic repulsion of the interstrand phosphates. In previous studies, the replacement of the 3-N atom of adenine with a C-H to afford 3-deazaadenine was shown to decrease the thermodynamic stability of DNA via a reduction in the enthalpic term. Using spectroscopic and calorimetric methods, we report herein a rigorous examination of the thermodynamics of DNA with 3-deazaadenine modifications, and report for the first time how the presence of a minor groove methyl group, i.e., 3-methyl-3-deazaadeine, affects DNA stability, hydration and cation binding. The methylation of adenine at the N3-position to yield N3-methyladenine represents an important reaction in the toxicity of many anticancer compounds. This minor groove lesion is unstable and cannot be readily studied in terms of its effect on DNA stability or structure. Our studies show that 3-methyl-3-deazaadenine, an isostere of N3-methyladenine, significantly destabilizes DNA (??G > 4 kcal�mol?1) due to a significant drop in the enthalpy (?H) term, which is associated with a lower hydration of the duplex relative to the unfolded state. PMID:20469878
Ganguly, Manjori; Wang, Ruo-Wen; Marky, Luis A.; Gold, Barry
Genetic Diversity within Schistosoma haematobium: DNA Barcoding Reveals Two Distinct Groups
Background Schistosomiasis in one of the most prevalent parasitic diseases, affecting millions of people and animals in developing countries. Amongst the human-infective species S. haematobium is one of the most widespread causing urogenital schistosomiasis, a major human health problem across Africa, however in terms of research this human pathogen has been severely neglected. Methodology/Principal Findings To elucidate the genetic diversity of Schistosoma haematobium, a DNA �barcoding� study was performed on parasite material collected from 41 localities representing 18 countries across Africa and the Indian Ocean Islands. Surprisingly low sequence variation was found within the mitochondrial cytochrome oxidase subunit I (cox1) and the NADH-dehydrogenase subunit 1 snad1). The 61 haplotypes found within 1978 individual samples split into two distinct groups; one (Group 1) that is predominately made up of parasites from the African mainland and the other (Group 2) that is made up of samples exclusively from the Indian Ocean Islands and the neighbouring African coastal regions. Within Group 1 there was a dominance of one particular haplotype (H1) representing 1574 (80%) of the samples analyzed. Population genetic diversity increased in samples collected from the East African coastal regions and the data suggest that there has been movement of parasites between these areas and the Indian Ocean Islands. Conclusions/Significance The high occurrence of the haplotype (H1) suggests that at some point in the recent evolutionary history of S. haematobium in Africa the population may have passed through a genetic �bottleneck� followed by a population expansion. This study provides novel and extremely interesting insights into the population genetics of S. haematobium on a large geographic scale, which may have consequence for control and monitoring of urogenital schistosomiasis. PMID:23145200
Webster, Bonnie L.; Emery, Aiden M.; Webster, Joanne P.; Gouvras, Anouk; Garba, Amadou; Diaw, Oumar; Seye, Mohmoudane M.; Tchuente, Louis Albert Tchuem; Simoonga, Christopher; Mwanga, Joseph; Lange, Charles; Kariuki, Curtis; Mohammed, Khalfan A.; Stothard, J. Russell; Rollinson, David
Characterization of polymorphisms in the mitochondrial DNA of twelve ethnic groups in the Guizhou province of China.
Abstract To characterize the genetic profiles and relationships between ancient ethnic populations, we analyzed polymorphisms in mitochondrial DNA (mtDNA) isolated from the blood of 753 members of 12 ethnic groups (Buyi, Dong, Gelao, Hui, Man, Miao, Menggu, Mulao, Maonan, Qiang, She and Zhuang) living in the Guizhou Province of China. The 9-bp deletion of mtDNA was detected by the polymerase chain reaction (PCR) and PCR-PAGE, and 11 SNPs by restriction fragment length polymorphism and mini-sequencing. Thereafter, these genotyping results were verified by PCR-DNA sequencing. The mtDNA of these populations exhibited considerable diversity, both with respect to the haplogroups M and N, and subgroups thereof. The differences between the major ethnic groups reflected the maternal inheritance. These ethnic groups in Guizhou demonstrated a genetic profile that differed considerably from that of other Asian populations. Our findings indicate that the matrilineal genetic profiles of Guizhou groups are relatively complex and distinct, showing relationships that reflect national history and geography. PMID:24660920
He, Yan; Ren, Ling-Yan; Shan, Ke-Ren; Zhang, Ting; Wang, Chan-Juan; Guan, Zhi-Zhong
NSDL National Science Digital Library
In this activity, students extract DNA from their cheek cells and relate the steps in the procedure to the characteristics of cells and biological molecules. Students learn key concepts about the function of DNA during the intervals required for the extraction procedure. A second optional section develops student understanding of the fundamentals of DNA structure, function and replication; this section includes hands-on modeling of DNA replication. This activity, together with our activity, "From Gene to Protein - Transcription and Translation", can be used to teach the basic concepts of molecular biology.
Jennifer Doherty
Activation of Group II Metabotropic Glutamate Receptors Promotes DNA Demethylation in the Mouse Brain
Activation of group II metabotropic glutamate receptors (mGlu2 and -3 receptors) has shown a potential antipsychotic activity, yet the underlying mechanism is only partially known. Altered epigenetic mechanisms contribute to the pathogenesis of schizophrenia and currently used medications exert chromatin remodeling effects. Here, we show that systemic injection of the brain-permeant mGlu2/3 receptor agonist (?)-2-oxa-4-aminobicyclo[3.1.0]hexane-4,6-dicarboxylic acid (LY379268; 0.3�1 mg/kg i.p.) increased the mRNA and protein levels of growth arrest and DNA damage 45-? (Gadd45-?), a molecular player of DNA demethylation, in the mouse frontal cortex and hippocampus. Induction of Gadd45-? by LY379268 was abrogated by the mGlu2/3 receptor antagonist (2S)-2-amino-2-[(1S,2S)-2-carboxycycloprop-1-yl]-3-(xanth-9-yl) propanoic acid (LY341495; 1 mg/kg i.p.). Treatment with LY379268 also increased the amount of Gadd45-? bound to specific promoter regions of reelin, brain-derived neurotrophic factor (BDNF), and glutamate decarboxylase-67 (GAD67). We directly assessed gene promoter methylation in control mice and in mice pretreated for 7 days with the methylating agent methionine (750 mg/kg i.p.). Both single and repeated injections with LY379268 reduce cytosine methylation in the promoters of the three genes, although the effect on the GAD67 was significant only in response to repeated injections. Single and repeated treatment with LY379268 could also reverse the defect in social interaction seen in mice pretreated with methionine. The action of LY379268 on Gadd45-? was mimicked by valproate and clozapine but not haloperidol. These findings show that pharmacological activation of mGlu2/3 receptors has a strong impact on the epigenetic regulation of genes that have been linked to the pathophysiology of schizophrenia. PMID:21505039
Dong, Erbo; Gavin, David Peter; Nicoletti, Ferdinando; Guidotti, Alessandro
Acinetobacter variabilis sp. nov. (formerly DNA group 15 sensu Tjernberg & Ursing), isolated from humans and animals.
We aimed to define the taxonomic status of 16 strains which were phenetically congruent with Acinetobacter DNA group 15 described by Tjernberg & Ursing in 1989. The strains were isolated from a variety of human and animal specimens in geographically distant places over the last three decades. Taxonomic analysis was based on an Acinetobacter-targeted, genus-wide approach that included the comparative sequence analysis of housekeeping, protein-coding genes, whole-cell profiling based on matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS), an array of in-house physiological and metabolic tests, and whole-genome comparative analysis. Based on analyses of the rpoB and gyrB genes, the 16 strains formed respective, strongly supported clusters clearly separated from the other species of the genus Acinetobacter. The distinctness of the group at the species level was indicated by average nucleotide identity values of ?82?% between the whole genome sequences of two of the 16 strains (NIPH 2171(T) and NIPH 899) and those of the known species. In addition, the coherence of the group was also supported by MALDI-TOF MS. All 16 strains were non-haemolytic and non-gelatinase-producing, grown at 41 �C and utilized a rather limited number of carbon sources. Virtually every strain displayed a unique combination of metabolic and physiological features. We conclude that the 16 strains represent a distinct species of the genus Acinetobacter, for which the name Acinetobacter variabilis sp. nov. is proposed to reflect its marked phenotypic heterogeneity. The type strain is NIPH 2171(T) (?=?CIP 110486(T)?=?CCUG 26390(T)?=?CCM 8555(T)). PMID:25510976
Krizova, Lenka; McGinnis, Jana; Maixnerova, Martina; Nemec, Matej; Poirel, Laurent; Mingle, Lisa; Sedo, Ondrej; Wolfgang, William; Nemec, Alexandr
Transforming Region of Group A, B, and C Adenoviruses: DNA Homology Studies with Twenty-Nine Human Adenovirus Serotypes
The 31 human adenovirus (Ad) serotypes form five groups based upon DNA genome homologies: group A (Ad12, 18, 31), group B (Ad3, 7, 11, 14, 16, 21), group C (Ad1, 2, 5, 6), group D (Ad8, 9, 10, 13, 15, 17, 19, 20, 22-30), and group E (Ad4) (M. Green, J. Mackey, W. Wold, and P. Rigden, Virology, in press). Group A Ads are highly oncogenic in newborn hamsters, group B Ads are weakly oncogenic, and other Ads are nononcogenic. However, most or all Ads transform cultured cells. We have studied the homology of Ad5, Ad7, and Ad12 transforming restriction endonuclease DNA fragments with DNAs of 29 Ad types. Ad5 HindIII-G (map position 0-7.3), Ad7 XhoI-C (map position 0-10.8), and Ad12 (strain Huie) EcoRI-C (map position 0-16) and SalI-C (map position 0-10.6) fragments were purified, labeled in vitro (nick translation), and annealed with DNAs of Ad1 to Ad16, Ad18 to Ad24, and Ad26 to Ad31. Hybrids were assayed by using hydroxylapatite. Ad5 HindIII-G hybridized 98 to 100% with DNAs of group C Ads, but only 1 to 15% with DNAs of other types. Ad7 XhoI-C fragment hybridized 85 to 99% with DNAs of group B Ads, but only 6 to 21% with DNAs of other types. Ad12 (Huie) EcoRI-C hybridized 53 to 68% with DNAs of five other Ad12 strains, 53% with Ad18 DNA, 56% with Ad31 DNA, but only 3 to 13% with DNAs of other types. In vitro-labeled Ad12 (Huie) SalI-C hybridized 35 to 71% with DNAs of 6 other Ad12 strains, 44% with Ad18 DNA, 52% with Ad31 DNA, but only 2 to 7% with DNAs Ad7, Ad2, Ad26, or Ad4. When assayed using S-1 nuclease, SalI-C annealed 17 to 44% with DNAs of group A Ads. The melting temperatures of the hybrids of Ad5 HindIII-G with all group C Ad DNAs were 84�C in 0.12 M sodium phosphate (pH 6.8). The melting temperature of the Ad12 (Huie) EcoRI-C hybrid with Ad12 (Huie) DNA was 83�C, but was only 71 to 77�C with DNAs of other group A Ads. Thus, group C and group B Ads both have very homologous transforming regions that are not represented in DNAs of non-group C Ads or non-group B Ads, respectively. Similarily, group A Ads have unique but less homologous transforming regions. These different transforming nucleotide sequences may be reflected in the different oncogenic properties of group A, B, and C Ads. Images PMID:448795
Mackey, Jesse K.; Wold, William S. M.; Rigden, Patricia; Green, Maurice
ERIC Educational Resources Information Center
Structural form, bonding scheme, and chromatin structure of and gene-modification experiments with deoxyribonucleic acid (DNA) are described. Indicates that DNA's double helix is variable and also flexible as it interacts with regulatory and other molecules to transfer hereditary messages. (DH)
Felsenfeld, Gary
The dnaK gene as a molecular marker for the classification and discrimination of the Lactobacillus casei group
It is hard to accurately identify specific species of the Lactobacillus casei group using phenotypic techniques alone. Some strains of this species group are considered to be probiotic and are widely\\u000a applied in the food industry. In this study, we compared the use of two phylogenetic markers, the 16S rRNA and dnaK genes, for species discrimination of the members of
Chien-Hsun Huang; Fwu-Ling Lee
Overexpression of matrix metalloproteinase 1 in dermal fibroblasts from DNA repair-deficient\\/cancer-prone xeroderma pigmentosum group C patients
Xeroderma pigmentosum (XP) is a rare, recessively inherited genetic disease characterized by skin cancer proneness and premature aging in photoexposed area. The disease results from defective nucleotide excision repair of ultraviolet (UV)-induced DNA lesions. Reconstruction of group C (XP-C) skin in vitro previously suggested that patients' dermal fibroblasts might be involved in promoting skin cancer development, as they elicited microinvasions
M Fr�chet; E Warrick; C Vioux; O Chevallier; A Spatz; S Benhamou; A Sarasin; F Bernerd; T Magnaldo
Distinct DNA-Binding Properties of the High Mobility Group Domain of Murine and Human SRY Sex-Determining Factors
The mammalian sex-determining gene SRY (sex-determining region on Y chromosome) encodes a member of the high mobility group (HMG) family of regulatory proteins. The HMG domain of the SRY protein represents a DNA binding motif that displays rather unusually weak evolutionary conservation of amino acids between human and mouse sequences. Together with the previous finding that the human (h) SRY
Klaus Giese; John Pagel; Rudolf Grosschedl
Reproducibility of mtDNA analysis between laboratories: a report of the European DNA profiling group (EDNAP)
The aim of this collaborative exercise was to determine whether uniformity of mtDNA sequencing results could be achieved among different EDNAP laboratories. Laboratories were asked to sequence mtDNAHV1 region (16024�16365) from three bloodstains, proceeding in accordance with the protocol and strategies currently used in each individual laboratory. Cycle sequencing was used by 11 laboratories and solid phase single stranded sequencing
A. Carracedo; E. D'Aloja; B. Dupuy; A. Jangblad; M. Karjalainen; C. Lambert; W. Parson; H. Pfeiffer; H. Pfitzinger; M. Sabatier; D. Syndercombe Court; C. Vide
Pyramidal and chiral groupings of gold nanocrystals assembled using DNA scaffolds.
Nanostructures constructed from metal and semiconductor nanocrystals conjugated to and organized by DNA are an emerging class of materials with collective optical properties. We created discrete pyramids of DNA with gold nanocrystals at the tips. By taking small-angle X-ray scattering measurements from solutions of these pyramids, we confirmed that this pyramidal geometry creates structures which are more rigid in solution than linear DNA. We then took advantage of the tetrahedral symmetry to demonstrate construction of chiral nanostructures. PMID:19331419
Mastroianni, Alexander J; Claridge, Shelley A; Alivisatos, A Paul
Pyramidal and Chiral Groupings of Gold Nanocrystals Assembled Using DNA Scaffolds
Nanostructures constructed from metal and semiconductor nanocrystals conjugated to, and organized by DNA are an emerging class of material with collective optical properties. We created discrete pyramids of DNA with gold nanocrystals at the tips. By taking small angle X-ray scattering (SAXS) measurments from solutions of these pyramids we confirmed that this pyramidal geometry creates structures which are more rigid in solution than linear DNA. We then took advantage of the tetrahedral symmetry to demonstrate construction of chiral nanostructures. PMID:19331419
Mastroianni, Alexander; Claridge, Shelley; Alivisatos, A. Paul
Pyramidal and Chiral Groupings of Gold Nanocrystals Assembled Using DNA Scaffolds
Nanostructures constructed from metal and semiconductor nanocrystals conjugated to, and organized by DNA are an emerging class of material with collective optical properties. We created discrete pyramids of DNA with gold nanocrystals at the tips. By taking small angle X-ray scattering (SAXS) measurments from solutions of these pyramids we confirmed that this pyramidal geometry creates structures which are more rigid in solution than linear DNA. We then took advantage of the tetrahedral symmetry to demonstrate construction of chiral nanostructures.
Mastroianni, Alexander; Claridge, Shelley; Alivisatos, A. Paul
A small insertion in the SSU rDNA of the lichen fungus Arthonia lapidicola is a degenerate group-I intron
Insertions of less than 100 nt occurring in highly conserved regions of the small subunit ribosomal DNA (SSU rDNA) may represent\\u000a degenerate forms of the group-I introns observed at the same positions in other organisms. A 63-nt insertion at SSU rDNA position\\u000a 1512 (relative to theEscherichia coli SSU rDNA) of the lichen-forming fungusArthonia lapidicola can be folded into a secondary
Martin Grube; Andrea Gargas; Paula T. DePriest
Aeromonas jandaei (formerly genospecies DNA group 9 A. sobria), a new sucrose-negative species isolated from clinical specimens.
A large numerical taxonomy study conducted in 1988 of 165 mostly clinical Aeromonas strains from diverse geographic sources produced a cluster (S = 84%, SSM) of four sucrose-negative strains that included the DNA definition strain for DNA group 9 A. sobria (CDC 0787-80). These four strains, together with five additional strains received in 1989, were subjected to DNA-DNA hybridization (hydroxyapatite, 32P, 60 and 75 degrees C), and all eight strains were closely related to the ninth labeled DNA group 9 definition strain CDC 0787-80 (73 to 86% relatedness at 60 degrees C and 68 to 80% relatedness at 75 degrees C; percent divergence, 2.0 to 3.5). Type strains and DNA definition strains for all other established Aeromonas species were only 35 to 72% related (60 degrees C) to CDC 0787-80. We propose the name Aeromonas jandaei for this highly related group of nine strains, formerly known as DNA group 9 A. sobria. The type strain was designated ATCC 49568 (CDC 0787-80). The nine strains were examined at 36 degrees C and were found to be resistant to 0/129 (vibriostatic agent) and uniformly positive for oxidase, gas production from glucose, indole, lysine decarboxylase, arginine dihydrolase, o-nitrophenyl-beta-D-galactopyranoside, motility (25 degrees C), nitrate reduction, citrate utilization, hemolysis on sheep blood agar, and growth in Trypticase soy broth with no added NaCl. They all fermented D-glucose, D-mannitol, and mannose but did not ferment sucrose, cellobiose, L-arabinose, inositol, salicin, or D-sorbitol. They were uniformly negative for esculin and urea hydrolysis, elastase production, ornithine decarboxylation, and the string test. The antibiogram of A. jandaei resembled that of other aeromonads (resistance to ampicillin and cephalothin), but it differed from most other aeromonads because of resistance to single dilution of colistin and differed from clinical A. veronii biogroup sorbria (formerly A. sobria) by its nearly uniform resistance to cephalothin. The esculin-, sucrose-, and cellobiose-negative and colistin-resistant profile distinguished A. jandaei from other Aeromonas species. These A. jandaei strains were isolated from blood (two strains), wounds (two strains), diarrheal stools (four strains), and a prawn (one strain). The blood and wound isolates, in particular, suggest that there is a possible clinical significance for this species and justify identification of and further research on this group of motile aeromonads. PMID:2037673
Carnahan, A; Fanning, G R; Joseph, S W
DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group: the ants of Madagascar
The role of DNA barcoding as a tool to accelerate the inventory and analysis of diversity for hyperdiverse arthropods is tested using ants in Madagascar. We demonstrate how DNA barcoding helps address the failure of current inventory methods to rapidly respond to pressing biodiversity needs, specifically in the assessment of richness and turnover across landscapes with hyperdiverse taxa. In a
M. Alex Smith; Brian L. Fisher; Paul D. N. Hebert
Hyperbranched poly(amino ester)s with different terminal amine groups for DNA delivery.
Hyperbranched poly(amino ester)s containing tertiary amines in the core and primary, secondary, and tertiary amines in the periphery, respectively, were evaluated for DNA delivery in vitro. The same core structure facilitated the investigation on the effects of the terminal amine type on the properties of hyperbranched poly(amino ester)s for DNA delivery. The hydrolysis of the poly(amino ester)s was monitored using (1)H NMR. The results reflected that the terminal amine type had negligible effects on the hydrolysis rate but was much slower than that of linear poly(amino ester)s, probably due to the compact hyperbranched spatial structure preventing the accessibility of water. In comparison with PEI 25 K, the hyperbranched poly(amino ester)s showed much lower cytotoxicity in Cos7, HEK293, and HepG2 cells. Gel electrophoresis indicated that poly(amino ester)s could condense DNA efficiently, and the zeta potentials and sizes of the complexes formed with different weight ratios of hyperbranched poly(amino ester)s and DNA were measured. Remarkably, all the hyperbranched poly(amino ester)s showed DNA transfection efficiency comparable to PEI 25 K in Cos7, HEK293, and HepG2 cells regardless of the terminal amine type. Therefore, the terminal amine type had insignificant effects on the hydrolysis rate, cytotoxicity, DNA condensation capability, and in vitro DNA transfection efficiency of the hyperbranched poly(amino ester)s. PMID:16768410
Wu, Decheng; Liu, Ye; Jiang, Xuan; He, Chaobin; Goh, Suat Hong; Leong, Kam W
ERIC Educational Resources Information Center
This history for molecular genetics and its explanation of DNA begins with an analysis of the Golden Jubilee essay papers, 1955. The paper ends stating that the higher nervous system is the one major frontier of biological inquiry which still offers some romance of research. (Author/VW)
Stent, Gunther S.
New epistasis group for the repair of DNA damage in bacteriophage T4: replication repair
The gene 32 mutation amA453 sensitizes bacteriophage T4 to the lethal effects of ultraviolet (UV) irradiation, methyl methanesulfonate and angelicin-mediated photodynamic irradiation when treated particles are plated on amber-suppressing host cells. The increased UV sensitivity caused by amA453 is additive to that caused by mutations in both the T4 excision repair (denV) and recombination repair (uvsWXY) systems, suggesting the operation of third kind of repair system. The mutation uvs79, with many similarities to amA453 but mapping in gene 41, is largely epistatic to amA453. The mutation mms1, also with many similarities to amA453, maps close to amA453 within gene 32 and is largely epistatic to uvs79. Neither amA453 nor uvs79 affect the ratio of UV-induced mutational to lethal hits, nor does amA453 affect spontaneous or UV-enhanced recombination frequencies. Gene 32 encode the major T4 ssDNA-binding protein (the scaffolding of the DNA replication) and gene 41 encodes a DNA helicase, both being required for T4 DNA replication. The authors conclude that a third repair process operates in phage T4 and suggest that it acts during rather than before of after DNA replication.
Wachsman, J.T.; Drake, J.W.
Multiple Group I Introns in the Small-Subunit rDNA of Botryosphaeria dothidea: Implication for Intraspecific Genetic Diversity
Botryosphaeria dothidea is a widespread and economically important pathogen on various fruit trees, and it often causes die-back and canker on limbs and fruit rot. In characterizing intraspecies genetic variation within this fungus, group I introns, rich in rDNA of fungi, may provide a productive region for exploration. In this research, we analysed complete small subunit (SSU) ribosomal DNA (rDNA) sequences of 37 B. dothidea strains, and found four insertions, designated Bdo.S943, Bdo.S1199-A, Bdo.S1199-B and Bdo.S1506, at three positions. Sequence analysis and structure prediction revealed that both Bdo.S943 and Bdo.S1506 belonged to subgroup IC1 of group I introns, whereas Bdo.S1199-A and Bdo.S1199-B corresponded to group IE introns. Moreover, Bdo.S1199-A was found to host an open reading frame (ORF) for encoding the homing endonuclease (HE), whereas Bdo.S1199-B, an evolutionary descendant of Bdo.S1199-A, included a degenerate HE. The above four introns were novel, and were the first group I introns observed and characterized in this species. Differential distribution of these introns revealed that all strains could be separated into four genotypes. Genotype III (no intron) and genotype IV (Bdo.S1199-B) were each found in only one strain, whereas genotype I (Bdo.S1199-A) and genotype II (Bdo.S943 and Bdo.S1506) occurred in 95% of the strains. There is a correlation between B. dothidea genotypes and hosts or geographic locations. Thus, these newly discovered group I introns can help to advance understanding of genetic differentiation within B. dothidea. PMID:23844098
Xu, Chao; Wang, Chunsheng; Sun, Xinyao; Zhang, Rong; Gleason, Mark L.; Eiji, Tanaka; Sun, Guangyu
DNA barcoding reveals both known and novel taxa in the Albitarsis Group (Anopheles: Nyssorhynchus) of Neotropical malaria vectors
Background Mosquitoes belonging to the Albitarsis Group (Anopheles: Nyssorhynchus) are of importance as malaria vectors across the Neotropics. The Group currently comprises six known species, and recent studies have indicated further hidden biodiversity within the Group. DNA barcoding has been proposed as a highly useful tool for species recognition, although its discriminatory utility has not been verified in closely related taxa across a wide geographic distribution. Methods DNA barcodes (658 bp of the mtDNA Cytochrome c Oxidase - COI) were generated for 565 An. albitarsis s.l. collected in Argentina, Brazil, Colombia, Paraguay, Trinidad and Venezuela over the past twenty years, including specimens from type series and type localities. Here we test the utility of currently advocated barcoding methodologies, including the Kimura-two-parameter distance model (K2P) and Neighbor-joining analysis (NJ), for determining species delineation within mosquitoes of the Neotropical Albitarsis Group of malaria vectors (Anopheles: Nyssorhynchus), and compare results with Bayesian analysis. Results Species delineation through barcoding analysis and Bayesian phylogenetic analysis, fully concur. Analysis of 565 sequences (302 unique haplotypes) resolved nine NJ tree clusters, with less than 2% intra-node variation. Mean intra-specific variation (K2P) was 0.009 (range 0.002 - 0.014), whereas mean inter-specific divergence were several-fold higher at 0.041 (0.020 - 0.056), supporting the reported "barcoding gap". These results show full support for separate species status of the six known species in the Albitarsis Group (An. albitarsis s.s., An. albitarsis F, An. deaneorum, An. janconnae, An. marajoara and An. oryzalimnetes), and also support species level status for two previously detected lineages - An. albitarsis G &An. albitarsis I (designated herein). In addition, we highlight the presence of a unique mitochondrial lineage close to An. deaneorum and An. marajoara (An. albitarsis H) from Rond�nia and Mato Grosso in southwestern Brazil. Further integrated studies are required to confirm the status of this lineage. Conclusions DNA barcoding provides a reliable means of identifying both known and undiscovered biodiversity within the closely related taxa of the Albitarsis Group. We advocate its usage in future studies to elucidate the vector competence and respective distributions of all eight species in the Albitarsis Group and the novel mitochondrial lineage (An. albitarsis H) recovered in this study. PMID:22353437
A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses
Background Viruses are known to be the most abundant organisms on earth, yet little is known about their collective origin and evolutionary history. With exceptionally high rates of genetic mutation and mosaicism, it is not currently possible to resolve deep evolutionary histories of the known major virus groups. Metagenomics offers a potential means of establishing a more comprehensive view of viral evolution as vast amounts of new sequence data becomes available for comparative analysis. Results Bioinformatic analysis of viral metagenomic sequences derived from a hot, acidic lake revealed a circular, putatively single-stranded DNA virus encoding a major capsid protein similar to those found only in single-stranded RNA viruses. The presence and circular configuration of the complete virus genome was confirmed by inverse PCR amplification from native DNA extracted from lake sediment. The virus genome appears to be the result of a RNA-DNA recombination event between two ostensibly unrelated virus groups. Environmental sequence databases were examined for homologous genes arranged in similar configurations and three similar putative virus genomes from marine environments were identified. This result indicates the existence of a widespread but previously undetected group of viruses. Conclusions This unique viral genome carries implications for theories of virus emergence and evolution, as no mechanism for interviral RNA-DNA recombination has yet been identified, and only scant evidence exists that genetic exchange occurs between such distinct virus lineages. Reviewers This article was reviewed by EK, MK (nominated by PF) and AM. For the full reviews, please go to the Reviewers' comments section. PMID:22515485
Complete mtDNA genomes of Filipino ethnolinguistic groups: a melting pot of recent and ancient lineages in the Asia-Pacific region.
The Philippines is a strategic point in the Asia-Pacific region for the study of human diversity, history and origins, as it is a cross-road for human migrations and consequently exhibits enormous ethnolinguistic diversity. Following on a previous in-depth study of Y-chromosome variation, here we provide new insights into the maternal genetic history of Filipino ethnolinguistic groups by surveying complete mitochondrial DNA (mtDNA) genomes from a total of 14 groups (11 groups in this study and 3 groups previously published) including previously published mtDNA hypervariable segment (HVS) data from Filipino regional center groups. Comparison of HVS data indicate genetic differences between ethnolinguistic and regional center groups. The complete mtDNA genomes of 14 ethnolinguistic groups reveal genetic aspects consistent with the Y-chromosome, namely: diversity and heterogeneity of groups, no support for a simple dichotomy between Negrito and non-Negrito groups, and different genetic affinities with Asia-Pacific groups that are both ancient and recent. Although some mtDNA haplogroups can be associated with the Austronesian expansion, there are others that associate with South Asia, Near Oceania and Australia that are consistent with a southern migration route for ethnolinguistic group ancestors into the Asia-Pacific, with a timeline that overlaps with the initial colonization of the Asia-Pacific region, the initial colonization of the Philippines and a possible separate post-colonization migration into the Philippine archipelago. PMID:23756438
Delfin, Frederick; Min-Shan Ko, Albert; Li, Mingkun; Gunnarsd�ttir, Ellen D; Tabbada, Kristina A; Salvador, Jazelyn M; Calacal, Gayvelline C; Sagum, Minerva S; Datar, Francisco A; Padilla, Sabino G; De Ungria, Maria Corazon A; Stoneking, Mark
Complete mtDNA genomes of Filipino ethnolinguistic groups: a melting pot of recent and ancient lineages in the Asia-Pacific region
The Philippines is a strategic point in the Asia-Pacific region for the study of human diversity, history and origins, as it is a cross-road for human migrations and consequently exhibits enormous ethnolinguistic diversity. Following on a previous in-depth study of Y-chromosome variation, here we provide new insights into the maternal genetic history of Filipino ethnolinguistic groups by surveying complete mitochondrial DNA (mtDNA) genomes from a total of 14 groups (11 groups in this study and 3 groups previously published) including previously published mtDNA hypervariable segment (HVS) data from Filipino regional center groups. Comparison of HVS data indicate genetic differences between ethnolinguistic and regional center groups. The complete mtDNA genomes of 14 ethnolinguistic groups reveal genetic aspects consistent with the Y-chromosome, namely: diversity and heterogeneity of groups, no support for a simple dichotomy between Negrito and non-Negrito groups, and different genetic affinities with Asia-Pacific groups that are both ancient and recent. Although some mtDNA haplogroups can be associated with the Austronesian expansion, there are others that associate with South Asia, Near Oceania and Australia that are consistent with a southern migration route for ethnolinguistic group ancestors into the Asia-Pacific, with a timeline that overlaps with the initial colonization of the Asia-Pacific region, the initial colonization of the Philippines and a possible separate post-colonization migration into the Philippine archipelago. PMID:23756438
Delfin, Frederick; Min-Shan Ko, Albert; Li, Mingkun; Gunnarsd�ttir, Ellen D; Tabbada, Kristina A; Salvador, Jazelyn M; Calacal, Gayvelline C; Sagum, Minerva S; Datar, Francisco A; Padilla, Sabino G; De Ungria, Maria Corazon A; Stoneking, Mark
[Sequencing the 16S rDNA of representative strain of new rhizobial group and determining of its phylogenetic relationship].
The full-length 16S rDNA sequence of representative strain SH2672 were sequenced by the dideoxy-mediated chain-termination method. This sequence was compared with that of type strains of all known rhizobia and related bacteria. An unrooted phylogenetic tree was produced. In this tree, strain SH2672, Mesorhizobium loti, M. huakuii, M. tianshanense, M. mediterraneum, and M. ciceri constituted a branch. Within this branch, the similarity values of 16S rDNA sequences between strain SH2672 and M. loti, M. huakuii, M. tianshanense, M. mediterraneum and M. ciceri were 96.3%, 96.4%, 97.2%, 95.1% and 95.6% respectively. All similarity values was more than 95%, this indicated that these species should belong to the same genus. The values of DNA-DNA homology between type strains of these species were less than 70%, which showed that strain SH2672 (representative strain of new group) represented a new rhizobial species. PMID:11189370
Tan, Z; Chen, W
Single nucleotide polymorphisms of mitochondrial DNA HVS-I and HVS-II in Chinese Bai ethnic group.
For forensic and population genetic purposes, a total of 125 unrelated volunteers' blood samples were collected from Chinese Bai ethnic minority group to analyze sequence variation of two hypervariable segments (HVS-I and HVS-II) in the mitochondrial DNA control region. Comparing the HVS-I and HVS-II sequences of the 125 Chinese Bais to the Anderson reference sequence, we found 86 polymorphic loci in HVS-I and 40 in HVS-II in mitochondrial DNA sequences of the Chinese Bai ethnic minority group, which defined 93 and 53 different haplotypes, respectively. Haplotype diversity and the mean pairwise differences were 0.992 � 0.003 and 6.553 in HVS-I, and 0.877 � 0.027 and 2.407 in HVS-II, respectively. We defined four macrohaplogroups R, M, N and D with the proportions ranging from 9.6% to 40.0%. With the analysis of the hypervariable domain from nucleotide 16�180-16�193 in HVS-I, our study revealed new haplotypes of sequence variations. In addition, the Fst metric, phylogenetic tree, and principal component analysis demonstrated a close genetic relationship between the Bai group and Chinese Han populations from South China, Changsha, and Guangdong. The results support that the Bai group is a multiorigin ethnic minority that has merged with the Chinese Han population. PMID:25488882
Chen, Feng; Yin, Cai-Yong; Qian, Xiao-Qin; Fan, Han-Ting; Deng, Ya-Jun; Zhang, Yu-Dang; Meng, Hao-Tian; Shen, Chun-Mei; Yang, Chun-Hua; Jin, Rui; Zhu, Bo-Feng; Xu, Peng
Comprehensive Phylogenetic Analysis of Bacterial Group II Intron-Encoded ORFs Lacking the DNA Endonuclease Domain Reveals New Varieties
Group II introns are self-splicing RNAs that act as mobile retroelements in the organelles of plants, fungi and protists. They are also widely distributed in bacteria, and are generally assumed to be the ancestors of nuclear spliceosomal introns. Most bacterial group II introns have a multifunctional intron-encoded protein (IEP) ORF within the ribozyme domain IV (DIV). This ORF encodes an N-terminal reverse transcriptase (RT) domain, followed by a putative RNA-binding domain with RNA splicing or maturase activity and, in some cases, a C-terminal DNA-binding (D) region followed by a DNA endonuclease (En) domain. In this study, we focused on bacterial group II intron ORF phylogenetic classes containing only reverse transcriptase/maturase open reading frames, with no recognizable D/En region (classes A, C, D, E, F and unclassified introns). On the basis of phylogenetic analyses of the maturase domain and its C-terminal extension, which appears to be a signature characteristic of ORF phylogenetic class, with support from the phylogeny inferred from the RT domain, we have revised the proposed new class F, defining new intron ORF varieties. Our results increase knowledge of the lineage of group II introns encoding proteins lacking the En-domain. PMID:23355907
Toro, Nicol�s; Mart�nez-Abarca, Francisco
Preparation of carboxyl group-modified palladium nanoparticles in an aqueous solution and their conjugation with DNA
NASA Astrophysics Data System (ADS)
The use of nanomaterials in biomolecular labeling and their corresponding detection has been attracting much attention, recently. There are currently very few studies on palladium nanoparticles (Pd NPs) due to their lack of appropriate surface functionalities for conjugation with DNA. In this paper, we thus firstly present an approach to prepare carboxyl group-modified Pd NPs (with an average size of 6 nm) by the use of 11-mercaptoundecanoic acid (MUDA) as a stabilizer in the aqueous solution. The effect of the various reducing reaction conditions on the morphology of the Pd NPs was investigated. The particles were further characterized by TEM, UV-vis, FT-IR and XPS techniques. DNA was finally covalently conjugated to the surface of the Pd NPs through the activation of the carboxyl group, which was confirmed by agarose gel electrophoresis and fluorescence analysis. The resulting Pd NPs-DNA conjugates show high single base pair mismatch discrimination capabilities. This work therefore sets a good foundation for further applications of Pd NPs in bio-analytical research.
Wang, Zhifei; Li, Hongying; Zhen, Shuang; He, Nongyue
mtDNA polymorphisms in five French groups: importance of regional sampling
According to classical markers, France has been reported to be regionally heterogeneous. Here, we propose to test the homogeneity of the French mitochondrial gene pool by analysing D-Loop and coding regions polymorphisms in 210 individuals stemming from five regions. The data set obtained was also used to test the ability of mitochondrial DNA to detect well historically established admixtures (admixtures
Vincent Dubut; Lionel Chollet; Pascal Murail; Fran�ois Cartault; Eliane B�raud-Colomb; Myriam Serre; N�rina Mogentale-Profizi
Hydration of the Phosphate Group in Double-Helical DNA Bohdan Schneider,* Ketan Patel,#
; Chalikian et al., 1994a) that there are differences in the properties of the solvent and counterions by neutron quasielastic scattering (Schreiner et al., 1988). The lower mobility of water at the DNA surface. Release of this partially or- dered water upon binding of charged molecules is a source of entropic force
Schneider, Bohdan
A small insertion in the SSU rDNA of the lichen fungus Arthonia lapidicola is a degenerate group-I intron.
Insertions of less than 100 nt occurring in highly conserved regions of the small subunit ribosomal DNA (SSU rDNA) may represent degenerate forms of the group-I introns observed at the same positions in other organisms. A 63-nt insertion at SSU rDNA position 1512 (relative to the Escherichia coli SSU rDNA) of the lichen-forming fungus Arthonia lapidicola can be folded into a secondary structure with two stem loops and a pairing of the insertion and flanking sequences. The two stem loops may correspond to the P1 and P2, and the insertion-flanking pairing to the P10, of a group-I intron. Considering these small insertions as degenerate introns provides important clues to the evolution and catalytic function of group-I introns. Keywords Ribosomal DNA middle dot Small subunit middle dot 18s middle dot Degenerate introns middle dot Ascomycetes PMID:8662198
Grube, M; Gargas, A; DePriest, P T
Development of cDNA probes for typing group A bovine rotaviruses on the basis of VP4 specificity.
Dot and Northern (RNA) blot hybridization assays were developed for the P typing of group A bovine rotaviruses (BRV) by using cDNA probes prepared from gene segment 4. The probes were prepared by polymerase chain reaction amplification of hyperdivergent regions (nucleotides 211 to 686) of BRV strain UK, IND, NCDV, and Cr VP4 cDNA by using specific oligonucleotide primers. The probes were P type specific (VP4) and exhibited little or no cross-reactivity with double-stranded RNA from heterologous rotavirus P types. Our studies indicate that at least three P types, as defined by polymerase chain reaction-derived VP4 gene probes from the UK, NCDV, and Cr strains, exist among the seven BRV isolates tested. Images PMID:1383267
Parwani, A V; Rosen, B I; McCrae, M A; Saif, L J
Phylogeny of the Sphaerotilus-Leptothrix group inferred from morphological comparisons, genomic fingerprinting, and 16S ribosomal DNA sequence analyses.
Phase-contrast light microscopy revealed that only one of eight cultivated strains belonging to the Sphaerotilus-Leptothrix group of sheathed bacteria actually produced a sheath in standard growth media. Two Sphaerotilus natans strains produced branched cells, but other morphological characteristics that were used to identify these bacteria were consistent with previously published descriptions. Genomic fingerprints, which were obtained by performing PCR amplification with primers corresponding to enterobacterial repetitive intergenic consensus sequences, were useful for distinguishing between the genera Sphaerotilus and Leptothrix, as well as among individual strains. The complete 16S ribosomal DNA (rDNA) sequences of two strains of "Leptothrix discophora" (strains SP-6 and SS-1) were determined. In addition, partial sequences (approximately 300 nucleotides) of one strain of Leptothrix cholodnii (strain LMG 7171), an unidentified Leptothrix strain (strain NC-1), and four strains of Sphaerotilus natans (strains ATCC 13338T [T = type strain], ATCC 15291, ATCC 29329, and ATCC 29330) were determined. We found that two of the S. natans strains (ATCC 15291 and ATCC 13338T), which differed in morphology and in their genomic fingerprints, had identical sequences in the 300-nucleotide region sequenced. Both parsimony and distance matrix methods were used to infer the evolutionary relationships of the eight strains in a comparison of the 16S rDNA sequences of these organisms with 16S rDNA sequences obtained from ribosomal sequence databases. All of the strains clustered in the Rubrivivax subdivision of the beta subclass of the Proteobacteria, which confirmed previously published conclusions concerning selected individual strains. Additional analyses revealed that all of the S. natans strains clustered in one closely related group, while the Leptothrix strains clustered in two separate lineages that were approximately equidistant from the S. natans cluster. This finding suggests that the tentative species "L. discophora" needs to be more clearly defined and compared with other species belonging to the genus Leptothrix. PMID:8573492
Siering, P L; Ghiorse, W C
Integrated DNA methylation and copy-number profiling identify three clinically and biologically relevant groups of anaplastic glioma.
The outcome of patients with anaplastic gliomas varies considerably. Whether a molecular classification of anaplastic gliomas based on large-scale genomic or epigenomic analyses is superior to histopathology for reflecting distinct biological groups, predicting outcomes and guiding therapy decisions has yet to be determined. Epigenome-wide DNA methylation analysis, using a platform which also allows the detection of copy-number aberrations, was performed in a cohort of 228 patients with anaplastic gliomas (astrocytomas, oligoastrocytomas, and oligodendrogliomas), including 115 patients of the NOA-04 trial. We further compared these tumors with a group of 55 glioblastomas. Unsupervised clustering of DNA methylation patterns revealed two main groups correlated with IDH status: CpG island methylator phenotype (CIMP) positive (77.5�%) or negative (22.5�%). CIMP(pos) (IDH mutant) tumors showed a further separation based on copy-number status of chromosome arms 1p and 19q. CIMP(neg) (IDH wild type) tumors showed hallmark copy-number alterations of glioblastomas, and clustered together with CIMP(neg) glioblastomas without forming separate groups based on WHO grade. Notably, there was no molecular evidence for a distinct biological entity representing anaplastic oligoastrocytoma. Tumor classification based on CIMP and 1p/19q status was significantly associated with survival, allowing a better prediction of outcome than the current histopathological classification: patients with CIMP(pos) tumors with 1p/19q codeletion (CIMP-codel) had the best prognosis, followed by patients with CIMP(pos) tumors but intact 1p/19q status (CIMP-non-codel). Patients with CIMP(neg) anaplastic gliomas (GBM-like) had the worst prognosis. Collectively, our data suggest that anaplastic gliomas can be grouped by IDH and 1p/19q status into three molecular groups that show clear links to underlying biology and a significant association with clinical outcome in a prospective trial cohort. PMID:25008768
Wiestler, Benedikt; Capper, David; Sill, Martin; Jones, David T W; Hovestadt, Volker; Sturm, Dominik; Koelsche, Christian; Bertoni, Anna; Schweizer, Leonille; Korshunov, Andrey; Wei�, Elisa K; Schliesser, Maximilian G; Radbruch, Alexander; Herold-Mende, Christel; Roth, Patrick; Unterberg, Andreas; Hartmann, Christian; Pietsch, Torsten; Reifenberger, Guido; Lichter, Peter; Radlwimmer, Bernhard; Platten, Michael; Pfister, Stefan M; von Deimling, Andreas; Weller, Michael; Wick, Wolfgang
Sequence analysis of a cDNA encoding a Group 3 LEA mRNA inducible by ABA or dehydration stress in wheat
A cDNA clone (pMA2005) of a Group 3 LEA (late embryogenesis abundant) protein has been sequenced from wheat. The wheat cDNA clone codes for a protein with ten tandem repeats of an 11 amino acid sequence and has homology to other Group 3 LEAs reported in barley, carrot, cotton and rape (L. Dure et al., Plant Mol Biol 12: 475�486,
Jeanne Curry; Craig F. Morris; M. K. Walker-Simmons
Chromosome 9: gene for blood group, Matt RidleySite: DNA Interactive (www.dnai.org)
NSDL National Science Digital Library
Interviewee: Matt Ridley DNAi Location:Genome>tour>genome spots>Blood groups Location: chromosome 9 gene name: ABO (galactosyl transferase) The ABO gene codes for an enzyme called galactosyl transferase and determines your blood group. In people with A and B blood groups, the gene differs by seven basepairs, four of which have an effect on the type, shape and activity of the enzyme. People with O blood group have a single deletion in the gene that causes an inactive protein to be made.
-base non 1-Base non Watson-Crick DNA Hybridization Simulation O O DNA Hybridization SimulationIntelligence Lab. School of Computer Science and Engineering, Seoul National University 1-Base non Watson-Crick DNA DNA . #12;Watson-Crick base pair 1-base dangling end hybridization . PCR
Complementation of DNA repair defect in xeroderma pigmentosum cells of group C by the transfer of human chromosome 5
Complementation of DNA excision repair defect in xeroderma pigmentosum cells of group C (XP-C) has been achieved by the transfer of human chromosome 5. Individual human chromosomes tagged with a selectable marker were transferred to XP-C cells by microcell fusion from mouse-human hybrid cell lines each bearing a single different human chromosome. Analysis of the chromosome transfer clones revealed that introduction of chromosome 5 into XP-C cells corrected the DNA repair defect as well as UV-sensitive phenotypes, while chromosomes 2, 6, 7, 9, 13, 15, 17, and 21 failed to complement. The introduced chromosome 5 in complemented UV[sup r] clones was distinguished from the parental XP-C chromosomes by polymorphism for dinucleotide (CA)[sub n] repeats at two loci, D5S117 and D5S209. In addition, an intact marked chromosome 5 was rescued into mouse cells from a complemented UV[sup r] clone by microcell fusion. Five subclones of a complemented clone that had lost the marked chromosome 5 exhibited UV-sensitive and repair-deficient phenotypes identical to parental XP-C cells. Concordant loss of the transferred chromosome and reappearance of XP-C phenotype further confirmed the presence of a DNA repair gene on human chromosome 5. 38 refs., 7 figs., 1 tab.
Kaur, G.P.; Athwal, R.S. (New Jersey Medical School, Newark (United States))
Syntheses of Two 5-Hydroxymethyl-2?-DeoxyCytidine Phosphoramidites with TBDMS as the 5-hydroxyl protecting group and Their Incorporation into DNA
5-Hydroxymethylcytosine (5-hmC) is a newly discovered DNA base modification in mammalian genomic DNA that is proposed to be a major epigenetic mark. We report here the syntheses of two new versions of phosphoramidites III and IV from dU in 18 and 32% overall yields, respectively, with TBDMS as the 5-hydroxyl protecting group. Phosphoramidites III and IV allow efficient incorporation of 5-hmC into DNA and a �one-step� deprotection procedure to cleanly remove all the protecting groups. A �two-step� deprotection strategy is compatible with ultra-mild DNA synthesis, which enables the synthesis of 5hmC-containing DNA with additional modifications. PMID:21462947
Song, Chun-Xiao; Pan, Tao; He, Chuan
Genome-wide DNA polymorphisms in seven rice cultivars of temperate and tropical japonica groups.
Elucidation of the rice genome is expected to broaden our understanding of genes related to the agronomic characteristics and the genetic relationship among cultivars. In this study, we conducted whole-genome sequencings of 6 cultivars, including 5 temperate japonica cultivars and 1 tropical japonica cultivar (Moroberekan), by using next-generation sequencing (NGS) with Nipponbare genome as a reference. The temperate japonica cultivars contained 2 sake brewing (Yamadanishiki and Gohyakumangoku), 1 landrace (Kameji), and 2 modern cultivars (Koshihikari and Norin 8). Almost >83% of the whole genome sequences of the Nipponbare genome could be covered by sequenced short-reads of each cultivar, including Omachi, which has previously been reported to be a temperate japonica cultivar. Numerous single nucleotide polymorphisms (SNPs), insertions, and deletions were detected among the various cultivars and the Nipponbare genomes. Comparison of SNPs detected in each cultivar suggested that Moroberekan had 5-fold more SNPs than the temperate japonica cultivars. Success of the 2 approaches to improve the efficacy of sequence data by using NGS revealed that sequencing depth was directly related to sequencing coverage of coding DNA sequences: in excess of 30� genome sequencing was required to cover approximately 80% of the genes in the rice genome. Further, the contigs prepared using the assembly of unmapped reads could increase the value of NGS short-reads and, consequently, cover previously unavailable sequences. These approaches facilitated the identification of new genes in coding DNA sequences and the increase of mapping efficiency in different regions. The DNA polymorphism information between the 7 cultivars and Nipponbare are available at NGRC_Rices_Build1.0 (http://www.nodai-genome.org/oryza_sativa_en.html). PMID:24466017
Arai-Kichise, Yuko; Shiwa, Yuh; Ebana, Kaworu; Shibata-Hatta, Mari; Yoshikawa, Hirofumi; Yano, Masahiro; Wakasa, Kyo
Genome-Wide DNA Polymorphisms in Seven Rice Cultivars of Temperate and Tropical Japonica Groups
Elucidation of the rice genome is expected to broaden our understanding of genes related to the agronomic characteristics and the genetic relationship among cultivars. In this study, we conducted whole-genome sequencings of 6 cultivars, including 5 temperate japonica cultivars and 1 tropical japonica cultivar (Moroberekan), by using next-generation sequencing (NGS) with Nipponbare genome as a reference. The temperate japonica cultivars contained 2 sake brewing (Yamadanishiki and Gohyakumangoku), 1 landrace (Kameji), and 2 modern cultivars (Koshihikari and Norin 8). Almost >83% of the whole genome sequences of the Nipponbare genome could be covered by sequenced short-reads of each cultivar, including Omachi, which has previously been reported to be a temperate japonica cultivar. Numerous single nucleotide polymorphisms (SNPs), insertions, and deletions were detected among the various cultivars and the Nipponbare genomes. Comparison of SNPs detected in each cultivar suggested that Moroberekan had 5-fold more SNPs than the temperate japonica cultivars. Success of the 2 approaches to improve the efficacy of sequence data by using NGS revealed that sequencing depth was directly related to sequencing coverage of coding DNA sequences: in excess of 30� genome sequencing was required to cover approximately 80% of the genes in the rice genome. Further, the contigs prepared using the assembly of unmapped reads could increase the value of NGS short-reads and, consequently, cover previously unavailable sequences. These approaches facilitated the identification of new genes in coding DNA sequences and the increase of mapping efficiency in different regions. The DNA polymorphism information between the 7 cultivars and Nipponbare are available at NGRC_Rices_Build1.0 (http://www.nodai-genome.org/oryza_sativa_en.html). PMID:24466017
Arai-Kichise, Yuko; Shiwa, Yuh; Ebana, Kaworu; Shibata-Hatta, Mari; Yoshikawa, Hirofumi; Yano, Masahiro; Wakasa, Kyo
The DNA-binding Polycomb-group protein Pleiohomeotic maintains both active and repressed transcriptional states through a single site
Although epigenetic maintenance of either the active or repressed transcriptional state often involves overlapping regulatory elements, the underlying basis of this is not known. Epigenetic and pairing-sensitive silencing are related properties of Polycomb-group proteins, whereas their activities are generally opposed by the trithorax group. Both groups modify chromatin structure, but how their opposing activities are targeted to allow differential maintenance remains a mystery. Here, we identify a strong pairing-sensitive silencing (PSS) element at the 3' border of the Drosophila even skipped (eve) locus. This element can maintain repression during embryonic as well as adult eye development. Transgenic dissection revealed that silencing activity depends on a binding site for the Polycomb-group protein Pleiohomeotic (Pho) and on pho gene function. Binding sites for the trithorax-group protein GAGA factor also contribute, whereas sites for the known Polycomb response element binding factors Zeste and Dsp1 are dispensible. Normally, eve expression in the nervous system is maintained throughout larval stages. An enhancer that functions fully in embryos does not maintain expression, but the adjacent PSS element confers maintenance. This positive activity also depends on pho gene activity and on Pho binding. Thus, a DNA-binding complex requiring Pho is differentially regulated to facilitate epigenetic transcriptional memory of both the active and the repressed state. PMID:19029043
Fujioka, Miki; Yusibova, Galina L.; Zhou, Jian; Jaynes, James B.
Testing the validity of Northern European species in the Chrysis ignita species group (Hymenoptera: Chrysididae) with DNA barcoding.
Containing more than a hundred species, the Chrysis ignita species group is the largest and one of the most taxonomically challenging groups in its genus. It has not been possible to resolve the taxonomy of the group using traditional methods due to the lack of robust diagnostic morphological characters. Here we present the results of a molecular analysis designed to delimit species in the Chrysis ignita group for the first time; using mitochondrial sequence data for 364 in-group specimens consisting of all 18 species known to occur in Northern Europe. Two mitochondrial loci were analysed: a COI gene fragment, and a continuous DNA sequence consisting of 16S rRNA, tRNAVal, 12S rRNA and ND4. Two approaches were employed for delimiting species: (1) genetic distance analysis based on the standard COI barcode sequences and; (2) phylogenetic analysis of the COI fragment together with rRNA genes. Both analyses yielded trees with similar topology, but support values for nodes were higher using the second approach. Fifteen species were distinguished in all analyses: Chrysis angustula Schenck, 1856, C. brevitarsis Thomson, 1870, C. clarinicollis Linsenmaier, 1951, C. corusca Valkeila, 1971, C. fulgida Linnaeus, 1761, C. ignita (Linnaeus, 1758), C. impressa Schenck, 1856, C. iris Christ, 1791, C. leptomandibularis Niehuis, 2000, C. longula Abeille de Perrin, 1879, C. ruddii Shuckard, 1837, C. schencki Linsenmaier, 1968, C. subcoriacea Linsenmaier, 1959, C. terminata Dahlbom, 1854 and C. vanlithi Linsenmaier, 1959. The specific status of C. mediata Linsenmaier, 1951 and C. solida Haupt, 1957 was not resolved. Included unidentified specimens grouped in three clusters, two of which are distinctly delimited and apparently represent cryptic species. The specific status of the unidentified samples in the third cluster remained unclear. Moreover, our data suggest the existence of additional cryptic species currently lumped under the names C. pseudobrevitarsis Linsenmaier, 1951 and C. schencki Linsenmaier, 1968. In conclusion, our results derived from analysis of mitochondrial loci strongly support the specific status of the majority of currently recognised species in the Chrysis ignita species group, and suggest the existence of additional cryptic species in Northern Europe. Thus, considering the difficulties that often arise during species determination based on morphological characters, the mtDNA loci used here appear highly suitable for assisting species delimitation in this group as well as identification of specimens.� PMID:24869539
Soon, Villu; Budrys, Eduardas; Orlovskyt?, Svetlana; Paukkunen, Juho; Odegaard, Frode; Ljubomirov, Toshko; Saarma, Urmas
Both the folate cycle and betaine-homocysteine methyltransferase contribute methyl groups for DNA methylation in mouse blastocysts.
The embryonic pattern of global DNA methylation is first established in the inner cell mass (ICM) of the mouse blastocyst. The methyl donor S-adenosylmethionine (SAM) is produced in most cells through the folate cycle, but only a few cell types generate SAM from betaine (N,N,N-trimethylglycine) via betaine-homocysteine methyltransferase (BHMT), which is expressed in the mouse ICM. Here, mean ICM cell numbers decreased from 18-19 in controls to 11-13 when the folate cycle was inhibited by the antifolate methotrexate and to 12-14 when BHMT expression was knocked down by antisense morpholinos. Inhibiting both pathways, however, much more severely affected ICM development (7-8 cells). Total SAM levels in mouse blastocysts decreased significantly only when both pathways were inhibited (from 3.1 to 1.6 pmol/100 blastocysts). DNA methylation, detected as 5-methylcytosine (5-MeC) immunofluorescence in isolated ICMs, was minimally affected by inhibition of either pathway alone but decreased by at least 45-55% when both BHMT and the folate cycle were inhibited simultaneously. Effects on cell numbers and 5-MeC levels in the ICM were completely rescued by methionine (immediate SAM precursor) or SAM. Both the folate cycle and betaine/BHMT appear to contribute to a methyl pool required for normal ICM development and establishing initial embryonic DNA methylation.-Zhang, B., Denomme, M.M., White, C. R., Leung, K.-Y., Lee, M. B., Greene, N. D. E., Mann, M. R. W., Trasler, J. M., Baltz, J. M. Both the folate cycle and betaine-homocysteine methyltransferase contribute methyl groups for DNA methylation in mouse blastocysts. PMID:25466894
Zhang, Baohua; Denomme, Michelle M; White, Carlee R; Leung, Kit-Yi; Lee, Martin B; Greene, Nicholas D E; Mann, Mellissa R W; Trasler, Jacquetta M; Baltz, Jay M
Rapid plant identification using species- and group-specific primers targeting chloroplast DNA.
Plant identification is challenging when no morphologically assignable parts are available. There is a lack of broadly applicable methods for identifying plants in this situation, for example when roots grow in mixture and for decayed or semi-digested plant material. These difficulties have also impeded the progress made in ecological disciplines such as soil- and trophic ecology. Here, a PCR-based approach is presented which allows identifying a variety of plant taxa commonly occurring in Central European agricultural land. Based on the trnT-F cpDNA region, PCR assays were developed to identify two plant families (Poaceae and Apiaceae), the genera Trifolium and Plantago, and nine plant species: Achillea millefolium, Fagopyrum esculentum, Lolium perenne, Lupinus angustifolius, Phaseolus coccineus, Sinapis alba, Taraxacum officinale, Triticum aestivum, and Zea mays. These assays allowed identification of plants based on size-specific amplicons ranging from 116 bp to 381 bp. Their specificity and sensitivity was consistently high, enabling the detection of small amounts of plant DNA, for example, in decaying plant material and in the intestine or faeces of herbivores. To increase the efficacy of identifying plant species from large number of samples, specific primers were combined in multiplex PCRs, allowing screening for multiple species within a single reaction. The molecular assays outlined here will be applicable manifold, such as for root- and leaf litter identification, botanical trace evidence, and the analysis of herbivory. PMID:22253728
Wallinger, Corinna; Juen, Anita; Staudacher, Karin; Schallhart, Nikolaus; Mitterrutzner, Evi; Steiner, Eva-Maria; Thalinger, Bettina; Traugott, Michael
Rapid Plant Identification Using Species- and Group-Specific Primers Targeting Chloroplast DNA
Plant identification is challenging when no morphologically assignable parts are available. There is a lack of broadly applicable methods for identifying plants in this situation, for example when roots grow in mixture and for decayed or semi-digested plant material. These difficulties have also impeded the progress made in ecological disciplines such as soil- and trophic ecology. Here, a PCR-based approach is presented which allows identifying a variety of plant taxa commonly occurring in Central European agricultural land. Based on the trnT-F cpDNA region, PCR assays were developed to identify two plant families (Poaceae and Apiaceae), the genera Trifolium and Plantago, and nine plant species: Achillea millefolium, Fagopyrum esculentum, Lolium perenne, Lupinus angustifolius, Phaseolus coccineus, Sinapis alba, Taraxacum officinale, Triticum aestivum, and Zea mays. These assays allowed identification of plants based on size-specific amplicons ranging from 116 bp to 381 bp. Their specificity and sensitivity was consistently high, enabling the detection of small amounts of plant DNA, for example, in decaying plant material and in the intestine or faeces of herbivores. To increase the efficacy of identifying plant species from large number of samples, specific primers were combined in multiplex PCRs, allowing screening for multiple species within a single reaction. The molecular assays outlined here will be applicable manifold, such as for root- and leaf litter identification, botanical trace evidence, and the analysis of herbivory. PMID:22253728
Staudacher, Karin; Schallhart, Nikolaus; Mitterrutzner, Evi; Steiner, Eva-Maria; Thalinger, Bettina; Traugott, Michael
Phylogeny of All Major Groups of Cetaceans Based on DNA Sequences from Three Mitochondrial Genes
Traditionally, living cetaceans (order Cetacea) are classified into two highly distinct suborders: the echolocating toothed whales, Odontoceti, and the filter-feeding baleen whales, Mysticeti. A molecular phylogeny based on 1,352 base pairs of two mitochondrial ribosomal gene segments and the mitochondrial cytochrome b gene for all major groups of cetaceans contradicts this long-accepted taxonomic subdivision. One group of toothed whales, the
Michel C. Milinkovitch; Jeffrey R. Powell
Functions of the high mobility group protein, Abf2p, in mitochondrial DNA segregation, recombination and copy number in Saccharomyces cerevisiae.
Previous studies have established that the mitochondrial high mobility group (HMG) protein, Abf2p, of Saccharomyces cerevisiae influences the stability of wild-type (rho+) mitochondrial DNA (mtDNA) and plays an important role in mtDNA organization. Here we report new functions for Abf2p in mtDNA transactions. We find that in homozygous deltaabf2 crosses, the pattern of sorting of mtDNA and mitochondrial matrix protein is altered, and mtDNA recombination is suppressed relative to homozygous ABF2 crosses. Although Abf2p is known to be required for the maintenance of mtDNA in rho+ cells growing on rich dextrose medium, we find that it is not required for the maintenance of mtDNA in p cells grown on the same medium. The content of both rho+ and rho- mtDNAs is increased in cells by 50-150% by moderate (two- to threefold) increases in the ABF2 copy number, suggesting that Abf2p plays a role in mtDNA copy control. Overproduction of Abf2p by > or = 10-fold from an ABF2 gene placed under control of the GAL1 promoter, however, leads to a rapid loss of rho+ mtDNA and a quantitative conversion of rho+ cells to petites within two to four generations after a shift of the culture from glucose to galactose medium. Overexpression of Abf2p in rho- cells also leads to a loss of mtDNA, but at a slower rate than was observed for rho+ cells. The mtDNA instability phenotype is related to the DNA-binding properties of Abf2p because a mutant Abf2p that contains mutations in residues of both HMG box domains known to affect DNA binding in vitro, and that binds poorly to mtDNA in vivo, complements deltaabf2 cells only weakly and greatly lessens the effect of overproduction on mtDNA instability. In vivo binding was assessed by colocalization to mtDNA of fusions between mutant or wild-type Abf2p and green fluorescent protein.These findings are discussed in the context of a model relating mtDNA copy number control and stability to mtDNA recombination. PMID:9581629
Zelenaya-Troitskaya, O; Newman, S M; Okamoto, K; Perlman, P S; Butow, R A
Examination of species boundaries in the Acropora cervicornis group (Scleractinia, cnidaria) using nuclear DNA sequence analyses.
Although Acropora is the most species-rich genus of the scleractinian (stony) corals, only three species occur in the Caribbean: A. cervicornis, A. palmata and A. prolifera. Based on overall coral morphology, abundance and distribution patterns, it has been suggested that A. prolifera may be a hybrid between A. cervicornis and A. palmata. The species boundaries among these three morphospecies were examined using DNA sequence analyses of the nuclear Pax-C 46/47 intron and the ribosomal DNA Internal Transcribed Spacer (ITS1 and ITS2) and 5.8S regions. Moderate levels of sequence variability were observed in the ITS and 5.8S sequences (up to 5.2% overall sequence difference), but variability within species was as large as between species and all three species carried similar sequences. Since this is unlikely to represent a shared ancestral polymorphism, the data suggest that introgressive hybridization occurs among the three species. For the Pax-C intron, A. cervicornis and A. palmata had very distinct allele frequencies and A. cervicornis carried a unique allele at a frequency of 0.769 (although sequence differences between alleles were small). All A. prolifera colonies examined were heterozygous for the Pax-C intron, whereas heterozygosity was only 0.286 and 0.333 for A. cervicornis and A. palmata, respectively. These data support the hypothesis that A. prolifera is the product of hybridization between two species that have a different allelic composition for the Pax-C intron, i.e. A. cervicornis and A. palmata. We therefore suggest that A. prolifera is a hybrid between A. cervicornis and A. palmata, which backcrosses with the parental species at low frequency. PMID:10972775
Oppen, M J; Willis, B L; Vugt, H W; Miller, D J
Group I introns in small subunit ribosomal DNA of several Phaeosphaeria species
Technology Transfer Automated Retrieval System (TEKTRAN)
In a study of small subunit ribosomal RNA (SSU-rRNA) gene sequences in Phaeosphaeria species, group I introns were found in 9 of 10 P. avenaria f.sp. avenaria (Paa) isolates, 1 of 2 Phaeosphaeria sp. (P-rye) isolates from Polish rye (Sn48-1), 1 Phaeosphaeria sp. from dallis grass (P-dg) (S-93-48) an...
Cloning of the bovine and rat Fanconi anemia group C cDNA
Fanconi anemia (FA) is a rare autosomal recessive disorder characterized by a diverse array of symptoms including congenital malformations, progressive pancytopenia, predisposition to the development of malignancies, and cellular hypersensitivity to DNAcrosslinking agents (Strathdee and Buchwald 1992). The clinical heterogeneity of FA may be attributable to genetic heterogeneity in the disease. Five genetic complementation groups, A, B, C, D, and
Jasmine Ching Ying Wong; Noa Alon; Manuel Buchwald
Microsatellite DNA analysis shows that greater sage grouse leks are not kin groups.
The spectacular social courtship displays of lekking birds are thought to evolve via sexual selection, but this view does not easily explain the participation of many males that apparently fail to mate. One of several proposed solutions to this 'lek skew paradox' is that kin selection favours low-ranking males joining leks to increase the fitness of closely related breeders. We investigated the potential for kin selection to operate in leks of the greater sage grouse, Centrocercus urophasianus, by estimating relatedness between lekking males using microsatellite DNA markers. We also calibrated these estimates using data from known families. Mean relatedness within leks was statistically indistinguishable from zero. We also found no evidence for local clustering of kin during lek display, although males tended to range closer to kin when off the lek. These results make kin selection an unlikely solution to the lek skew paradox in sage grouse. Together with other recent studies, they also raise the question of why kin selection apparently promotes social courtship in some lekking species, but not in others. PMID:16313605
Gibson, Robert M; Pires, Debra; Delaney, Kathleen S; Wayne, Robert K
DNA methylation of polycomb group target genes in cores taken from breast cancer centre and periphery
We previously demonstrated that methylation of neugogenic differentiation 1 (NEUROD1) gene, a polycomb group target (PCGT) gene is a predictor of response to neoadjuvant chemotherapy in breast cancer. Here,\\u000a we address the question whether NEUROD1 methylation provides clinical information independent from its expression level, and whether PCGT methylation is homogeneous\\u000a in breast cancer. We examined: (1) NEUROD1 methylation and mRNA
Evangelia-Ourania Fourkala; Cornelia Hauser-Kronberger; Sophia Apostolidou; Matthew Burnell; Allison Jones; Johannes Grall; Roland Reitsamer; Heidi Fiegl; Ian Jacobs; Usha Menon; Martin Widschwendter
Identification of Vibrio parahaemolyticus Pandemic Group-Specific DNA Sequence by Genomic Subtraction
Vibrio parahaemolyticus is a major cause of seafood-borne gastroenteritis, frequently associated with the consumption of raw or undercooked seafood (2). Although various serovars of the bacterium can cause infections, O3:K6, O4:K68, and sev- eral other serovars producing thermostable direct hemolysin (TDH) have been recognized as the predominant group re- sponsible for most outbreaks occurring worldwide since 1996 (6, 8). Past
Masatoshi Okura; Ro Osawa; Eiji Arakawa; Jun Terajima; Haruo Watanabe
Mitochondrial DNA diversity in two ethnic groups in southeastern Kenya: perspectives from the northeastern periphery of the Bantu expansion
The Bantu languages are widely distributed throughout sub-Saharan Africa. Genetic research supports linguists and historians who argue that migration played an important role in the spread of this language family, but the genetic data also indicates a more complex process involving substantial gene flow with resident populations. In order to understand the Bantu expansion process in east Africa, mtDNA hypervariable region I variation in 352 individuals from the Taita and Mijikenda ethnic groups was analyzed, and we evaluated the interactions that took place between the Bantu- and non-Bantu-speaking populations in east Africa. The Taita and Mijikenda are Bantu-speaking agropastoralists from southeastern Kenya, at least some of whose ancestors probably migrated into the area as part of Bantu migrations that began around 3,000 BCE. Our analyses indicate that they show some distinctive differences that reflect their unique cultural histories. The Taita are genetically more diverse than the Mijikenda with larger estimates of genetic diversity. The Taita cluster with other east African groups, having high frequencies of haplogroups from that region, while the Mijikenda have high frequencies of central African haplogroups and cluster more closely with central African Bantu-speaking groups. The non-Bantu speakers who lived in southeastern Kenya before Bantu speaking groups arrived were at least partially incorporated into what are now Bantu-speaking Taita groups. In contrast, gene flow from non-Bantu speakers into the Mijikenda was more limited. These results suggest a more complex demographic history where the nature of Bantu and non-Bantu interactions varied throughout the area. PMID:23382080
Batai, Ken; Babrowski, Kara B.; Arroyo, Juan Pablo; Kusimba, Chapurukha M.; Williams, Sloan R.
Survey of chimeric IStron elements in bacterial genomes: multiple molecular symbioses between group I intron ribozymes and DNA transposons
IStrons are chimeric genetic elements composed of a group I intron associated with an insertion sequence (IS). The group I intron is a catalytic RNA providing the IStron with self-splicing ability, which renders IStron insertions harmless to the host genome. The IS element is a DNA transposon conferring mobility, and thus allowing the IStron to spread in genomes. IStrons are therefore a striking example of a molecular symbiosis between unrelated genetic elements endowed with different functions. In this study, we have conducted the first comprehensive survey of IStrons in sequenced genomes that provides insights into the distribution, diversity, origin and evolution of IStrons. We show that IStrons have a restricted phylogenetic distribution limited to two bacterial phyla, the Firmicutes and the Fusobacteria. Nevertheless, diverse IStrons representing two major groups targeting different insertion site motifs were identified. This taken with the finding that while the intron components of all IStrons belong to the same structural class, they are fused to different IS families, indicates that multiple intron�IS symbioses have occurred during evolution. In addition, introns and IS elements related to those that were at the origin of IStrons were also identified. PMID:25324310
Tourasse, Nicolas J.; Stabell, Fredrik B.; Kolst�, Anne-Brit
Molecular changes in the d -bifunctional protein cDNA sequence in australasian patients belonging to the bifunctional protein complementation group
The cDNA sequence for the human d-bifunctional protein (D-BP: 17?-hydroxysteroid dehydrogenase IV) was investigated in patients with peroxisomal disorders\\u000a belonging to the BP complementation group (CG). In three cases, analysis of polymerase chain reaction products generated from\\u000a the patients' cDNA indicated the presence of a deletion within the region corresponding to nucleotides 209�537 of the normal\\u000a cDNA sequence. Subsequent sequencing
Barbara C. Paton; Anthony N. Pollard
Chemical synthesis of H-phosphonate DNA without using N-protecting groups.
Oligodeoxyribonucleotides were synthesized by using N-unprotected H-phosphonate monomers. It was found that the amino groups of nucleosides were not modified during condensation where benzotriazolyloxy carbonium and phosphonium types of compounds were employed as condensing reagents. The most effective condensing reagent for rapid internucleotidic bond formation was found to be 2-(benzotriazol-1-yloxy)-1,1-dimethyl-2-(pyrrolidin-1- yl)-1,3,2- diazaphospholidinium hexafluorophosphate (BOMP). In the present H-phosphonate approach, 2-benzenesulfonyl-3-(3-nitrophenyl)oxaziridine (BNO) was successfully employed as a new oxidizing reagent for oxidation of the H-phosphonate linkages under anhydrous conditions. PMID:9585978
Wada, T; Honda, F; Sato, Y; Kawahara, S; Sekine, M
Multicenter Clinical Evaluation of the illumigene Group A Streptococcus DNA Amplification Assay for Detection of Group A Streptococcus from Pharyngeal Swabs
Acute pharyngitis is a nonspecific symptom that can result from a number of viral or bacterial infections. For most etiologies, symptoms are self-limited and resolve without lasting effects; however, pharyngitis resulting from infection with Streptococcus pyogenes (a group A Streptococcus [GAS]) can be associated with serious sequelae, including acute rheumatic fever and acute glomerulonephritis. Rapid accurate detection of GAS in pharyngeal specimens from individuals suffering from pharyngitis aids in the management and selection of antibiotic therapy for these patients. A total of 796 pharyngeal swabs were collected at three separate clinical centers. Each specimen was analyzed using the illumigene group A strep DNA amplification assay (Meridian Bioscience Inc., Cincinnati, OH). To confirm GAS identification, the results were compared to those from direct and extracted culture methods using Gram staining and a GAS-specific latex agglutination test. Discrepant results were resolved using an alternative nucleic acid amplification test. The prevalence of culture-detected GAS in this study was 12.8% (102/796 specimens). The illumigene assay detected GAS in 74/74 direct culture-positive specimens (100% sensitivity) and 100/102 extracted culture-positive specimens (98.0% sensitivity). GAS was detected by the illumigene assay in an additional 42 specimens that were direct culture negative (94.2% specificity) and 16 specimens that were extracted culture negative (97.7% specificity). Discrepant analysis using an alternative molecular assay detected GAS nucleic acid in 13/16 (81.3%) false-positive specimens and 1/2 false-negative specimens, resulting in a final sensitivity of 99.0% and a specificity of 99.6% for the detection of GAS in pharyngeal swabs using the illumigene assay. PMID:23447639
Anderson, Neil W.; Buchan, Blake W.; Mayne, Donna; Mortensen, Joel E.; Mackey, Tami-Lea A.
NSDL National Science Digital Library
This interactive Flash applet models the measurement interpretation of division. A child or teacher chooses a total number of objects and a divisor representing the size of equal groups. The applet allows the user to move the objects into equal groups and links the process to jumps on a number line. The applet can be used to introduce children to remainders and to reinforce the language and notation of division. It works well on an interactive white board or projector. A teacher's guide to this collection of applets is cataloged separately.
1971 1976 (renormalzation group
RNARNA AUCG RNA Ribosome translation DNA DNA RNA RNA RNA AIDS RNA DNA DNA2006 8 676 / Go 19 20 DNA RNA DNA RNA 1971 1976 (renormalzation group 1998 2002 DNA (protein) 20 (amino acid) (main chain)(N) (C)( C ) 20 (side chain) (1s-1s) X
DNA Evidence on the Phylogenetic Systematics of New World Monkeys: Support for the Sister-Grouping of Cebus and Saimiri from Two Unlinked Nuclear Genes
Previous inferences from ?-globin gene sequences on cladistic relationships among the 16 extant genera of Ceboidea (the New World monkeys) were tested by strength of grouping and bootstrap values for the clades in the most parsimonious trees found: for this epsilon data set enlarged with additional Cebus and Saimiri orthologues; for another nuclear DNA sequence data set consisting of IRBP
M. L. Harada; H. Schneider; M. P. C. Schneider; I. Sampaio; J. Czelusniak; M. Goodman
Replacement of a Thiourea with an Amidine Group in a Monofunctional Platinum�acridine Antitumor Agent. Effect on DNA Interactions, DNA Adduct Recognition and Repair
A combination of biophysical, biochemical, and computational techniques was used to delineate mechanistic differences between the platinum�acridine hybrid agent [PtCl(en)(L)](NO3)2 (complex 1, en = ethane-1,2-diamine, L = 1-[2-(acridin-9-ylamino)ethyl]-1,3- dimethylthiourea) and a considerably more potent second-generation analogue containing L? = N-[2-(acridin-9-ylamino)ethyl]-Nmethylpropionamidine (complex 2). Calculations at the density functional theory level provide a rationale for the binding preference of both complexes for guanine-N7 and the relatively high level of adenine adducts observed for compound 1. A significant rate enhancement is observed for binding of the amidine-based complex 2 with DNA compared with the thiourea-based prototype 1. Studies conducted with chemical probes and on the bending and unwinding of model duplex DNA suggest that adducts of complex 2 perturb B-form DNA more severely than complex 1, however, without denaturing the double strand and significantly less than cisplatin. Circular and linear dichroism spectroscopies and viscosity measurements suggest that subtle differences exist between the intercalation modes and adduct geometries of the two complexes. The adducts formed by complex 2 most efficiently inhibit transcription of the damaged DNA by RNA polymerase II. Not only do complexes 1 and 2 cause less distortion to DNA than cisplatin, they also do not compromise the thermodynamic stability of the modified duplex. This leads to a decreased or negligible affinity of HMG domain proteins for the adducts formed by either Pt-acridine complex. In a DNA repair synthesis assay the lesions formed by complex 2 were repaired less efficiently than those formed by complex 1. These significant differences in DNA adduct formation, structure, and recognition between the two acridine complexes and cisplatin help to elucidate why compound 2 is highly active in cisplatin-resistant, repair proficient cancer cell lines. PMID:21806015
Kostrhunova, Hana; Malina, Jaroslav; Pickard, Amanda J.; Stepankova, Jana; Vojtiskova, Marie; Ka�p�rkova, Jana; Muchova, Tereza; Rohlfing, Matthew L.; Bierbach, Ulrich; Brabec, Viktor
SSX2 is a novel DNA-binding protein that antagonizes polycomb group body formation and gene repression.
Polycomb group (PcG) complexes regulate cellular identity through epigenetic programming of chromatin. Here, we show that SSX2, a germline-specific protein ectopically expressed in melanoma and other types of human cancers, is a chromatin-associated protein that antagonizes BMI1 and EZH2 PcG body formation and derepresses PcG target genes. SSX2 further negatively regulates the level of the PcG-associated histone mark H3K27me3 in melanoma cells, and there is a clear inverse correlation between SSX2/3 expression and H3K27me3 in spermatogenesis. However, SSX2 does not affect the overall composition and stability of PcG complexes, and there is no direct concordance between SSX2 and BMI1/H3K27me3 presence at regulated genes. This suggests that SSX2 antagonizes PcG function through an indirect mechanism, such as modulation of chromatin structure. SSX2 binds double-stranded DNA in a sequence non-specific manner in agreement with the observed widespread association with chromatin. Our results implicate SSX2 in regulation of chromatin structure and function. PMID:25249625
Gjerstorff, Morten Frier; Relster, Mette Marie; Greve, Katrine Buch Viden; Moeller, Jesper Bonnet; Elias, Daniel; Lindgreen, Jonas N�rrelund; Schmidt, Steffen; Mollenhauer, Jan; Voldborg, Bj�rn; Pedersen, Christina B�g; Br�ckmann, Nadine Heidi; M�llegaard, Niels Erik; Ditzel, Henrik J�rn
SSX2 is a novel DNA-binding protein that antagonizes polycomb group body formation and gene repression
Polycomb group (PcG) complexes regulate cellular identity through epigenetic programming of chromatin. Here, we show that SSX2, a germline-specific protein ectopically expressed in melanoma and other types of human cancers, is a chromatin-associated protein that antagonizes BMI1 and EZH2 PcG body formation and derepresses PcG target genes. SSX2 further negatively regulates the level of the PcG-associated histone mark H3K27me3 in melanoma cells, and there is a clear inverse correlation between SSX2/3 expression and H3K27me3 in spermatogenesis. However, SSX2 does not affect the overall composition and stability of PcG complexes, and there is no direct concordance between SSX2 and BMI1/H3K27me3 presence at regulated genes. This suggests that SSX2 antagonizes PcG function through an indirect mechanism, such as modulation of chromatin structure. SSX2 binds double-stranded DNA in a sequence non-specific manner in agreement with the observed widespread association with chromatin. Our results implicate SSX2 in regulation of chromatin structure and function. PMID:25249625
Gjerstorff, Morten Frier; Relster, Mette Marie; Greve, Katrine Buch Viden; Moeller, Jesper Bonnet; Elias, Daniel; Lindgreen, Jonas N�rrelund; Schmidt, Steffen; Mollenhauer, Jan; Voldborg, Bj�rn; Pedersen, Christina B�g; Br�ckmann, Nadine Heidi; M�llegaard, Niels Erik; Ditzel, Henrik J�rn
A DNA vaccine encoding a chimeric allergen derived from major group 1 allergens of dust mite can be used for specific immunotherapy
Immunization with DNA-based constructs has been shown to be against the antigen and the response is skewed in such a way as to ameliorate the symptoms of allergic disease. This approach is particularly useful in the treatment of allergic inflammatory diseases, such as asthma. The major group 1 allergen from house dust mites is one of the triggers of allergic asthma. This study explores whether a chimeric gene R8, derived from the major group 1 allergen of house dust mite species (Dermatophagoides farinae and Dermatophagoides pteronyssinus), can be expressed in Human Embryonic Kidney 293 cells (HEK 293T) and whether such a construct can be used as a DNA vaccine in asthma therapy. The eukaryotic expression vector pcDNA3.1 was used to express the R8 molecule in HEK 293T cells and successful expression of R8 was confirmed using a fluorescence microscope and western blot analysis. The efficacy of R8 as DNA vaccine was also assessed in a mouse asthma model. The in vivo data showed that R8 rectified the TH1/TH2 imbalance typical of allergic inflammation and stimulated the proliferation of regulatory T (Treg) cells. Immunization with the R8 construct also decreased serum allergen-specific IgE production in this mouse asthma model. Our findings suggest that R8 may be a feasible potential DNA vaccine for specific immunotherapy (SIT) in the treatment of allergic asthma. PMID:25337189
Sun, Tong; Yin, Kang; Wu, Lu-Yi; Jin, Wen-Jie; Li, Yang; Sheng, Bin; Jiang, Yu-Xin
Conjugative plasmids of enteric bacteria from many different incompatibility groups have similar genes for single-stranded DNA-binding proteins.
Among 30 conjugative plasmids of enteric bacteria from 23 incompatibility (Inc) groups, we found 19 (from 12 Inc groups) which can complement defects caused by a defective single-stranded DNA-binding protein of Escherichia coli K-12. The genes which are responsible for the complementation from three of these plasmids (Inc groups I1, Y, and 9) were cloned. These genes showed extensive homology with each other and with the E. coli F factor ssb gene (formerly denoted ssf), which codes for a single-stranded DNA binding protein. The proteins coded for by the cloned genes bound tightly to single-stranded DNA. Six other ssb- -complementing plasmids were tested for homology to the F factor ssb gene, and all of these showed homology, as did one of the ssb- -noncomplementing plasmids. Plasmids from a total of 13 different Inc groups of enteric bacteria were found to be likely to have genes with some homology to the ssb gene of the F factor. For plasmids from several different Inc groups, we found no evidence for strong homology with ssb of the F factor. Images PMID:3884590
Golub, E I; Low, K B
mtDNA G10398A variation provides risk to type 2 diabetes in population group from the Jammu region of India.
Mitochondrion plays an integral role in glucose metabolism and insulin secretion. Mitochondrial electron-transport chain (ETC) is involved in adenosine triphosphate (ATP) generation and ATP mediated insulin secretion in pancreatic ?-cells. ?-cell dysfunction is a critical component in the pathogenesis of type 2 diabetes (T2D). The mtDNA G10398A variation (amino acid change: Alanine�?�Threonine) within the NADH dehydrogenase (ND3) subunit of complex I of mtDNA ETC, has emerged as a variation of clinical significance in various disorders including T2D. This variation is supposed to result in altered complex I function, leading to an increased rate of electron leakage and reactive oxygen species (ROS) production, which might cause ?-cell damage and impaired insulin secretion. The aim of the study was to explore the association of mtDNA G10398A variation with T2D in a total of 439 samples (196 T2D cases and 243 healthy controls) belonging to the Jammu region of Jammu and Kashmir (J&K). The candidate gene association analyses showed significant association of mtDNA G10398A variant with T2D and the estimated odds ratio (OR) was 2.83 (1.64-4.90 at 95% CI) in the studied population group. The extent of genetic heterogeneity in T2D and diversity of the Indian population groups, make such replication studies pertinent to understand the etiology of T2D in these population groups. PMID:25606409
Sharma, Varun; Sharma, Indu; Singh, Vishav Pratap; Verma, Sonali; Pandita, Anil; Singh, Vinod; Rai, Ekta; Sharma, Swarkar
Dna Systems for B-Z Transition and Their Significance as Epigenetic Model: The Fundamental Role of the Methyl Group
Epigenetic systems involved in the dynamics of gene expression, which are fundamental to cell determination and function without alteration in DNA sequences, are based on methylation of the N-terminal tails of lysine residues and DNA methylation. We demonstrate the vital importance for genetic transfer by different (hydrogen) networks, suggesting a complex interaction between the two epigenetic modifications. In other words,
Henk M. Buck
Spectroscopic study on the interaction of ct-DNA with manganese Salen complex containing triphenyl phosphonium groups.
The DNA binding properties of a bulky and hydrophobic Schiff base complex of manganese(III) [N,N'-bis(5-(triphenyl phosphonium methyl)salicylidene)-1,2-ethylene diamine chloride Mn(III) acetate] was examined by spectroscopic techniques. UV-vis titration data indicate both hypo and hyperchromic effect with addition of DNA to complex. A competitive binding study showed that the enhanced emission intensity of ethidium bromide (EB) in the presence of DNA was quenched by adding Mn Salen complex. This finding indicates that Mn Salen complex displaces EB from its binding site in DNA. Helix melting studies indicate improvement in the helix stability, and an increase in the melting temperature. The analysis of CD spectra represents the structural changes in DNA due to the binding of Mn Salen complex. The binding constant has been calculated using absorbance and fluorescence data. The results also represent that the binding process proceeds by strong electrostatic and hydrophobic interactions. PMID:22306451
Dehkordi, Maryam Nejat; Bordbar, Abdol-Khalegh; Lincoln, Per; Mirkhani, Valiollah
Spectroscopic study on the interaction of ct-DNA with manganese Salen complex containing triphenyl phosphonium groups
NASA Astrophysics Data System (ADS)
The DNA binding properties of a bulky and hydrophobic Schiff base complex of manganese(III) [N,N'-bis(5-(triphenyl phosphonium methyl)salicylidene)-1,2-ethylene diamine chloride Mn(III) acetate] was examined by spectroscopic techniques. UV-vis titration data indicate both hypo and hyperchromic effect with addition of DNA to complex. A competitive binding study showed that the enhanced emission intensity of ethidium bromide (EB) in the presence of DNA was quenched by adding Mn Salen complex. This finding indicates that Mn Salen complex displaces EB from its binding site in DNA. Helix melting studies indicate improvement in the helix stability, and an increase in the melting temperature. The analysis of CD spectra represents the structural changes in DNA due to the binding of Mn Salen complex. The binding constant has been calculated using absorbance and fluorescence data. The results also represent that the binding process proceeds by strong electrostatic and hydrophobic interactions.
Dehkordi, Maryam Nejat; Bordbar, Abdol-Khalegh; Lincoln, Per; Mirkhani, Valiollah
Convenient and efficient approach to the permanent or reversible conjugation of RNA and DNA sequences with functional groups.
The conversion of 3',5'-disilylated 2'-O-(methylthiomethyl)ribonucleosides to 2'-O-(phthalimidooxymethyl)ribonucleosides is achieved in yields of 66% to 94%. Desilylation and dephtalimidation of these ribonucleosides by treatment with NH(4)F in MeOH produce 2'-O-aminooxymethylated ribonucleosides, which are efficient in producing stable and yet reversible 2'-conjugates upon reaction with 1-pyrenecarboxaldehyde. Exposure of 2'-pyrenylated ribonucleosides to 0.5 M tetra-n-butylammonium fluoride (TBAF) in THF or DMSO results in the cleavage of their iminoether functions to give the native ribonucleosides along with an innocuous nitrile side product. Conversely, the reaction of 2'-O-(aminooxymethyl)uridine with 5-cholesten-3-one leads to a permanent uridine 2'-conjugate, which is left unreacted when treated with TBAF. The versatility and uniqueness of 2'-O-(aminooxymethyl)ribonucleosides is demonstrated by the single or double incorporation of a reversible pyrenylated uridine 2'-conjugate into an RNA sequence. Furthermore, the conjugation of 2'-O-(aminooxymethyl)ribonucleosides with various aldehydes, including those generated from their acetals, is also presented. The preparation of 5'-O-(aminooxymethyl)thymidine is also achieved, albeit in modest yields, from the conversion of 5'-O-methylthiomethyl-3'-O-(levulinyl)thymidine to 5'-O-phthalimidooxymethyl-3'-O-(levuliny)lthymidine followed by hydrazinolysis of both 5'-phthalimido and 3'-levulinyl groups. Pyrenylation of the 5'-O-(aminooxymethyl)deoxyribonucleoside also provides a reversible 5'-conjugate that is sensitive to TBAF, thereby further demonstrating the usefulness of 5'-O-(aminooxymethyl)deoxyribonucleosides for permanent or reversible modification of DNA sequences. Curr. Protoc. Nucleic Acid Chem. 50:4.52.1-4.52.36. � 2012 by John Wiley & Sons, Inc. PMID:22956458
Cie?lak, Jacek; Aus�n, Cristina; Grajkowski, Andrzej; Beaucage, Serge L
NSDL National Science Digital Library
Students reinforce their knowledge that DNA is the genetic material for all living things by modeling it using toothpicks and gumdrops that represent the four biochemicals (adenine, thiamine, guanine, and cytosine) that pair with each other in a specific pattern, making a double helix. They investigate specific DNA sequences that code for certain physical characteristics such as eye and hair color. Student teams trade DNA "strands" and de-code the genetic sequences to determine the physical characteristics (phenotype) displayed by the strands (genotype) from other groups. Students extend their knowledge to learn about DNA fingerprinting and recognizing DNA alterations that may result in genetic disorders.
Integrated Teaching and Learning Program,
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DNA conjugation andDNA conjugation and reversibility onreversibility on chitosan surfaceschitosan surfaceschitosan surfaceschitosan surfaces Rubloff Research Group Accomplishments #12;DNA conjugation and reversibility onDNA conjugation and reversibility on chitosan surfaceschitosan surfaces Accomplishment Single
Rubloff, Gary W.
[Genetic diversity and relatives of the goitered gazelle (Gazella subgutturosa) groups from Uzbekistan, Turkmenistan, and Azerbaijan: analysis of the D-loop of mitochondrial DNA].
Polymorphism of the nucleotide sequence of a hypervariable fragment of the D-loop (985 bp) of mtDNA in 76 Goitered gazelles of subspecies Gazella subgutturosa subgutturosa from Uzbekistan, Turkmenistan, and Azerbaijan was studied. The genetic similarity of gazelles from Turkmenistan and Uzbekistan has been identified. The population of gazelles from Shirvanskaya steppe reserve (Azerbaijan) is unique and strictly isolated from other groups studied. A high haplotypic (H = 0.9649 +/- 0.0091) and relatively low nucleotide diversity (pi = 0.0212 +/- 0.0105) were noted for all investigated groups of gazelle based on this mtDNA fragment, which is probably related to ecological peculiarities of the species and the history of formation of regional populations. PMID:22292288
Sorokin, P A; Soldatova, N V; Lukarevski?, V S; Kholodova, M V
The sporadic occurrence of a group I intron-like element in the mtDNA rnl gene of Ophiostoma novo-ulmi subsp. americana.
The presence of group I intron-like elements within the U7 region of the mtDNA large ribosomal subunit RNA gene (rnl) was investigated in strains of Ophiostoma novo-ulmi subsp. americana from Canada, Europe and Eurasia, and in selected strains of O. ips, O. minus, O. piceae, O. ulmi, and O. himal-ulmi. This insertion is of interest as it has been linked previously to the generation of plasmid-like mtDNA elements in diseased strains of O. novo-ulmi. Among 197 O. novo-ulmi subsp. americana strains tested, 61 contained a 1.6kb insertion within the rnl-U7 region and DNA sequence analysis suggests the presence of a group I intron (IA1 type) that encodes a potential double motif LAGLIDADG homing endonuclease-like gene (HEG). Phylogenetic analysis of rnl-U7 intron encoded HEG-like elements supports the view that double motif HEGs originated from a duplication event of a single-motif HEG followed by a fusion event that combined the two copies into one open reading frame (ORF). The data also show that rnl-U7 intron encoded ORFs belong to a clade that includes ORFs inserted into different types of group I introns, e.g. IB, ID, IC3, IA1, present within a variety of different mtDNA genes, such as the small ribosomal subunit RNA gene (rns), apo-cytochrome b gene (cob), NADH dehydrogenase subunit 5 (nad5), cytochrome oxidase subunit 1 gene (coxI), and ATPase subunit 9 gene (atp9). We also compared the occurrence of the rnl-U7 intron in our collection of 227 strains with the presence of the rnl-U11 group I intron and concluded that the U7 intron appears to be an optional element and the U11 intron is probably essential among the strains tested. PMID:18406119
Sethuraman, Jyothi; Okoli, Chukwuemeka V; Majer, Anna; Corkery, Tamara L C; Hausner, Georg
Kinetic analysis of high-mobility-group proteins HMG1 and HMGI\\/Y binding to cholesterol-tagged DNA on a supported lipid monolayer
High-mobility-group proteins HMG-1 and HMG-I\\/Y bind to multiple sites within a 268 bp A\\/T-rich enhancer element of the pea plastocyanin gene (PetE). Within a 31 bp region of the enhancer, the binding site for HMG-1 overlaps with the binding site for HMG-I\\/Y. The kinetics of binding and the affinities of HMG-1 and HMG-I\\/Y for the 31 bp DNA were determined
Carl I. Webster; Matthew A. Cooper; Leonard C. Packman; Dudley H. Williams; John C. Gray
Structure-function relationships in human testis-determining factor SRY: an aromatic buttress underlies the specific DNA-bending surface of a high mobility group (HMG) box.
Human testis determination is initiated by SRY, a Y-encoded architectural transcription factor. Mutations in SRY cause 46 XY gonadal dysgenesis with female somatic phenotype (Swyer syndrome) and confer a high risk of malignancy (gonadoblastoma). Such mutations cluster in the SRY high mobility group (HMG) box, a conserved motif of specific DNA binding and bending. To explore structure-function relationships, we constructed all possible substitutions at a site of clinical mutation (W70L). Our studies thus focused on a core aromatic residue (position 15 of the consensus HMG box) that is invariant among SRY-related HMG box transcription factors (the SOX family) and conserved as aromatic (Phe or Tyr) among other sequence-specific boxes. In a yeast one-hybrid system sensitive to specific SRY-DNA binding, the variant domains exhibited reduced (Phe and Tyr) or absent activity (the remaining 17 substitutions). Representative nonpolar variants with partial or absent activity (Tyr, Phe, Leu, and Ala in order of decreasing side-chain volume) were chosen for study in vitro and in mammalian cell culture. The clinical mutation (Leu) was found to markedly impair multiple biochemical and cellular activities as respectively probed through the following: (i) in vitro assays of specific DNA binding and protein stability, and (ii) cell culture-based assays of proteosomal degradation, nuclear import, enhancer DNA occupancy, and SRY-dependent transcriptional activation. Surprisingly, however, DNA bending is robust to this or the related Ala substitution that profoundly impairs box stability. Together, our findings demonstrate that the folding, trafficking, and gene-regulatory function of SRY requires an invariant aromatic "buttress" beneath its specific DNA-bending surface. PMID:25258310
Racca, Joseph D; Chen, Yen-Shan; Maloy, James D; Wickramasinghe, Nalinda; Phillips, Nelson B; Weiss, Michael A
Thermostable group II intron reverse transcriptase fusion proteins and their use in cDNA synthesis and next-generation RNA sequencing
Mobile group II introns encode reverse transcriptases (RTs) that function in intron mobility (�retrohoming�) by a process that requires reverse transcription of a highly structured, 2�2.5-kb intron RNA with high processivity and fidelity. Although the latter properties are potentially useful for applications in cDNA synthesis and next-generation RNA sequencing (RNA-seq), group II intron RTs have been difficult to purify free of the intron RNA, and their utility as research tools has not been investigated systematically. Here, we developed general methods for the high-level expression and purification of group II intron-encoded RTs as fusion proteins with a rigidly linked, noncleavable solubility tag, and we applied them to group II intron RTs from bacterial thermophiles. We thus obtained thermostable group II intron RT fusion proteins that have higher processivity, fidelity, and thermostability than retroviral RTs, synthesize cDNAs at temperatures up to 81�C, and have significant advantages for qRT-PCR, capillary electrophoresis for RNA-structure mapping, and next-generation RNA sequencing. Further, we find that group II intron RTs differ from the retroviral enzymes in template switching with minimal base-pairing to the 3? ends of new RNA templates, making it possible to efficiently and seamlessly link adaptors containing PCR-primer binding sites to cDNA ends without an RNA ligase step. This novel template-switching activity enables facile and less biased cloning of nonpolyadenylated RNAs, such as miRNAs or protein-bound RNA fragments. Our findings demonstrate novel biochemical activities and inherent advantages of group II intron RTs for research, biotechnological, and diagnostic methods, with potentially wide applications. PMID:23697550
Mohr, Sabine; Ghanem, Eman; Smith, Whitney; Sheeter, Dennis; Qin, Yidan; King, Olga; Polioudakis, Damon; Iyer, Vishwanath R.; Hunicke-Smith, Scott; Swamy, Sajani; Kuersten, Scott; Lambowitz, Alan M.
DNA barcoding of rhodiola (crassulaceae): a case study on a group of recently diversified medicinal plants from the qinghai-tibetan plateau.
DNA barcoding, the identification of species using one or a few short standardized DNA sequences, is an important complement to traditional taxonomy. However, there are particular challenges for barcoding plants, especially for species with complex evolutionary histories. We herein evaluated the utility of five candidate sequences - rbcL, matK, trnH-psbA, trnL-F and the internal transcribed spacer (ITS) - for barcoding Rhodiola species, a group of high-altitude plants frequently used as adaptogens, hemostatics and tonics in traditional Tibetan medicine. Rhodiola was suggested to have diversified rapidly recently. The genus is thus a good model for testing DNA barcoding strategies for recently diversified medicinal plants. This study analyzed 189 accessions, representing 47 of the 55 recognized Rhodiola species in the Flora of China treatment. Based on intraspecific and interspecific divergence and degree of monophyly statistics, ITS was the best single-locus barcode, resolving 66% of the Rhodiola species. The core combination rbcL+matK resolved only 40.4% of them. Unsurprisingly, the combined use of all five loci provided the highest discrimination power, resolving 80.9% of the species. However, this is weaker than the discrimination power generally reported in barcoding studies of other plant taxa. The observed complications may be due to the recent diversification, incomplete lineage sorting and reticulate evolution of the genus. These processes are common features of numerous plant groups in the high-altitude regions of the Qinghai-Tibetan Plateau. PMID:25774915
Zhang, Jian-Qiang; Meng, Shi-Yong; Wen, Jun; Rao, Guang-Yuan
DNA Barcoding of Rhodiola (Crassulaceae): A Case Study on a Group of Recently Diversified Medicinal Plants from the Qinghai-Tibetan Plateau
DNA barcoding, the identification of species using one or a few short standardized DNA sequences, is an important complement to traditional taxonomy. However, there are particular challenges for barcoding plants, especially for species with complex evolutionary histories. We herein evaluated the utility of five candidate sequences � rbcL, matK, trnH-psbA, trnL-F and the internal transcribed spacer (ITS) � for barcoding Rhodiola species, a group of high-altitude plants frequently used as adaptogens, hemostatics and tonics in traditional Tibetan medicine. Rhodiola was suggested to have diversified rapidly recently. The genus is thus a good model for testing DNA barcoding strategies for recently diversified medicinal plants. This study analyzed 189 accessions, representing 47 of the 55 recognized Rhodiola species in the Flora of China treatment. Based on intraspecific and interspecific divergence and degree of monophyly statistics, ITS was the best single-locus barcode, resolving 66% of the Rhodiola species. The core combination rbcL+matK resolved only 40.4% of them. Unsurprisingly, the combined use of all five loci provided the highest discrimination power, resolving 80.9% of the species. However, this is weaker than the discrimination power generally reported in barcoding studies of other plant taxa. The observed complications may be due to the recent diversification, incomplete lineage sorting and reticulate evolution of the genus. These processes are common features of numerous plant groups in the high-altitude regions of the Qinghai-Tibetan Plateau. PMID:25774915
Zhang, Jian-Qiang; Meng, Shi-Yong; Wen, Jun; Rao, Guang-Yuan
Growth and grazing rates of bacteria groups with different apparent DNA content in the Gulf of Mexico
Growth rates and grazing losses of bacterioplankton were assessed by serial dilution experiments in surface waters in the Mississippi River plume, the northern Gulf of Mexico, a Texas coastal lagoon (Laguna Madre), southeast Gulf of Mexico surface water, and the chlorophyll subsurface maximum layer in the southeast Gulf of Mexico. Bacteria were quantified by flow cytometry after DNA staining with
F. J. Jochem; P. J. Lavrentyev; M. R. First
NSDL National Science Digital Library
In this forensics activity, learners solve a mystery using �DNA� taken from the scene of the crime. This activity describes how to collect a �DNA sample� (learner-invented DNA sequence on a roll of paper) from the culprit and from each learner in the group, then run the DNA on a �gel� that covers the floor of the classroom, a hallway, or gymnasium. The crime-scene investigation aspect can become as elaborate as you wish by including additional �clues� such as fingerprints, a ransom note written in a specific type of ink, cloth fibers, eyewitness accounts and more.
Irene Salter
RAD25 (SSL2), the yeast homolog of the human xeroderma pigmentosum group B DNA repair gene, is essential for viability
Xeroderma pigmentosum (XP) patients are extremely sensitive to ultraviolet (UV) light and suffer from a high incidence of skin cancers, due to a defect in nucleotide excision repair. The disease is genetically heterogeneous, and seven complementation groups, A-G, have been identified. Homologs of human excision repair genes ERCC1, XPDC/ERCC2, and XPAC have been identified in the yeast Saccharomyces cerevisiae. Since no homolog of human XPBC/ERCC3 existed among the known yeast genes, we cloned the yeast homolog by using XPBC cDNA as a hybridization probe. The yeast homolog, RAD25 (SSL2), encodes a protein of 843 amino acids (M[sub r] 95,356). The RAD25 (SSL2)- and XPCX-encoded proteins share 55% identical and 72% conserved amino acid residues, and the two proteins resemble one another in containing the conserved DNA helicase sequence motifs. A nonsense mutation at codon 799 that deletes the 45 C-terminal amino acid residues in RAD25 (SSL2) confers UV sensitivity. This mutation shows epistasis with genes in the excision repair group, whereas a synergistic increase in UN sensitivity occurs when it is combined with mutations in genes in other DNA repair pathways, indicating that RAD25 (SSL2) functions in excision repair but not in other repair pathways. We also show that RAD25 (SSL2) is an essential gene. A mutation of the Lys[sup 392] residue to arginine in the conserved Walker type A nucleotide-binding motif is lethal, suggesting an essential role of the putative RAD 25 (SSL2) ATPase/DNA helicase activity in viability. 40 refs., 3 figs., 1 tab.
Park, E.; Prakash, L. (Univ. of Rochester School of Medicine, NY (United States)); Guzder, S.N.; Prakash, S. (Univ. of Rochester, NY (United States)); Koken, M.H.M.; Jaspers-Dekker, I.; Weeda, G.; Hoeijmakers, H.J. (Erasmus Univ., Rotterdam (Netherlands))
DNA sequence recognition in the minor groove by crosslinked polyamides: The effect of N-terminal head group and linker length on binding affinity and specificity
Development of sequence-reading polyamides or �lexitropsins� with comparable DNA-binding affinities to cellular proteins raises the possibility of artificially regulated gene expression. Covalent linkage of polyamide ligands, with either a hairpin motif or crosslinking methylene bridge, has greatly improved binding affinity by ensuring their side-by-side register. Whereas hairpin polyamides have been investigated extensively, the optimized structure of crosslinked polyamides remains to be determined. This study examines a series of thiazole-imidazole-pyrrole (TIP) monomers and crosslinked dimers to evaluate the effects on selectivity and binding affinity of different N-terminal head groups attached to the leading thiazole ring and differing methylene linker lengths. Quantitative footprinting of a DNA sequence, containing potential match and mismatch sites for both maximum overlap and one-residue stagger binding modes, allowed measurement of binding constants at each putative site. Within an N-terminal amino TIP series, C7 and C8-linked compounds bound most strongly to these sites, whereas maximum binding affinity was observed for a C6 linker with a formyl head group. A C5 linker gave weak binding with either head group. A hydrogen or acetyl head group abrogated binding. Binding was confirmed by gel shift analyses. The highest specificity for the maximum overlap site over the one-residue stagger was observed with TIP-C7-amino. Selectivity of the leading thiazole was modulated by the head group, with N-terminal formyl TIP exhibiting up to 3-fold specificity for AGT over TGT, suggesting that N-formyl-thiazole may provide sequence discrimination of adenine over thymine. Moreover, the leading head group and methylene linker length significantly influences the binding characteristics of crosslinked polyamides. PMID:11756678
O'Hare, C. Caroline; Mack, Darcy; Tandon, Manju; Sharma, Sanjay K.; Lown, J. William; Kopka, Mary L.; Dickerson, Richard E.; Hartley, John A.
European Mitochondrial DNA Haplogroups and Metabolic Changes during Antiretroviral Therapy in AIDS Clinical Trials Group Study A5142
Background Mitochondrial DNA (mtDNA) influences metabolic diseases and perhaps antiretroviral therapy (ART) complications. We explored associations between European mtDNA haplogroups and metabolic changes among A5142 participants. Methods 757 ART-na�ve subjects were randomized to one of three class-sparing ART regimens including efavirenz and/or lopinavir/ritonavir with or without nucleoside reverse transcriptase inhibitors (NRTIs). Non-randomized NRTIs included stavudine, tenofovir, or zidovudine, each with lamivudine. Fasting lipid profiles and whole-body dual-energy X-ray absorptiometry (DEXA) were performed. Nine European mtDNA haplogroups were determined for 231 self-identified non-Hispanic white subjects. Metabolic changes from baseline to 96 weeks were analyzed by haplogroup. Results Median age was 39 years, 9% were female, and 37%, 32%, and 30% were randomized to NRTI-containing regimens with either efavirenz or lopinavir/ritonavir, and an NRTI-sparing regimen respectively. Among NRTI-containing regimens, 51% included zidovudine, 28% tenofovir, and 21% stavudine. Compared with other haplogroups, mtDNA haplogroup I (N=10) had higher baseline non-HDL cholesterol (160 mg/dL [interquartile range 137�171] vs. 120 mg/dL [104�136]; p=0.005), a decrease in non-HDL cholesterol over 96 weeks (?14% [?20-+6] vs. +25% [+8-+51]; p<0.001), tended to have more baseline extremity fat, and had more extremity fat loss by DEXA (?13% [?31-+12] vs. +9% [?13-+26]; p=0.08) and lipoatrophy (50% vs. 20%; p=0.04). Haplogroup W (N=5; all randomized to NRTI-sparing regimens) had the greatest increase in extremity fat (+35.5% [+26.8 - +54.9]; P=0.02). Conclusions Lipids and extremity fat were associated with European mtDNA haplogroups in this HIV-infected population. These preliminary results suggest that mitochondrial genomics may influence metabolic parameters before and during ART. PMID:20871389
Hulgan, Todd; Haubrich, Richard; Riddler, Sharon A.; Tebas, Pablo; Ritchie, Marylyn D.; McComsey, Grace A.; Haas, David W.; Canter, Jeffrey A.
Architectural DNA Binding by a High-Mobility-Group\\/Kinesin-Like Subunit in Mammalian SWI\\/SNF-Related Complexes
The SWI\\/SNF complex in yeast and Drosophila is thought to facilitate transcriptional activation of specific genes by antagonizing chromatin-mediated transcriptional repression. The mechanism by which it is targeted to specific genes is poorly understood and may involve direct DNA binding and\\/or interactions with specific or general transcription factors. We have previously purified a mammalian complex by using antibodies against BRG1,
Weidong Wang; Tianhuai Chi; Yutong Xue; Sharleen Zhou; Ann Kuo; Gerald R. Crabtree
Nuclear ribosomal DNA internal transcribed spacer regions (ITS1 and ITS2) define discrete biogeographic groups in Cladophora albida (Chlorophyta)
Nucleotide sequences of the nuclear ribosomal DNA internal transcribed spacers (ITS1 and ITS2), the 5.8S, and short stretches of the adjacent 18S and 26S coding regions were determined in isolates from four disjunct Cladophora albida (Huds.) K�tz. populations (NE-America, W-Europe, Japan, and W-Australia). The two Pacific isolates share nearly identical ITS sequences as do the two Atlantic isolates. In contrast,
Freek T. Bakker; Jeanine L. Olsen; Wytze T. Stam; Hoek van den C
Characterisation and Interpopulation Variability of a Complex HpaI Satellite DNA of Drosophila seriema (repleta Group)
A HpaI satellite DNA has been isolated and characterised from the genome of Drosophila seriema, a cactus-breeding species endemic to the rock fields of the Espinha�o Range in Brazil. The monomer sequences are slightly A + T rich (66%) and there is a significant variation of repetition length (343�391 bp). The length variability is mainly due to a 22 bp
Gustavo C. S. Kuhn; Fabio M. Sene
Ancient DNA from Hunter-Gatherer and Farmer Groups from Northern Spain Supports a Random Dispersion Model for the Neolithic Expansion into Europe
Background/Principal Findings The phenomenon of Neolithisation refers to the transition of prehistoric populations from a hunter-gatherer to an agro-pastoralist lifestyle. Traditionally, the spread of an agro-pastoralist economy into Europe has been framed within a dichotomy based either on an acculturation phenomenon or on a demic diffusion. However, the nature and speed of this transition is a matter of continuing scientific debate in archaeology, anthropology, and human population genetics. In the present study, we have analyzed the mitochondrial DNA diversity in hunter-gatherers and first farmers from Northern Spain, in relation to the debate surrounding the phenomenon of Neolithisation in Europe. Methodology/Significance Analysis of mitochondrial DNA was carried out on 54 individuals from Upper Paleolithic and Early Neolithic, which were recovered from nine archaeological sites from Northern Spain (Basque Country, Navarre and Cantabria). In addition, to take all necessary precautions to avoid contamination, different authentication criteria were applied in this study, including: DNA quantification, cloning, duplication (51% of the samples) and replication of the results (43% of the samples) by two independent laboratories. Statistical and multivariate analyses of the mitochondrial variability suggest that the genetic influence of Neolithisation did not spread uniformly throughout Europe, producing heterogeneous genetic consequences in different geographical regions, rejecting the traditional models that explain the Neolithisation in Europe. Conclusion The differences detected in the mitochondrial DNA lineages of Neolithic groups studied so far (including these ones of this study) suggest different genetic impact of Neolithic in Central Europe, Mediterranean Europe and the Cantabrian fringe. The genetic data obtained in this study provide support for a random dispersion model for Neolithic farmers. This random dispersion had a different impact on the various geographic regions, and thus contradicts the more simplistic total acculturation and replacement models proposed so far to explain Neolithisation. PMID:22563371
Hervella, Montserrat; Izagirre, Neskuts; Alonso, Santos; Fregel, Rosa; Alonso, Antonio; Cabrera, Vicente M.; de la R�a, Concepci�n
Universal Plant DNA Barcode Loci May Not Work in Complex Groups: A Case Study with Indian Berberis Species
Background The concept of DNA barcoding for species identification has gained considerable momentum in animals because of fairly successful species identification using cytochrome oxidase I (COI). In plants, matK and rbcL have been proposed as standard barcodes. However, barcoding in complex genera is a challenging task. Methodology and Principal Findings We investigated the species discriminatory power of four reportedly most promising plant DNA barcoding loci (one from nuclear genome- ITS, and three from plastid genome- trnH-psbA, rbcL and matK) in species of Indian Berberis L. (Berberidaceae) and two other genera, Ficus L. (Moraceae) and Gossypium L. (Malvaceae). Berberis species were delineated using morphological characters. These characters resulted in a well resolved species tree. Applying both nucleotide distance and nucleotide character-based approaches, we found that none of the loci, either singly or in combinations, could discriminate the species of Berberis. ITS resolved all the tested species of Ficus and Gossypium and trnH-psbA resolved 82% of the tested species in Ficus. The highly regarded matK and rbcL could not resolve all the species. Finally, we employed amplified fragment length polymorphism test in species of Berberis to determine their relationships. Using ten primer pair combinations in AFLP, the data demonstrated incomplete species resolution. Further, AFLP analysis showed that there was a tendency of the Berberis accessions to cluster according to their geographic origin rather than species affiliation. Conclusions/Significance We reconfirm the earlier reports that the concept of universal barcode in plants may not work in a number of genera. Our results also suggest that the matK and rbcL, recommended as universal barcode loci for plants, may not work in all the genera of land plants. Morphological, geographical and molecular data analyses of Indian species of Berberis suggest probable reticulate evolution and thus barcode markers may not work in this case. PMID:21060687
Roy, Sribash; Tyagi, Antariksh; Shukla, Virendra; Kumar, Anil; Singh, Uma M.; Chaudhary, Lal Babu; Datt, Bhaskar; Bag, Sumit K.; Singh, Pradhyumna K.; Nair, Narayanan K.; Husain, Tariq; Tuli, Rakesh
Phylogenetic analysis of LSU and SSU rDNA group I introns of lichen photobionts associated with the genera Xanthoria and Xanthomendoza (Teloschistaceae, lichenized Ascomycetes)
We studied group I introns in sterile cultures of selected groups of lichen photobionts, focusing on Trebouxia species associated with Xanthoria s. lat. (including Xanthomendoza spp.; lichen-forming ascomycetes). Group I introns were found inserted after position 798 (Escherichia coli numbering) in the large subunit (LSU) rRNA in representatives of the green algal genera Trebouxia and Asterochloris. The 798 intron was found in about 25% of Xanthoria photobionts including several reference strains obtained from algal culture collections. An alignment of LSU-encoded rDNA intron sequences revealed high similarity of these sequences allowing their phylogenetic analysis. The 798 group I intron phylogeny was largely congruent with a phylogeny of the Internal Transcribed Spacer Region (ITS), indicating that the insertion of the intron most likely occurred in the common ancestor of the genera Trebouxia and Asterochloris. The intron was vertically inherited in some taxa, but lost in others. The high sequence similarity of this intron to one found in Chlorella angustoellipsoidea suggests that the 798 intron was either present in the common ancestor of Trebouxiophyceae, or that its present distribution results from more recent horizontal transfers, followed by vertical inheritance and loss. Analysis of another group I intron shared by these photobionts at small subunit (SSU) position 1512 supports the hypothesis of repeated lateral transfers of this intron among some taxa, but loss among others. Our data confirm that the history of group I introns is characterized by repeated horizontal transfers, and suggests that some of these introns have ancient origins within Chlorophyta. PMID:24415800
Nyati, Shyam; Bhattacharya, Debashish; Werth, Silke; Honegger, Rosmarie
Phylogenetic analysis of LSU and SSU rDNA group I introns of lichen photobionts associated with the genera Xanthoria and Xanthomendoza (Teloschistaceae, lichenized Ascomycetes).
We studied group I introns in sterile cultures of selected groups of lichen photobionts, focusing on Trebouxia species associated with Xanthoria s. lat. (including Xanthomendoza spp.; lichen-forming ascomycetes). Group I introns were found inserted after position 798 (Escherichia coli numbering) in the large subunit (LSU) rRNA in representatives of the green algal genera Trebouxia and Asterochloris. The 798 intron was found in about 25% of Xanthoria photobionts including several reference strains obtained from algal culture collections. An alignment of LSU-encoded rDNA intron sequences revealed high similarity of these sequences allowing their phylogenetic analysis. The 798 group I intron phylogeny was largely congruent with a phylogeny of the Internal Transcribed Spacer Region (ITS), indicating that the insertion of the intron most likely occurred in the common ancestor of the genera Trebouxia and Asterochloris. The intron was vertically inherited in some taxa, but lost in others. The high sequence similarity of this intron to one found in Chlorella angustoellipsoidea suggests that the 798 intron was either present in the common ancestor of Trebouxiophyceae, or that its present distribution results from more recent horizontal transfers, followed by vertical inheritance and loss. Analysis of another group I intron shared by these photobionts at small subunit (SSU) position 1512 supports the hypothesis of repeated lateral transfers of this intron among some taxa, but loss among others. Our data confirm that the history of group I introns is characterized by repeated horizontal transfers, and suggests that some of these introns have ancient origins within Chlorophyta. PMID:24415800
Nyati, Shyam; Bhattacharya, Debashish; Werth, Silke; Honegger, Rosmarie
DNA evidence on the phylogenetic systematics of New World monkeys: support for the sister-grouping of Cebus and Saimiri from two unlinked nuclear genes.
Previous inferences from epsilon-globin gene sequences on cladistic relationships among the 16 extant genera of Ceboidea (the New World monkeys) were tested by strength of grouping and bootstrap values for the clades in the most parsimonious trees found: for this epsilon data set enlarged with additional Cebus and Saimiri orthologues; for another nuclear DNA sequence data set consisting of IRBP (interstitial retinol-binding protein gene) intron 1 orthologues; and for tandemly combined epsilon and IRBP sequences. Different ceboid species of the same genus always grouped strongly together as demonstrated by results on Cebus (capuchin monkeys), Saimiri (squirrel monkeys), Callicebus (titi monkeys), Aotus (night monkeys), Ateles (spider monkeys), and Alouatta (howler monkeys). Other strong groupings that could be represented as monophyletic taxa in a cladistic classification were: Cebuella (pygmy marmoset) and Callithrix (marmoset) into subtribe Callitrichina; Callitrichina, Callimico (Goeldi's monkey), Leontopithecus (lion tamarin), and Saguinus (tamarin) into subfamily Callitrichinae; Callitrichinae, Aotus, Cebus, and Saimiri into family Cebidae; Cacajao (uakari monkey) and Chiropotes (saki) into subtribe Chiropotina; Chiropotina and Pithecia (bearded saki) into tribe Pitheciini; Pitheciini and Callicebus into subfamily Pitheciinae; Brachyteles (woolly spider monkey), Lagothrix (woolly monkey), and Ateles into tribe Atelini; and Atelini and Alouatta into subfamily Atelinae. In addition the epsilon and IRBP results congruently grouped (but at lesser strengths) Brachyteles and Lagothrix into subtribe Brachytelina within Atelini, and also Cebus and Saimiri into subfamily Cebinae within Cebidae. Because the IRBP results weakly grouped Pitheciinae with Cebidae, whereas the epsilon results weakly grouped Pitheciinae with Atelinae, the present evidence is best represented in an interim cladistic classification of ceboids by dividing the superfamily Ceboidea into three families: Atelidae, Pitheciidae, and Cebidae. PMID:8845968
Harada, M L; Schneider, H; Schneider, M P; Sampaio, I; Czelusniak, J; Goodman, M
Characterization of polybacterial clinical samples using a set of group-specific broad-range primers targeting the 16S rRNA gene followed by DNA sequencing and RipSeq analysis.
The standard use of a single universal broad-range PCR in direct 16S rDNA sequencing from polybacterial samples leaves the minor constituents at risk of remaining undetected because all bacterial DNA will be competing for the same reagents. In this article we introduce a set of three broad-range group-specific 16S rDNA PCRs that together cover the clinically relevant bacteria and apply them in the investigation of 25 polybacterial clinical samples. Mixed DNA chromatograms from samples containing more than one species per primer group were analysed using RipSeq Mixed (iSentio, Norway), a web-based application for the interpretation of chromatograms containing up to three different species. The group-specific PCRs reduced complexity in the resulting DNA chromatograms and made the assay more sensitive in situations with unequal species concentrations. Together this allowed for identification of a significantly higher number of bacterial species than did standard direct sequencing with a single universal primer pair and RipSeq analysis (95 vs 51). The method could improve microbiological diagnostics for important groups of patients and can be established in any laboratory with experience in direct 16S rDNA sequencing. PMID:21436365
Kommedal, Oyvind; Lekang, Katrine; Langeland, Nina; Wiker, Harald G
DNA fingerprinting and anastomosis grouping reveal similar genetic diversity in Rhizoctonia species infecting turfgrasses in the transition zone of USA
Technology Transfer Automated Retrieval System (TEKTRAN)
Rhizoctonia blight (sensu lato) is a common and serious disease of many turfgrass species. The most widespread causal agent, R. solani, consists of several genetically different subpopulations. Though hyphal anastomosis reactions have been used to group Rhizoctonia species, they are time consuming a...
Solid-phase synthesis of thermolytic DNA oligonucleotides functionalized with a single 4-hydroxy-1-butyl or 4-phosphato-/thiophosphato-1-butyl thiophosphate protecting group.
Several thermolytic CpG-containing DNA oligonucleotides analogous to 1 have been synthesized to serve as potential immunotherapeutic oligonucleotide prodrug formulations for the treatment of infectious diseases in animal models. Specifically, the CpG motif (GACGTT) of each DNA oligonucleotide has been functionalized with either the thermolabile 4-hydroxy-1-butyl or the 4-phosphato-/thiophosphato-1-butyl thiophosphate protecting group. This functionalization was achieved through incorporation of activated deoxyribonucleoside phosphoramidite 8b into the oligonucleotide chain during solid-phase synthesis and, optionally, through subsequent phosphorylation effected by phosphoramidite 9. Complete conversion of CpG ODNs hbu1555, psb1555, and pob1555 to CpG ODN 1555 (homologous to 2) occurred under elevated temperature conditions, thereby validating the function of these diastereomeric oligonucleotides as prodrugs in vitro. Noteworthy is the significant increase in solubility of CpG ODN psb1555 and CpG pob1555 in water when compared to that of neutral CpG ODN fma1555 (homologous to 1). PMID:17253799
Grajkowski, Andrzej; Aus�n, Cristina; Kauffman, Jon S; Snyder, John; Hess, Sonja; Lloyd, John R; Beaucage, Serge L
Isolation of a DNA polymerase I (polA) mutant of Rhizobium leguminosarum that has significantly reduced levels of an IncQ-group plasmid.
A population of Tn5 mutagenized Rhizobium leguminosarum cells was screened for mutants affected in protein secretion by introducing a plasmid carrying the Erwinia chrysanthemi prtB gene and screening for mutants defective in secretion of the protease PrtB. One such mutant (A301) also appeared to be defective in secretion of the R. leguminosarum nodulation protein NodO. Genetic analysis showed that the defect in A301 was caused by the Tn5 insertion. However the DNA sequence adjacent to the site of Tn5 insertion had significant homology to the Escherichia coli polA gene, which encodes DNA polymerase I. The mutant A301 showed increased sensitivity to ultraviolet light, a characteristic of polA mutants of E. coli. The apparent defect in secretion by A301 was due to a large decrease in the copy number of the IncQ group replicon on which prtB and nodO were cloned and this decreased the total amounts of PrtB or NodO protein synthesised and secreted by the polA mutant. The polA mutant had a lower growth rate than the parent strain on both rich and minimal media, but there was no obvious effect of the polA mutation on the symbiosis of R. leguminosarum bv. viciae with pea. PMID:8190065
Crank, S F; Downie, J A
Functional constraints and evolutionary dynamics of the repeats in the rDNA internal transcribed spacer 2 of members of the Anopheles barbirostris group
Background The Anopheles barbirostris group is widely distributed in Southeast Asia. Although seven species have been formally described, a molecular analysis of the rDNA ITS2 and the mitochondrial cytochrome oxidase I gene suggests that the group includes species that are morphologically very similar or identical. We have previously shown that species in the Anopheles barbirostris Subgroup have an exceptionally large ITS2 (>1.5�kb), greater than in any other Anopheline group. However, the molecular processes responsible for generating such a large ITS2 have not previously been explored. Methods To determine the processes by which this large ITS2 is generated, we examined the sequence and secondary structure of the ITS2 of 51 specimens from five species of the Anopheles barbirostris Subgroup. These include the anthropophilic species An. campestris and three morphospecies of the Barbirostris Complex: An. vanderwulpi, An. barbirostris I and III, together with a previously undescribed member of this group (Clade IV). Results and conclusions All the specimens were found to have an ITS2 greater than 1.5�kb in length. The possibility that the spacer sequences amplified were pseudogenes was examined and discarded. The large size of ITS2 in the species studied is due to the presence of internal repeats of approximately 110�bp in length, confined to the central region of the spacer. Repeats varied markedly between the species examined, with respect to their organization, number and sequence similarity. The nucleotide diversity increased in direct relation to size variation and the presence of non-repeated elements. A secondary structure analysis showed that the repeats form hairpin structures with a wide range of free energy values. These hairpin structures are known to facilitate the subsequent processing of mature rRNA. An analysis of the repeats from the different species suggests they originate from a common ancestor, with the repeats appearing before speciation of the Barbirostris Group. PMID:24646478
Review of the Eulamprotes wilkella species-group based on morphology and DNA barcodes, with descriptions of new taxa (Lepidoptera, Gelechiidae).
The Eulamprotes wilkella species-group is revised based on morphological characters and on DNA barcodes of the mtCOI (Cytochrome c Oxidase 1) gene. Adult morphology combined with sequence information for 9 species supports the existence of 12 species, 7 of which are described as new to science: E. mirusella Huemer & Karsholt sp. nov. (France), E. baldizzonei Karsholt & Huemer sp. nov. (Italy, Slovenia, Croatia), E. atrifrontella Karsholt & Huemer sp. nov. (Turkey), E. wieseri Huemer & Karsholt sp. nov. (Kyrgizia), E. altaicella Huemer & Karsholt sp. nov. (Russia: Altai, Buryatia, Tuva Republic), E. kailai Karsholt & Huemer sp. nov. (Kazakhstan, Kyrgizia, Russia: Buryatia, Tuva Republic) and E. gemerensis Elsner sp. nov. (Slovakia). E. buvati Leraut, 1991 syn. nov. is synonymized with E. ochricapilla (Rebel, 1903). PMID:25113469
Huemer, Peter; Elsner, Gustav; Karsholt, Ole
True XP group E patients have a defective UV-damaged DNA binding protein complex and mutations in DDB2 which reveal the functional domains of its p48 product
Xeroderma pigmentosum (XP) is a skin cancer-prone autosomal recessive disease characterized by inability to repair UV-induced DNA damage. The major form of XP is defective in nucleotide excision repair (NER) and comprises seven complementation groups (A-G). The genes defective in all groups have been identified unambiguously with the exception of group E. The cells of some XP-E patients are deficient
V. Rapic-Otrin; Valentina Navazza; Tiziana Nardo; Elena Botta; Mary McLenigan; Dawn C. Bisi; Arthur S. Levine; Miria Stefanini
New Group-Specific 16S rDNA Primers for Monitoring Foaming Mycolata During Saline Waste-Water Treatment
Newly designed group-specific PCR primers for denaturing gradient gel electrophoresis (DGGE) were used to investigate foaming\\u000a mycolata from a bioreactor treating an industrial saline waste-water. Genetic profiles on DGGE gels were different with NaCl\\u000a at 1.65 and 8.24�g�l?1, demonstrating that mycolata community was affected by salinity. A semi-nested PCR strategy resulted in more bands in community\\u000a genetic profiles than direct
L. A. I. de Azeredo; C. D. da Cunha; A. S. Rosado; A. Macrae; D. M. G. Freire; L. C. S. Mendon�a-Hagler; G. L. Sant�Anna
Design, synthesis, and DNA binding characteristics of a group of orthogonally positioned diamino, N-formamido, pyrrole- and imidazole-containing polyamides.
Orthogonally positioned diamino/dicationic polyamides (PAs) have good water solubility and enhanced binding affinity, whilst retaining DNA minor groove and sequence specificity compared to their monoamino/monocationic counterparts. The synthesis and DNA binding properties of the following diamino PAs: f-IPI (3a), f-IPP (4), f-PIP (5), and f-PPP (6) are described. P denotes the site where a 1-propylamino group is attached to the N1-position of the heterocycle. Binding of the diamino PAs to DNA was assessed by DNase I footprinting, thermal denaturation, circular dichroism titration, biosensor surface plasmon resonance (SPR), and isothermal titration calorimetry (ITC) studies. According to SPR studies, f-IPI (3a) bound more strongly (K(eq)=2.4�10(8) M(-1)) and with comparable sequence selectivity to its cognate sequence 5'-ACGCGT-3' when compared to its monoamino analog f-IPI (1). The binding of f-IPI (3a) to 5'-ACGCGT-3' via the stacked dimer motif was balanced between enthalpy and entropy, and that was quite different from the enthalpy-driven binding of its monoamino parent f-IPI (1). f-IPP (4) also bound more strongly to its cognate sequence 5'-ATGCAT-3' (K(eq)=7.4�10(6) M(-1)) via the side-by-side stacked motif than its monoamino analog f-IPP (2a). Although f-PPP (6) bound via a 1:1 motif, it bound strongly to its cognate sequence 5'-AAATTT-3' (K(eq)=4.8�10(7) M(-1)), 15-times higher than the binding of its monoamino analog f-PPP (2c), albeit f-PPP bound via the stacked motif. Finally, f-PIP (5) bound to its target sequence 5'-ATCGAT-3' as a stacked dimer and it has the lowest affinity among the diamino PAs tested (Keq <1�10(5) M(-1)). This was about two times lower in affinity than the binding of its monoamino analog f-PIP (2b). The results further demonstrated that the 'core rules' of DNA recognition by monoamino PAs also apply to their diamino analogs. Specifically, PAs that contain a stacked IP core structure bind most strongly (highest binding constants) to their cognate GC doublet, followed by the binding of PAs with a stacked PP structure to two degenerate AT base pairs, and finally the binding of PAs with a PI core to their cognate CG doublet. PMID:23647824
Chavda, Sameer; Babu, Balaji; Patil, Pravin; Plaunt, Adam; Ferguson, Amanda; Lee, Megan; Tzou, Samuel; Sjoholm, Robert; Rice, Toni; Mackay, Hilary; Ramos, Joseph; Wang, Shuo; Lin, Shicai; Kiakos, Konstantinos; Wilson, W David; Hartley, John A; Lee, Moses
Influence of the stereoisomeric position of the reactive acetate groups of the benzo[b]acronycine derivative S23906-1 on its DNA alkylation, helix-opening, cytotoxic, and antitumor activities.
S23906-1 is a benzo[b]acronycine derivative acting as a DNA-alkylating agent through covalent bonding to the exocyclic amino group of guanines and subsequent local opening of the DNA helix. This compound was selected for phase I clinical trials based on its efficient antitumor activity in experimental models and its unique mode of action. S23906-1 is the racemate of cis-1,2-diacetoxy-6-methoxy-3,3,14-trimethyl-1,2,3,14-tetrahydro-7H-benzo[b]pyrano[3,2-h]acridin-7-one. Here, we evaluated the cytotoxic and antitumor activities of the two pure cis-enantiomers and investigated the mechanism of action of both cis- and trans-racemates and their enantiomers in terms of DNA alkylation potency and locally drug-induced DNA helix opening process. Reaction with glutathione, as a detoxification process, was also studied. The trans-compounds, both as racemate or separated enantiomers, were found less potent than the corresponding cis-derivatives. Among the cis-enantiomers, the most efficient one regarding DNA alkylation bears the acetate on the reactive C1 position in the R configuration, both on purified DNA and genomic DNA extracted from cell cultures. By contrast, the most cytotoxic and tumor-active enantiomer bears the C1-acetate in the S configuration. Distinct cellular DNA-alkylation levels or covalent bonding to glutathione could not explain the differences. However, we showed that the S and R orientations of the acetate on C1 asymmetric carbon lead to different local opening of the DNA, as visualized using nuclease S1 mapping. These different interactions could lead to modulated DNA-repair, protein/DNA interaction, and apoptosis processes. PMID:19752199
Depauw, Sabine; Gaslonde, Thomas; L�once, St�phane; Kraus-Berthier, Laurence; Laine, William; Lenglet, Ga�lle; Chiaroni, Ang�le; Pfeiffer, Bruno; Bailly, Christian; Michel, Sylvie; Tillequin, Fran�ois; Pierr�, Alain; David-Cordonnier, Marie-H�l�ne
Molecular cloning, sequence, and expression of a human GDP-L-fucose:. beta. -D-galactoside 2-. alpha. -L-fucosyltransferase cDNA that can form the H blood group antigen
The authors have previously used a gene-transfer scheme to isolate a human genomic DNA fragment that determines expression of a GDP-L-fucose:{beta}D-galactoside 2-{alpha}-L-fucosyltransferase. Although this fragment determined expression of an {alpha}(1,2)FT whose kinetic properties mirror those of the human H blood group {alpha}(1,2)FT, their precise nature remained undefined. They describe here the molecular cloning, sequence, and expression of a human of cDNA corresponding to these human genomic sequences. When expressed in COS-1 cells, the cDNA directs expression of cell surface H structures and a cognate {alpha}(1,2)FT activity with properties analogous to the human H blood group {alpha}(1,2)FT. The cDNA sequence predicts a 365-amino acid polypeptide characteristic of a type II transmembrane glycoprotein with a domain structure analogous to that of other glycosyltransferases but without significant primary sequence similarity to these or other known proteins. To directly demonstrate that the cDNA encodes an {alpha}(1,2)FT, the COOH-terminal domain predicted to be Golgi-resident was expressed in COS-1 cells as a catalytically active, secreted, and soluble protein A fusion peptide. Southern blot analysis showed that this cDNA identified DNA sequences syntenic to the human H locus on chromosome 19. These results strongly suggest that this cloned {alpha}(1,2)FT cDNA represents the product of the human H blood group locus.
Larsen, R.D.; Ernst, L.K.; Nair, R.P.; Lowe, J.B. (Univ. of Michigan, Ann Arbor (USA))
Germ-line variants in methyl-group metabolism genes and susceptibility to DNA methylation in normal tissues and human primary tumors.
Aberrant DNA methylation is recognized as being a common feature of human neoplasia.CpG island hypermethylation and global genomic hypomethylation occur simultaneously in the cancer cell. However, very little is known about the interindividual inherited susceptibility to these epigenetic processes. To address this matter, we have genotyped in 233 cancer patients (with colorectal, breast, or lung tumors), four germ-line variants in three key genes involved in the metabolism of the methyl group, methylene-tetrahydrofolate reductase, methionine synthase, and cystathionine beta-synthase, and analyzed their association with DNA methylation parameters. The epigenetic features analyzed were the 5-methylcytosine content in the genome of the tumors and their normal counterparts, and the presence of CpG island hypermethylation of tumor suppressor genes (p16(INK4a), p14(ARF), hMLH1, MGMT, APC, LKB1, DAPK, GSTP1, BRCA1, RAR beta 2, CDH1, and RASSF1). Two positive associations were found. First, carriers of genotypes containing the methylene-tetrahydrofolate reductase 677T allele show constitutive low levels of 5-methylcytosine in their genomes (P = 0.002), and tumors in these patients do not achieve severe degrees of global hypomethylation (P = 0.047). Second, tumors occurring in homozygous carriers of the methionine synthase 2756G allele show a lower number of hypermethylated CpG islands of tumor suppressor genes (P = 0.029). The existence of these associations may provide another example of the interplay between genetic and epigenetic factors in the cancer cell. PMID:12154064
Paz, Maria F; Avila, Sonia; Fraga, Mario F; Pollan, Marina; Capella, Gabriel; Peinado, Miquel Angel; Sanchez-Cespedes, Montserrat; Herman, James G; Esteller, Manel
DNA content analysis of colorectal cancer defines a distinct �microsatellite and chromosome stable� group but does not predict response to radiotherapy
Colorectal cancers (CRC) are thought to have genetic instability in the form of either microsatellite instability (MSI) or chromosomal instability (CIN). Recently, tumours have been described without either MSI or CIN, that is, microsatellite and chromosome stable (MACS) CRCs. We investigated the (i) frequency of the MACS-CRCs and (ii) whether this genotype predicted responsiveness to neoadjuvant chemoradiotherapy. To examine the frequency of MACS-CRCs, DNA content (ploidy) was examined in 89 sporadic microsatellite-stable CRCs using flow cytometry. The tumours were also screened for mutations in KRAS/BRAF/TP53/PIK3CA by QMC-PCR. To examine the value of tumour ploidy in predicting response to chemoradiotherapy, DNA content was tested in a separate group of 62 rectal cancers treated with neoadjuvant chemoradiotherapy. Fifty-one of 89 CRCs (57%) were aneuploid and 38 (43%) were diploid. There was no significant association between mutations in TP53/KRAS/BRAF/PIK3CA and ploidy. Testing of association between mutations revealed only mutual exclusivity of KRAS/BRAF mutation (P?0.001). Of the 62 rectal cancers treated with neoadjuvant chemoradiotherapy, 22 had responded (Mandard tumour regression grade 1/2) and 40 failed to respond (Grade 3�5). Twenty-five of 62 (40%) tumours were diploid, but there was no association between ploidy and response to therapy. We conclude that MACS-CRCs form a significant proportion of microsatellite-stable CRCs with a mutation profile overlapping that of CRCs with CIN. A diploid genotype does not, however, predict the responsiveness to radiotherapy. PMID:24456329
Fadhil, Wakkas; Kindle, Karin; Jackson, Darryl; Zaitoun, Abed; Lane, Nina; Robins, Adrian; Ilyas, Mohammad
Ectopic Expression of DREF Induces DNA Synthesis, Apoptosis, and Unusual Morphogenesis in the Drosophila Eye Imaginal Disc: Possible Interaction with Polycomb and trithorax Group Proteins
The promoters of Drosophila genes encoding DNA replication-related proteins contain transcription regulatory element DRE (5?-TATCGATA) in addition to E2F recognition sites. A specific DRE-binding factor, DREF, positively regulates DRE-containing genes. In addition, it has been reported that DREF can bind to a sequence in the hsp70 scs? chromatin boundary element that is also recognized by boundary element-associated factor, and thus DREF may participate in regulating insulator activity. To examine DREF function in vivo, we established transgenic flies in which ectopic expression of DREF was targeted to the eye imaginal discs. Adult flies expressing DREF exhibited a severe rough eye phenotype. Expression of DREF induced ectopic DNA synthesis in the cells behind the morphogenetic furrow, which are normally postmitotic, and abolished photoreceptor specifications of R1, R6, and R7. Furthermore, DREF expression caused apoptosis in the imaginal disc cells in the region where commitment to R1/R6 cells takes place, suggesting that failure of differentiation of R1/R6 photoreceptor cells might cause apoptosis. The DREF-induced rough eye phenotype was suppressed by a half-dose reduction of the E2F gene, one of the genes regulated by DREF, indicating that the DREF overexpression phenotype is useful to screen for modifiers of DREF activity. Among Polycomb/trithorax group genes, we found that a half-dose reduction of some of the trithorax group genes involved in determining chromatin structure or chromatin remodeling (brahma, moira, and osa) significantly suppressed and that reduction of Distal-less enhanced the DREF-induced rough eye phenotype. The results suggest a possibility that DREF activity might be regulated by protein complexes that play a role in modulating chromatin structure. Genetic crosses of transgenic flies expressing DREF to a collection of Drosophila deficiency stocks allowed us to identify several genomic regions, deletions of which caused enhancement or suppression of the DREF-induced rough eye phenotype. These deletions should be useful to identify novel targets of DREF and its positive or negative regulators. PMID:11585906
Hirose, Fumiko; Ohshima, Nobuko; Shiraki, Michina; Inoue, Yoshihiro H.; Taguchi, Osamu; Nishi, Yoshimi; Matsukage, Akio; Yamaguchi, Masamitsu
Results of collaborative study regarding the standardization of the Y-linked STR system DYS385 by the European DNA Profiling (EDNAP) group.
Y-chromosome linked short tandem repeat (STR) loci are inherited as a closely linked haplotype, which appears to remain stable in a given paternal lineage over many generations. In forensic cases, Y-linked STRs are particularly useful for the identification of human remains as well as in rape cases with mixed male/female stain samples. DYS385 is derived from tandemly duplicated segments of the Y chromosome thus giving rise to two fragments of variable length which do not behave like alleles but genotypes. The European DNA Profiling (EDNAP) group has carried out a collaborative exercise among 14 participating laboratories using DYS385 for typing of five unknown bloodstains and a control sample. Furthermore, population data from eight different European countries with samples sizes between 91 and 150 male individuals were collected. The results confirm previous observations that DYS385 is one of the most informative Y-linked STR loci. It could also be demonstrated that reproducible results can be obtained independently from the electrophoretic separation and detection methods used. Thus DYS385 may serve as a useful complementation to the routinely used autosomal STR systems in special cases. PMID:10464931
Schneider, P M; d'Aloja, E; Dupuy, B M; Eriksen, B; Jangblad, A; Kloosterman, A D; Kratzer, A; Lareu, M V; Pfitzinger, H; Rand, S; Scheithauer, R; Schmitter, H; Skitsa, I; Syndercombe-Court, D; Vide, M C
Efficient rejoining of radiation-induced DNA double-strand breaks in vertebrate cells deficient in genes of the RAD52 epistasis group
Rejoining of ionizing radiation (IR) induced DNA DSBs usually follows biphasic kinetics with a fast (t50: 5�30 min) component attributed to DNA-PK-dependent non-homologous endjoining (NHEJ) and a slow (t50: 1�20 h), as of yet uncharacterized, component. To examine whether homologous recombination (HR) contributes to DNA DSB rejoining, a systematic genetic study was undertaken using the hyper-recombinogenic DT40 chicken cell line
Huichen Wang; Zhao-Chong Zeng; Tu-Anh Bui; Eiichiro Sonoda; Minoru Takata; Shunichi Takeda; George Iliakis
DNA Nanotechnology-- Architectures Designed with DNA
NASA Astrophysics Data System (ADS)
As the genetic information storage vehicle, deoxyribonucleic acid (DNA) molecules are essential to all known living organisms and many viruses. It is amazing that such a large amount of information about how life develops can be stored in these tiny molecules. Countless scientists, especially some biologists, are trying to decipher the genetic information stored in these captivating molecules. Meanwhile, another group of researchers, nanotechnologists in particular, have discovered that the unique and concise structural features of DNA together with its information coding ability can be utilized for nano-construction efforts. This idea culminated in the birth of the field of DNA nanotechnology which is the main topic of this dissertation. The ability of rationally designed DNA strands to self-assemble into arbitrary nanostructures without external direction is the basis of this field. A series of novel design principles for DNA nanotechnology are presented here, from topological DNA nanostructures to complex and curved DNA nanostructures, from pure DNA nanostructures to hybrid RNA/DNA nanostructures. As one of the most important and pioneering fields in controlling the assembly of materials (both DNA and other materials) at the nanoscale, DNA nanotechnology is developing at a dramatic speed and as more and more construction approaches are invented, exciting advances will emerge in ways that we may or may not predict.
Han, Dongran
Long-range repression by multiple polycomb group (PcG) proteins targeted by fusion to a defined DNA-binding domain in Drosophila.
A tethering assay was developed to study the effects of Polycomb group (PcG) proteins on gene expression in vivo. This system employed the Su(Hw) DNA-binding domain (ZnF) to direct PcG proteins to transposons that carried the white and yellow reporter genes. These reporters constituted naive sensors of PcG effects, as bona fide PcG response elements (PREs) were absent from the constructs. To assess the effects of different genomic environments, reporter transposons integrated at nearly 40 chromosomal sites were analyzed. Three PcG fusion proteins, ZnF-PC, ZnF-SCM, and ZnF-ESC, were studied, since biochemical analyses place these PcG proteins in distinct complexes. Tethered ZnF-PcG proteins repressed white and yellow expression at the majority of sites tested, with each fusion protein displaying a characteristic degree of silencing. Repression by ZnF-PC was stronger than ZnF-SCM, which was stronger than ZnF-ESC, as judged by the percentage of insertion lines affected and the magnitude of the conferred repression. ZnF-PcG repression was more effective at centric and telomeric reporter insertion sites, as compared to euchromatic sites. ZnF-PcG proteins tethered as far as 3.0 kb away from the target promoter produced silencing, indicating that these effects were long range. Repression by ZnF-SCM required a protein interaction domain, the SPM domain, which suggests that this domain is not primarily used to direct SCM to chromosomal loci. This targeting system is useful for studying protein domains and mechanisms involved in PcG repression in vivo. PMID:11333237
Roseman, R R; Morgan, K; Mallin, D R; Roberson, R; Parnell, T J; Bornemann, D J; Simon, J A; Geyer, P K
Phosphorus-nitrogen compounds: Part 28. Syntheses, structural characterizations, antimicrobial and cytotoxic activities, and DNA interactions of new phosphazenes bearing vanillinato and pendant ferrocenyl groups
NASA Astrophysics Data System (ADS)
The gradually Cl replacement reactions of spirocyclic mono (1 and 2) and bisferrocenyl cyclotriphosphazenes (3-5) with the potassium salt of 4-hydroxy-3-methoxybenzaldehyde (potassium vanillinate) gave mono (1a-5a), geminal (gem-1b-5b), non-geminal (cis-1b, cis-5b and trans-2b-5b), tri (1c-5c) and tetra-substituted phosphazenes (1d-5d). Some phosphazenes have stereogenic P-center(s). The chirality of 4c was verified using chiral HPLC column. Electrochemical behaviors were influenced only by the number of ferrocene groups, but not the length of the amine chains and the substituent(s). The structures of the new phosphazenes were determined by FTIR, MS, 1H, 13C and 31P NMR, HSQC and HMBC spectral data. The solid-state structures of cis-1b and 4d were examined by single crystal X-ray diffraction techniques. The twelve phosphazene derivatives were screened for antimicrobial activity and the compounds 5a, cis-1b and 2c exhibited the highest antibacterial activity against G(+) and G(-) bacteria. In addition, it was found that overall gem-1b inhibited the growth of Mycobacterium tuberculosis. The compounds 1d, 2d and 4d were tested in HeLa cancer cell lines. Among these compounds, 2d had cytotoxic effect on HeLa cell in the first 48 h. Moreover, interactions between compounds 2a, gem-1b, gem-2b, cis-1b, 2c, 3c, 4c, 5c, 1d, 2d and 4d, and pBR322 plasmid DNA were investigated.
T�mer, Yasemin; Asmafiliz, Nuran; K?l?�, Zeynel; H�kelek, Tuncer; Yasemin Ko�, L.; A�?k, Leyla; Yola, Mehmet L�tfi; Solak, Ali Osman; �ner, Ya?mur; D�ndar, Devrim; Yavuz, Makbule
Changes in Fat Mitochondrial DNA and Function in Subjects Randomized to Abacavir-Lamivudine or Tenofovir DF�Emtricitabine With Atazanavir-Ritonavir or Efavirenz: AIDS Clinical Trials Group Study A5224s, Substudy of A5202
Background.?The effect of nonthymidine nucleoside reverse-transcriptase inhibitors (NRTIs) on fat mitochondrial DNA (mtDNA) content and function is unclear. Methods.?A5202 randomized antiretroviral therapy�naive human immunodeficiency virus�infected subjects to abacavir-lamivudine (ABC/3TC) versus tenofovir DF�emtricitabine (TDF/FTC) with efavirenz (EFV) or atazanavir-ritonavir (ATV/r). A5224s, substudy of A5202, enrolled 269 subjects with fat measurements by dual-energy x-ray absorptiometry and computed tomography. A subset of subjects underwent fat biopsies at baseline and week 96 for mtDNA content (real-time polymerase chain reaction) and oxidative phosphorylation nicotinamide adenine dinucleotide (reduced) dehydrogenase (complex I) and cytochrome c oxidase (complex IV) activity levels (immunoassays). Intent-to-treat analyses were performed using analysis of variance and paired t tests. Results.?Fifty-six subjects (87% male; median age, 39 years) were included; their median body mass index, CD4 cell count, and fat mtDNA level were 26 kg/m2, 227 cells/?L, and 1197 copies/cell, respectively. Fat mtDNA content decreased within the ABC/3TC and TDF/FTC groups (combining EFV and ATV/r arms; median change, ?341 [interquartile range, ?848 to 190; P = .03] and ?400 [?661 to ?221; P < .001] copies/cell, respectively), but these changes did not differ significantly between the 2 groups (P = .57). Complex I and IV activity decreased significantly in the TDF/FTC group (median change, ?12.45 [interquartile range, ?24.70 to 2.90; P = .003] and ?8.25 [?13.90 to ?1.30; P < .001], optical density � 103/�g, respectively) but not the ABC/3TC group. Differences between the ABC/3TC and TDF/FTC groups were significant for complex I (P = .03). Conclusions.?ABC/3TC and TDF/FTC significantly and similarly decreased fat mtDNA content, but only TDF/FTC decreased complex I and complex IV activity levels. Clinical Trials Registration.?NCT00118898. PMID:23204164
McComsey, Grace A.; Daar, Eric S.; O'Riordan, MaryAnn; Collier, Ann C.; Kosmiski, Lisa; Santana, Jorge L.; Fichtenbaum, Carl J.; Fink, Heidi; Sax, Paul E.; Libutti, Daniel E.; Gerschenson, Mariana
Differentiation of Spotted Fever Group Rickettsiae by Sequencing and Analysis of Restriction Fragment Length Polymorphism of PCR Amplified DNA of the Gene Encoding the Protein rOmpA
Currently, the genotypic identification of the spotted fever group (SFG) rickettsiae is based on restriction fragmentlengthpolymorphismanalysisofPCR-amplifiedgenescodingfortheenzymecitratesynthaseandthe surfaceproteinsrOmpAandrOmpB.Asetofusefulrestrictionendonucleaseswasfoundfollowingcomparison ofRickettsiarickettsiiandR.prowazekiisequences.However,byusingthreePCRamplificationsandfourenzyme digestions with this set, it was impossible to differentiate between all of the known serotypes of the SFG rickettsiae. We amplified by PCR and sequenced using an automated laser fluorescent DNA sequencer a fragment of the gene encoding the protein rOmpA from
Nanotechnology with DNA DNA Nanodevices
Nanotechnology with DNA DNA Nanodevices Friedrich C. Simmel* and Wendy U. Dittmer A DNA actuator. Introduction.............285 2. Overview: DNA Nanotechnology.......285 3. Prototypes of Nanomechanical DNA overview of DNA nanotechnology as a whole is given. The most important properties of DNA molecules
Ludwig-Maximilians-Universität, München
Evolution of eukaryotic single-stranded DNA viruses of the Bidnaviridae family from genes of four other groups of widely different viruses
NASA Astrophysics Data System (ADS)
Single-stranded (ss)DNA viruses are extremely widespread, infect diverse hosts from all three domains of life and include important pathogens. Most ssDNA viruses possess small genomes that replicate by the rolling-circle-like mechanism initiated by a distinct virus-encoded endonuclease. However, viruses of the family Bidnaviridae, instead of the endonuclease, encode a protein-primed type B DNA polymerase (PolB) and hence break this pattern. We investigated the provenance of all bidnavirus genes and uncover an unexpected turbulent evolutionary history of these unique viruses. Our analysis strongly suggests that bidnaviruses evolved from a parvovirus ancestor from which they inherit a jelly-roll capsid protein and a superfamily 3 helicase. The radiation of bidnaviruses from parvoviruses was probably triggered by integration of the ancestral parvovirus genome into a large virus-derived DNA transposon of the Polinton (polintovirus) family resulting in the acquisition of the polintovirus PolB gene along with terminal inverted repeats. Bidnavirus genes for a receptor-binding protein and a potential novel antiviral defense modulator are derived from dsRNA viruses (Reoviridae) and dsDNA viruses (Baculoviridae), respectively. The unusual evolutionary history of bidnaviruses emphasizes the key role of horizontal gene transfer, sometimes between viruses with completely different genomes but occupying the same niche, in the emergence of new viral types.
Krupovic, Mart; Koonin, Eugene V.
1. DNA microarray DNA (spot) . DNA probe , probe (hybridization) . DNA microarray cDNA oligonucleotide oligonucleotide cDNA probe . oligonucleotide microarray , DNA , probe . oligonucleotide microarray probe
We have begun to characterize a variety of codes, motivated by potential implementation as (quaternary) DNA n-sequences, with letters denoted A, C The first codes we studied are the most reminiscent of conventional group codes. For these codes, Hamming similarity was generalized so that the score for matched letters takes more than one value, depending upon which letters are matched [2]. These codes consist of n-sequences satisfying an upper bound on the similarities, summed over the letter positions, of distinct codewords. We chose similarity 2 for matches of letters A and T and 3 for matches of the letters C and G, providing a rough approximation to double-strand bond energies in DNA. An inherent novelty of DNA codes is 'reverse complementation'. The latter may be defined, as follows, not only for alphabets of size four, but, more generally, for any even-size alphabet. All that is required is a matching of the letters of the alphabet: a partition into pairs. Then, the reverse complement of a codeword is obtained by reversing the order of its letters and replacing each letter by its match. For DNA, the matching is AT/CG because these are the Watson-Crick bonding pairs. Reversal arises because two DNA sequences form a double strand with opposite relative orientations. Thus, as will be described in detail, because in vitro decoding involves the formation of double-stranded DNA from two codewords, it is reasonable to assume - for universal applicability - that the reverse complement of any codeword is also a codeword. In particular, self-reverse complementary codewords are expressly forbidden in reverse-complement codes. Thus, an appropriate distance between all pairs of codewords must, when large, effectively prohibit binding between the respective codewords: to form a double strand. Only reverse-complement pairs of codewords should be able to bind. For most applications, a DNA code is to be bi-partitioned, such that the reverse-complementary pairs are separated across the two blocks. For the foregoing reasons, these two blocks of codewords suffice as the hooks and loops of a digital Velcro. We began our investigations of such codes by constructing quaternary BCH reverse-complement codes, using cyclic codes and conventional Hamming distance [4]. We also obtained upper and lower bounds on the rate of reverse-complement codes with a metric function based on the foregoing similarities [3]. For most applications involving DNA, however, the reverse-complementary analogue of codes based on the insertion-deletion distance is more advantageous. This distance equals the codeword length minus the longest length of a common (not necessarily contiguous) subsequence. (The 'aligned' codes described above may be used under special experimental conditions), The advantage arises because, under the assumption that DNA is very flexible, the sharing of sufficiently long subsequences between codewords would be tantamount to the ability of one of their reverse complements to form a double strand with the other codeword. Thus far, using the random coding method, we have derived an asymptotic lower bound on the rate of reverse-complement insertion-deletion codes, as a function of the insertion-deletion distance fraction and of the alphabet size [1]. For the quaternary DNA alphabet of primary importance, this lower bound yields an asymptotically positive rate if the insertion-deletion-distance fraction does not exceed the threshold {approx} 0.19. Extensions of the Varsamov-Tenengol'ts construction of insertion-deletion codes [5] for reverse-complement insertion-deletion codes will be described. Experiments have been performed involving some of our DNA codes.
Torney, D. C. (David C.)
Reduced Expression of DNA Damage Repair Genes High Mobility Group Box1 and Poly(ADP-ribose) Polymerase1 in Inactive Carriers of Hepatitis B Virus Infection-A Possible Stage of Viral Integration
Background High mobility group box1 (HMGB1) and poly(ADP-ribose) polymerase1 (PARP1) proteins repair cellular DNA damage. Reduced expression of the corresponding genes can lead to an impaired DNA damage repair mechanism. Intracellular replication of hepatitis B virus (HBV) in such conditions can favor the integration of viral DNA into host genome leading to the development of hepatocellular carcinoma (HCC). Objective This study was performed to assess the expression of HMGB1 and PARP1 mRNAs in conjunction with the estimation of HBV replication intermediate pregenomic RNA (PgRNA) in various phases of HBV infection. Materials Eighty eight patients and 26 voluntary blood donors as controls were included in the study. Patients were grouped in to acute (AHB; n�=�15), inactive carriers (IC; n�=�36), cirrhosis (Cirr; n�=�25) and hepatocellular carcinoma (HCC; n�=�12). Serum HBV DNA was quantified by real time polymerase chain reaction (PCR) assay. Expression of HMGB1, PARP1 and PgRNA were evaluated using peripheral blood mononuclear cells (PBMCs) derived RNA by reverse transcription PCR (RT-PCR) and densitometry. Results Significant reduction of HMGB1 and PARP1 gene expressions (P�<�0.05) were observed in patients than controls with more explicit decline of PARP1 (P�=�0.0002). Both genes were significantly downregulated (P�<�0.001) in ICs than controls. In ICs, HMGB1 was significantly lowered than cirrhosis (P�=�0.002) and HCC (P�=�0.0006) while PARP1 declined significantly (P�=�0.04) than HCC. Level of PgRNA was comparable in all the disease categories. Conclusion In conclusion, our findings indicate impaired DNA damage repair mechanisms in HBV infected cells of ICs. This, along with low viral load but higher level of PgRNA in this group is suggestive of the diversion of HBV replication pathway that might facilitate viral DNA integration in to host genome. Intrusion of HBV PgRNA reverse transcription in early stage of infection might appear advantageous to thwart the development of HCC.
Mukherjee, Rathindra M.; Shravanti, Gelli V.; Jakkampudi, Aparna; Kota, Ramya; Jangala, Asha L.; Reddy, Panyala B.; Rao, Padaki N.; Gupta, Rajesh; Reddy, Duvvuru N.
Immobilization of DNA in polyacrylamide gel for the manufacture of DNA and DNA-oligonucleotide microchips.
Activated DNA was immobilized in aldehyde-containing polyacrylamide gel for use in manufacturing the MAGIChip (microarrays of gel-immobilized compounds on a chip). First, abasic sites were generated in DNA by partial acidic depurination. Amino groups were then introduced into the abasic sites by reaction with ethylenediamine and reduction of the aldimine bonds formed. It was found that DNA could be fragmented at the site of amino group incorporation or preserved mostly unfragmented. In similar reactions, both amino-DNA and amino-oligonucleotides were attached through their amines to polyacrylamide gel derivatized with aldehyde groups. Single- and double-stranded DNA of 40 to 972 nucleotides or base pairs were immobilized on the gel pads to manufacture a DNA microchip. The microchip was hybridized with fluorescently labeled DNA-specific oligonucleotide probes. This procedure for immobilization of amino compounds was used to manufacture MAGIChips containing both DNA and oligonucleotides.
Proudnikov, D.; Timofeev, E.; Mirzabekov, A.; Center for Mechanistic Biology and Biotechnology; Engelhardt Inst. of Molecular Biology
Maternal exposure to potential inhibitors of DNA topoisomerase II and infant leukemia (United States): A report from the Children's Cancer Group
Nearly 80 percent of infant leukemias present with an abnormality involving the MLL gene at 11q23. Moreover, secondary acute myeloid leukemias (AML) that occur as the result of chemotherapy agents, which are known to inhibit DNA topoisomerase II, often manifest the same MLL abnormalities. It has been hypothesized that de novo infant leukemias may occur as a result of maternal
Julie A. Ross; John D. Potter; Gregory H. Reaman; Thomas W. Pendergrass; Leslie L. Robison
Functional regulation of the DNA damage-recognition factor DDB2 by ubiquitination and interaction with xeroderma pigmentosum group C protein
In mammalian nucleotide excision repair, the DDB1�DDB2 complex recognizes UV-induced DNA photolesions and facilitates recruitment of the XPC complex. Upon binding to damaged DNA, the Cullin 4 ubiquitin ligase associated with DDB1�DDB2 is activated and ubiquitinates DDB2 and XPC. The structurally disordered N-terminal tail of DDB2 contains seven lysines identified as major sites for ubiquitination that target the protein for proteasomal degradation; however, the precise biological functions of these modifications remained unknown. By exogenous expression of mutant DDB2 proteins in normal human fibroblasts, here we show that the N-terminal tail of DDB2 is involved in regulation of cellular responses to UV. By striking contrast with behaviors of exogenous DDB2, the endogenous DDB2 protein was stabilized even after UV irradiation as a function of the XPC expression level. Furthermore, XPC competitively suppressed ubiquitination of DDB2 in vitro, and this effect was significantly promoted by centrin-2, which augments the DNA damage-recognition activity of XPC. Based on these findings, we propose that in cells exposed to UV, DDB2 is protected by XPC from ubiquitination and degradation in a stochastic manner; thus XPC allows DDB2 to initiate multiple rounds of repair events, thereby contributing to the persistence of cellular DNA repair capacity. PMID:25628365
Matsumoto, Syota; Fischer, Eric S.; Yasuda, Takeshi; Dohmae, Naoshi; Iwai, Shigenori; Mori, Toshio; Nishi, Ryotaro; Yoshino, Ken-ichi; Sakai, Wataru; Hanaoka, Fumio; Thom�, Nicolas H.; Sugasawa, Kaoru
DNA barcoding uses specific regions of DNA in order to identify species. Initiatives are taking place around the world to generate DNA barcodes for all groups of living organisms and to make these data publically available in order to help understand, conserve, and utilize the world's biodiversity. For land plants the core DNA barcode markers are two sections of coding regions within the chloroplast, part of the genes, rbcL and matK. In order to create high quality databases, each plant that is DNA barcoded needs to have a herbarium voucher that accompanies the rbcL and matK DNA sequences. The quality of the DNA sequences, the primers used, and trace files should also be accessible to users of the data. Multiple individuals should be DNA barcoded for each species in order to check for errors and allow for intraspecific variation. The world's herbaria provide a rich resource of already preserved and identified material and these can be used for DNA barcoding as well as by collecting fresh samples from the wild. These protocols describe the whole DNA barcoding process, from the collection of plant material from the wild or from the herbarium, how to extract and amplify the DNA, and how to check the quality of the data after sequencing. PMID:25373752
de Vere, Natasha; Rich, Tim C G; Trinder, Sarah A; Long, Charlotte
DNA BARCODING DNA barcoding of Cuban freshwater fishes: evidence for
DNA BARCODING DNA barcoding of Cuban freshwater fishes: evidence for cryptic species and taxonomic subunit I) were used to barcode 126 individuals, representing 27 taxonomically recognized species in 17 of the DNA barcodes for cataloguing Cuban freshwater fish species and for identifying those groups
Bernatchez, Louis
A biosensing of Toxoplasma gondii DNA with CdTe/Fe3O4 dual functional quantum dot as reporter group
NASA Astrophysics Data System (ADS)
Toxoplasma gondii is an intestinal coccidium that parasitizes members of the cat family as definitive hosts and has a wide range of intermediate hosts. Infection is common in many warm-blooded animals, including humans, the early detection of Toxoplasma gondii was concerned in recent years. In the current research, we presented a fast, specific, and sensitive sensing probe to detect Toxoplasma gondii DNA based on mechanism of fluorescence energy transfer (FRET), and a magnetic-fluorescent CdTe/Fe3O4 core-shell quantum dots (mQDs) was utilized as energy donor, and a commercial quencher (BHQ-2) was used as energy acceptor, respectively. The CdTe/Fe3O4 mQDs were prepared by layer-by-layer (LBL) process at ambient temperature. The sensing probe was fabricated through labeling a stem-loop Toxoplasma gondii DNA oligonucleotide with mQDs at the 5' end and BHQ-2 at 3' end, respectively, and the resulting sensing probe can be simply isolated and purified from the reactant with a common magnet. Properties of mQDs and sensing probe were determined by transmission electron microscopy (TEM) and fluorescence spectrum (FS). The TEM data demonstrated that the size of mQDs was ~20nm. the FS data indicated fluorescence intensity (FI) was doubled after the complete complimentary target Toxoplasma gondii DNA was introduced comparing with the FI before addition of target Toxoplasma gondii DNA. Moreover, only weak FI change was observed when the target DNA with one-mismatch base pair was added, this result revealed the sensing probe has high sensitivity and specificity. The current sensing probe will has great potential applications in the life science and related research.
Liang, Chu; Xu, Shichao; Yang, Juan; Zhang, Jimei; Dai, Zhao; Sun, Bo; Sun, Shuqing; Feng, Tielin; Zi, Yan; Liu, Jingwei; Luo, Hao
Evaluation of Group B Streptococcus Molecular Assay with Automated Ampliprep DNA Extraction and LightCycler 2.0 Amplifi cation and Detection
Background: Federal guidelines from the CDC recommend surveillance in pregnant women for Group B Streptococcus carriage to reduce mortality and morbidity in newborn infants. Recent papers have demonstrated that molecular methods can increase identifi cation of Group B Strep carriage by approximately 12%. We have optimized the molecular detection of Group B Streptococcus using the Ampliprep? and LightCycler instruments. Methods:
K. Hocker MT; R. C. Fader; A. Rao
DNA Structural Nanotechnology Duke University
DNA Structural Nanotechnology John Reif Duke University Graduate Students: Harish Chandran and Nikhil Gopalkrishnan Recent Graduated Phds: Urmi Majumder, Sudheer Sahu, & Peng Yin DNA Nanostructure Group John Reif & Thomas H. LaBean #12;Introduction to DNA Self-Assembly #12;Self-Assembly in Nature
Reif, John H.
Report of the European DNA profiling group (EDNAP): an investigation of the complex STR loci D21S11 and HUMFIBRA (FGA)
This paper describes a collaborative exercise which was intended to demonstrate whether uniformity of DNA profiling results could be achieved between European laboratories using two complex short tandem repeat (STR) loci. The loci D21S11 and HUMFIBRA (FGA) were chosen because they are commonly used by different European laboratories. D21S11 has approximately 14 common alleles (f>0.001), whereas HUMFIBRA has 19 common
Peter Gill; E d'Aloja; J Andersen; B Dupuy; M Jangblad; V Johnsson; A. D Kloosterman; A Kratzer; M. V Lareu; M Meldegaard; C Phillips; H Pfitzinger; S Rand; M Sabatier; R Scheithauer; H Schmitter; P Schneider; M. C Vide
Plasma Epstein-Barr virus DNA predicts outcome in advanced Hodgkin lymphoma: correlative analysis from a large North American cooperative group trial.
Epstein-Barr virus (EBV) is associated with Hodgkin lymphoma (HL) and can be detected by in situ hybridization (ISH) of viral nucleic acid (EBER) in tumor cells. We sought to determine whether plasma EBV-DNA could serve as a surrogate for EBER-ISH and to explore its prognostic utility in HL. Specimens from the Cancer Cooperative Intergroup Trial E2496 were used to compare pretreatment plasma EBV-DNA quantification with EBV tumor status by EBER-ISH. A cutoff of >60 viral copies/100 �L plasma yielded 96% concordance with EBER-ISH. Pretreatment and month 6 plasma specimens were designated EBV(-) or EBV(+) by this cutoff. Patients with pretreatment EBV(+) plasma (n = 54) had inferior failure-free survival (FFS) compared with those with pretreatment EBV(-) plasma (n = 274), log-rank P = .009. By contrast, no difference in FFS was observed when patients were stratified by EBER-ISH. Pretreatment plasma EBV positivity was an independent predictor of treatment failure on multivariate analyses. At month 6, plasma EBV(+) patients (n = 7) had inferior FFS compared with plasma EBV(-) patients (n = 125), log-rank P = .007. These results confirm that plasma EBV-DNA is highly concordant with EBER-ISH in HL and suggest that it may have prognostic utility both at baseline and after therapy. This trial was registered at www.clinicaltrials.gov as #NCT00003389. PMID:23386127
Kanakry, Jennifer A; Li, Hailun; Gellert, Lan L; Lemas, M Victor; Hsieh, Wen-son; Hong, Fangxin; Tan, King L; Gascoyne, Randy D; Gordon, Leo I; Fisher, Richard I; Bartlett, Nancy L; Stiff, Patrick; Cheson, Bruce D; Advani, Ranjana; Miller, Thomas P; Kahl, Brad S; Horning, Sandra J; Ambinder, Richard F
DNA Computing Hamiltonian path
2014 DNA DNA #12;DNA Computing � Feynman � Adleman � DNASIMD � ... � � � � � DNADNA #12;DNA � DNA � � � � DNA � � #12;2000 2005 2010 1995 Hamiltonian path DNA tweezers DNA tile DNA origami DNA box Sierpinski DNA tile self assembly DNA logic gates Whiplash PCR DNA automaton DNA spider MAYA
Hagiya, Masami
DNA methylation is one of the most intensely studied epigenetic modifications in mammals. In normal cells, it assures the proper regulation of gene expression and stable gene silencing. DNA methylation is associated with histone modifications and the interplay of these epigenetic modifications is crucial to regulate the functioning of the genome by changing chromatin architecture. The covalent addition of a methyl group occurs generally in cytosine within CpG dinucleotides which are concentrated in large clusters called CpG islands. DNA methyltransferases are responsible for establishing and maintenance of methylation pattern. It is commonly known that inactivation of certain tumor-suppressor genes occurs as a consequence of hypermethylation within the promoter regions and a numerous studies have demonstrated a broad range of genes silenced by DNA methylation in different cancer types. On the other hand, global hypomethylation, inducing genomic instability, also contributes to cell transformation. Apart from DNA methylation alterations in promoter regions and repetitive DNA sequences, this phenomenon is associated also with regulation of expression of noncoding RNAs such as microRNAs that may play role in tumor suppression. DNA methylation seems to be promising in putative translational use in patients and hypermethylated promoters may serve as biomarkers. Moreover, unlike genetic alterations, DNA methylation is reversible what makes it extremely interesting for therapy approaches. The importance of DNA methylation alterations in tumorigenesis encourages us to decode the human epigenome. Different DNA methylome mapping techniques are indispensable to realize this project in the future. PMID:20920744
Kulis, Marta; Esteller, Manel
Molecular Cloning, Sequence, and Expression of a Human GDP-L-Fucose: beta-D-Galactoside 2-alpha-L-Fucosyltransferase cDNA that can Form the H Blood Group Antigen
We have previously used a gene-transfer scheme to isolate a human genomic DNA fragment that determines expression of a GDP-L-fucose:beta-D-galactoside 2-alpha-L-fucosyltransferase [alpha(1,2)FT EC 22.214.171.124]. Although this fragment determined expression of an alpha(1, 2)FT whose kinetic properties mirror those of the human H blood group alpha(1,2)FT, their precise nature remained undefined. We describe here the molecular cloning, sequence, and expression of
Robert D. Larsen; Linda K. Ernst; Rajan P. Nair; John B. Lowe
NSDL National Science Digital Library
This animated YouTube video, created by�Southwest Center for Microsystems Education (SCME), illustrates how DNA hybridization works in the context of nanofabrication. The animation and associated narration describe "DNA hybridization is when a single-stranded DNA (ssDNA) molecule bonds with a complementary ssDNA molecule from another source forming a "hybrid". This animation shows a double-stranded DNA (dsDNA) molecule dividing into two ssDNA strands. One ssDNA remains on the substrate as the "probe". A complementary ssDNA from another source (a ssDNA with a complementary base pair sequence) joins with the probe forming a 'hybrid'�dsDNA molecule." A supporting learning module and activities can be downloaded from the SCME website.
NSDL National Science Digital Library
The discovery of enzymes that could cut and paste DNA made genetic engineering possible. Restriction enzymes, found naturally in bacteria, can be used to cut DNA fragment at specific sequences, while another enzyme, DNA ligase, can attach or rejoin DNA fragments with complementary ends. This animation from Cold Spring Harbor Laboratory's Dolan DNA Learning Center presents DNA restriction through a series of illustrations of processes involved.
NSDL National Science Digital Library
Stanley Cohen and Herbert Boyer's historic experiment used techniques to cut and paste DNA to create the first custom-made organism containing recombined or 'recombinant' DNA. Cohen and Boyer inserted the recombinant DNA molecule they created into E. coli bacteria by means of a plasmid, thereby inducing the uptake and expression of a foreign DNA sequence known as 'transformation.' This animation from Cold Spring Harbor Laboratory's Dolan DNA Learning Center presents DNA transformation through a series of illustrations of the processes involved.
Synthesis, spectral characterization, crystal structure and in vitro DNA/protein binding studies of phosphorous ylide palladacyclic complexes containing azide group.
The reaction between (4-nitrobenzoylmethylene)triphenylphosphorane Pd(II) complex [Pd{?(2)(C,C)-C6H4PPh2C(H)CO(C6H4NO2-4)}(?-Cl)]2 and excess of NaN3 resulted in the ?-N3 bridged Pd(II) complex [Pd{?(2)(C,C)-C6H4PPh2C(H)CO(C6H4NO2-4)}(?-N3)]2 (1), which underwent bridge cleavage reactions with monodentate ligands to afford the monomeric, neutral complexes [Pd{?(2)(C,C)-C6H4PPh2C(H)CO(C6H4NO2-4)}N3(L)] (L=Me3Py (1a), PPh3 (1b)). The complexes were identified and characterized by elemental analyses, infrared (IR), ((1))H, ((13))C{((1))H} and ((31))P{((1))H} NMR spectroscopy. The molecular structure of 1b was determined by single-crystal X-ray diffraction. The interactions of complexes with FS-DNA were investigated using UV absorption and fluorescence spectra. The results suggested that both complexes could interact with FS-DNA through the intercalation mode and follow the binding affinity order of 1a>1b. The reactivity toward protein BSA revealed that the quenching of BSA fluorescence by the two complexes are static quenching, and complex 1a exhibits a higher BSA-binding ability than the complex 1b. PMID:25668144
Karami, Kazem; Shirani-Sarmazeh, Zahra; Hosseini-Kharat, Mahboubeh; Lipkowski, Janusz; Saeidifar, Maryam
NSDL National Science Digital Library
This animated YouTube video, created by�Southwest Center for Microsystems Education (SCME), illustrates how DNA microarrays work in the context of nanofabrication. The animation and associated narration describe "how a DNA microarray identifies complementary DNA (cDNA) strands from a sample. On the substrate of the array are synthetic ssDNA stands or oligonucleotides (oligos). Each grid in the microarray contains hundreds to thousands of oligos with a unique DNA sequence. These oligos hybridize with cDNA from one of two samples. There are thousands of grids on the array allowing for the simultaneous identification of thousands of different DNA sequences. Each sample cDNA is "tagged" with the red or green tag as shown in the animation. The "tags" enable an interpretation of the DNA hybridizations."�A supporting learning module and activities can be downloaded from the SCME website.
DNA vaccines use eukaryotic expression vectors to produce immunizing proteins in the vaccinated host. Popular methods of delivery are intramuscular and intradermal saline injections of DNA and gene gun bombardment of skin with DNA-coated gold beads. The method of DNA inoculation (gene gun versus intramuscular injection) and the form of the DNA-expressed antigen (cell-associated versus secreted) determine whether T-cell help
Harriet L. Robinson; Celia Aurora Tiglao Torres
Conformation-dependent DNA attraction
NASA Astrophysics Data System (ADS)
Understanding how DNA molecules interact with other biomolecules is related to how they utilize their functions and is therefore critical for understanding their structure-function relationships. For a long time, the existence of Z-form DNA (a left-handed double helical version of DNA, instead of the common right-handed B-form) has puzzled the scientists, and the definitive biological significance of Z-DNA has not yet been clarified. In this study, the effects of DNA conformation in DNA-DNA interactions are explored by molecular dynamics simulations. Using umbrella sampling, we find that for both B- and Z-form DNA, surrounding Mg2+ ions always exert themselves to screen the Coulomb repulsion between DNA phosphates, resulting in very weak attractive force. On the contrary, a tight and stable bound state is discovered for Z-DNA in the presence of Mg2+ or Na+, benefiting from their hydrophobic nature. Based on the contact surface and a dewetting process analysis, a two-stage binding process of Z-DNA is outlined: two Z-DNA first attract each other through charge screening and Mg2+ bridges to phosphate groups in the same way as that of B-DNA, after which hydrophobic contacts of the deoxyribose groups are formed via a dewetting effect, resulting in stable attraction between two Z-DNA molecules. The highlighted hydrophobic nature of Z-DNA interaction from the current study may help to understand the biological functions of Z-DNA in gene transcription.Understanding how DNA molecules interact with other biomolecules is related to how they utilize their functions and is therefore critical for understanding their structure-function relationships. For a long time, the existence of Z-form DNA (a left-handed double helical version of DNA, instead of the common right-handed B-form) has puzzled the scientists, and the definitive biological significance of Z-DNA has not yet been clarified. In this study, the effects of DNA conformation in DNA-DNA interactions are explored by molecular dynamics simulations. Using umbrella sampling, we find that for both B- and Z-form DNA, surrounding Mg2+ ions always exert themselves to screen the Coulomb repulsion between DNA phosphates, resulting in very weak attractive force. On the contrary, a tight and stable bound state is discovered for Z-DNA in the presence of Mg2+ or Na+, benefiting from their hydrophobic nature. Based on the contact surface and a dewetting process analysis, a two-stage binding process of Z-DNA is outlined: two Z-DNA first attract each other through charge screening and Mg2+ bridges to phosphate groups in the same way as that of B-DNA, after which hydrophobic contacts of the deoxyribose groups are formed via a dewetting effect, resulting in stable attraction between two Z-DNA molecules. The highlighted hydrophobic nature of Z-DNA interaction from the current study may help to understand the biological functions of Z-DNA in gene transcription. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr03235c
Li, Weifeng; Nordenski�ld, Lars; Zhou, Ruhong; Mu, Yuguang
Genetic variation and demographic history of the Haplochromis laparogramma group of Lake Victoria--An analysis based on SINEs and mitochondrial DNA
Genetic variation and demographic history of the Haplochromis laparogramma group of Lake Victoria More than 500 endemic haplochromine cichlid species inhabit Lake Victoria. This striking species and population structure of closely related Lake Victoria cichlids and in showing the importance of applying
Development of a DNA vaccine for chicken infectious anemia and its immunogenicity studies using high mobility group box 1 protein as a novel immunoadjuvant indicated induction of promising protective immune responses.
Chicken infectious anaemia (CIA) is an economically important and emerging poultry disease reported worldwide. Current CIA vaccines have limitations like, the inability of the virus to grow to high titres in embryos/cell cultures, possession of residual pathogenicity and a risk of reversion to virulence. In the present study, a DNA vaccine, encoding chicken infectious anaemia virus (CIAV) VP1 and VP2 genes, was developed and co-administered with truncated chicken high mobility group box 1 (HMGB1?C) protein in young chicks for the evaluation of vaccine immune response. CIAV VP1 and VP2 genes were cloned in pTARGET while HMGB1?C in PET32b vector. In vitro expression of these gene constructs was evaluated by Western blotting. Further, recombinant HMGB1?C was evaluated for its biological activity. The CIAV DNA vaccine administration in specific pathogen free chicks resulted in moderately protective ELISA antibody titres in the range of 4322.87 � 359.72 to 8288.19 � 136.38, increased CD8(+) cells, and a higher titre was observed by co-administration of novel adjuvant (HMGB1?C) and booster immunizations. The use of vaccine with adjuvant showed achieving antibody titres nearly 8500, titre considered as highly protective, which indicates that co-immunization of HMGB1?C may have a strong adjuvant activity on CIAV DNA vaccine induced immune responses. The able potential of HMGB1 protein holding strong adjuvant activity could be exploited further with trials with vaccines for other important pathogens for achieving the required protective immune responses. PMID:25448094
Sawant, Pradeep Mahadev; Dhama, Kuldeep; Rawool, Deepak Bhiva; Wani, Mohd Yaqoob; Tiwari, Ruchi; Singh, Shambhu Dayal; Singh, Raj Kumar
Genetic variation and demographic history of the Haplochromis laparogramma group of Lake Victoria-An analysis based on SINEs and mitochondrial DNA.
More than 500 endemic haplochromine cichlid species inhabit Lake Victoria. This striking species diversity is a classical example of recent explosive adaptive radiation thought to have happened within the last approximately 15,000 years. In this study, we examined the population structure and historical demography of 3 pelagic haplochromine cichlid species that resemble in morphology and have similar niche, Haplochromis (Yssichromis) laparogramma, Haplochromis (Y.) pyrrhocephalus, and Haplochromis (Y.) sp. "glaucocephalus". We investigated the sequences of the mitochondrial DNA control region and the insertion patterns of short interspersed elements (SINEs) of 759 individuals. We show that sympatric forms are genetically differentiated in 4 of 6 cases, but we also found apparent weakening of the genetic differentiation in areas with turbid water. We estimated the timings of population expansion and species divergence to coincide with the refilling of the lake at the Pleistocene/Holocene boundary. We also found that estimates can be altered significantly by the choice of the shape of the molecular clock. If we employ the nonlinear clock model of evolutionary rates in which the rates are higher towards the recent, the population expansion was dated at around the event of desiccation of the lake ca. 17,000 YBP. Thus, we succeeded in clarifying the species and population structure of closely related Lake Victoria cichlids and in showing the importance of applying appropriate clock calibrations in elucidating recent evolutionary events. PMID:19837145
Mzighani, Semvua I; Nikaido, Masato; Takeda, Miyuki; Seehausen, Ole; Budeba, Yohana L; Ngatunga, Benjamin P; Katunzi, Egid F B; Aibara, Mitsuto; Mizoiri, Shinji; Sato, Tetsu; Tachida, Hidenori; Okada, Norihiro
Complex group-I introns in nuclear SSU rDNA of red and green algae: evidence of homing-endonuclease pseudogenes in the Bangiophyceae
The green alga Scenedesmus pupukensis and the red alga Porphyra spiralis contain large group-IC1 introns in their nuclear small subunit ribosomal RNA genes due to the presence of open reading frames\\u000a at the 5? end of the introns. The putative 555 amino-acid Scenedesmus-encoded protein harbors a sequence motif resembling the bacterial S9 ribosomal proteins. The Porphyra intron self-splices in?vitro, and
Peik Haugen; Volker A. R. Huss; Henrik Nielsen; Steinar Johansen
Plasma Concentrations of High-Mobility Group Box Protein 1, Soluble Receptor for Advanced Glycation End-Products and Circulating DNA in Patients with Acute Pancreatitis
Aims: High-mobility group box protein 1 (HMGB1), a late-acting proinflammatory cytokine, is secreted actively by inflammatory cells, and released passively from necrotic cells. From the aspect that both inflammation and necrosis are involved in the pathogenesis in acute pancreatitis, the aim of the study was a joint investigation of the plasma concentrations of HMGB1, its soluble receptor for advanced glycation
�. K. Kocsis; A. Szabolcs; P. Hofner; T. Tak�cs; G. Farkas; K. Boda; Y. M�ndi
Solution confirmation of the (-)-trans-anti-5-Methylchrysene-dG adduct oppposite dC in a DNA duplex: DNA bending associated with wedging of the Methyl group of 5-Methylchrysene to the 3{prime}-side of the modification site
This paper reports on NMR-molecular mechanics structural studies of the (-)-trans-anti-[MC]dG adduct positioned opposite dC in the sequence context of the d(Cl-C2-A3-T4-C5-[MC]G6-C7-T8-A9-C10-C11){sm_bullet}d(G12-G13-T14-A15-G16-C17-G 18-A19-T20-G21-G22) duplex [designated (-)-trans-anti-[MC]dG{sm_bullet}dC 11-mer duplex]. This adduct is derived from the trans addition at C{sup 4} of (-)-anti-1(S),2(R)-dihydroxy-3(R),4(S)-epoxy-1,2,3,4-tetrahydro-5-methylchrysene [(-)-anti-5-MeCDE] to the N{sup 2} position of dG6 in this duplex sequence. The 5-methyl group is located adjacent to the MC(C{sup 4}) binding site, with these groups juxtaposed in a sterically crowded bay region in the adduct duplex. The 5-methylchrysenyl and the nucleic acid exchangeable and nonexchangeable protons were assigned following analysis of two-dimensional NMR data sets in H{sub 2}O and D{sub 2}O buffer solution. The solution structure of the trans-anti-[MC]dG{sm_bullet}dC 11-mer duplex has been determined by incorporating DNA-DNA and carcinogen-DNA proton-proton distances defined by lower and upper bounds deduced from NOESY data sets as restraints in molecular mechanics computations in torsion angle space. The results establish that the [MC]dG6{sm_bullet}dC17 base pair and flanking dC5{sm_bullet}dG18 and dC7{sm_bullet}dG16 base pairs retain Watson-Crick alignments upon adduct formation. 61 refs., 9 figs., 2 tabs.
Cosman, M.; Patel, D.J. [Memorial Sloan-Kettering Cancer Center, New York, NY (United States)] [and others
A phosphate group at the cos ends of phage lambda DNA is not a prerequisite for in vitro packaging: an alternative method for constructing genomic libraries using a new phasmid vector, lambda pGY97.
It is shown here that the phosphate groups at the cos ends of phage lambda DNA are not a prerequisite for in vitro packaging. Molecules with phosphatase-treated cos ends are packaged in vitro as efficiently as native lambda DNA. This observation can be used for an alternative strategy to improve the efficiency of gene library construction, since cos-cos ligation decreases in vitro encapsidation and infectivity. Dephosphorylated cos ends and a new phasmid vector lambda pGY97 have been used to construct a representative gene bank of alfalfa in a Mcr- (5-methylcytosine restriction deficient) Escherichia coli host strain. These recombinant clones can be propagated as phages or more conveniently as plasmids in recA- E. coli, to prevent possible homologous recombination events between repetitive sequences of the insert that would otherwise interfere with clone stability. The 5-19-kb inserts can be easily recloned as plasmids from the recombinant phasmids with simple EcoRI digestion and re-ligation. This observation also implies that the construction of gene libraries in cosmid vectors can be made more efficient if cos-cos ligates were cleaved by lambda terminase just before in vitro packaging. PMID:2148297
Vincze, E; Kiss, G B
NSDL National Science Digital Library
CSI: DNA provides DNA fingerprints in the form of fluorescent electrophoregrams for use as evidence in crime scenes. It includes explanations of fluorescent genotyping, variable number tandem repeats (VNTRs), and probability in forensics.
Rebecca Reiss (New Mexico Tech; )
NSDL National Science Digital Library
This animation, which shows DNA replication and the interactions of the various enzymes, can be used to illustrate to students the order of events in DNA replication, as well as emphasize which enzymes are involved in the process.
American Society For Microbiology
NSDL National Science Digital Library
Many of the revolutionary changes that have occurred in biology since 1970 can be attributed directly to the ability to manipulate DNA in defined ways. The principal tools for this recombinant DNA technology are enzymes that can "cut and "paste" DNA. Restriction enzymes are the "chemical scissors" of the molecular biologist; these enzymes cut DNA at specific nucleotide sequences. A sample of someone's DNA, incubated with restriction enzymes, is reduced to millions of DNA fragments of varying sizes. A DNA sample from a different person would have a different nucleotide sequence and would thus be enzymatically "chopped up" into a very different collection of fragments. We have been asked to apply DNA fingerprinting to determine which suspect should be charged with a crime perpetrated in our city.
BEGIN:VCARD VERSION:2.1 FN:Suzanne Black N:Black; Suzanne ORG:Inglemoor High School REV:2005-04-09 END:VCARD
ERIC Educational Resources Information Center
Provides background information for teachers on mitochondrial DNA, pointing out that it may have once been a free-living organism. Includes a ready-to-duplicate exercise titled "Using Microchondrial DNA to Measure Evolutionary Distance." (JN)
Wright, Russell G.; Bottino, Paul J.
of architecture and computer software. Sequences of DNA should also be acknowledged as eligible for copyright protection. Unaltered genomic DNA sequences would seem poor candidates for copyright protection. The case is stronger for copyright protection...
Torrance, Andrew W.
NSDL National Science Digital Library
This animation from Cold Spring Harbor Laboratory's Dolan DNA Learning Center presents DNA arrays. The animation contains information on Pat Brown's discovery and the purpose of DNA arrays to study gene expression as well as its role in the development of pharmacogenomic treatment for diseases such as cancer.
NSDL National Science Digital Library
In this activity, learners explore deoxyribonucleic acid (DNA), a nanoscale structure that occurs in nature. Learners extract a sample of DNA from split peas and put the sample in an Eppendorf tube to take home. Learners discover that nanoscientists study DNA to understand its biological function and use it to make other nanoscale materials and devices.
Nanoscale Informal Science Education Network
Cinnamate-based DNA photolithography
As demonstrated by means of DNA nanoconstructs[1], as well as DNA functionalization of nanoparticles[2-4] and micrometre-scale colloids[5-8], complex self-assembly processes require components to associate with particular partners in a programmable fashion. In many cases the reversibility of the interactions between complementary DNA sequences is an advantage[9]. However, permanently bonding some or all of the complementary pairs may allow for flexibility in design and construction[10]. Here, we show that the substitution of a pair of complementary bases by a cinnamate group provides an efficient, addressable, UV light-based method to covalently bond complementary DNA. To show the potential of this approach, we wrote micrometre-scale patterns on a surface via UV light and demonstrate the reversible attachment of conjugated DNA and DNA-coated colloids. Our strategy enables both functional DNA photolithography and multi-step, specific binding in self-assembly processes. PMID:23685865
Romulus, Joy; Li, Minfeng; Sha, Ruojie; Royer, John; Wu, Kun-Ta; Xu, Qin
DNA demethylation by DNA repair
Active DNA demethylation underlies key facets of reproduction in flowering plants and mammals and serves a general genome housekeeping function in plants. A family of 5-methylcytosine DNA glycosylases catalyzes plant ...
Gehring, Mary
A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.
Tabor, Stanley (Cambridge, MA); Richardson, Charles C. (Chestnut Hill, MA)
DNA-looping mechanisms are part of networks that regulate all aspects of DNA metabolism, including transcription, replication, and recombination. DNA looping is involved in regulation of transcriptional initiation in prokaryotic operons, including ara, gal, lac, and deo, and in phage systems. Similarly, in eukaryotic organisms, the effects of enhancers appear to be mediated at least in part by loop formation, and examples of DNA looping by hormone receptor proteins and developmental regulatory proteins have been found. In addition, instances of looped structures have been found in replication and in recombination in both prokaryotes and eukaryotes. DNA loop formation may have different functions in different cellular contexts; in some cases, the loop itself is requisite for regulation, while in others the increase in the effective local concentration of protein may account for the effects observed. The ability of DNA to form loops is affected by the distance between binding sites; by the DNA sequence, which determines deformability and bendability; and by the presence of other proteins that exert an influence on the conformation of a particular sequence. Alteration of the stability of DNA loops and/or protein-DNA binding by extra- or intracellular signals provides responsivity to changing metabolic or environmental conditions. The fundamental property of site-specific protein binding to DNA can be combined with protein-protein and protein-ligand interaction to generate a broad range of physiological states. PMID:1579106
Matthews, K S
NASA Astrophysics Data System (ADS)
Classic experimental and theoretical analyses led to a unified view of DNA as a semiflexible polymer, characterized by a bending persistence length, P, �50 nm (�150 bp). In this view, DNA lengths that are greater than P are, on average, spontaneously gently bent, and require relatively little force to bend significantly, while DNA lengths that are shorter than P are nearly straight, and require great force to bend significantly. Nevertheless, sharply bent DNA plays important roles in biology. We used the method of ligase catalyzed DNA cyclization to investigate the spontaneous looping of short DNAs. Remarkably, DNAs as short as 84 bp spontaneously bend into circles, and 94 bp DNA sequences cyclize up to 10^5 times more easily than predicted from classic theories of DNA bending. In subsequent studies we find that the twistability of sharply looped DNAs exceeds the prediction of classic theories by up to 400-fold. These results can only be understood by greatly enhanced DNA flexibility, not by permanent bends. Our results provide striking support for two new theories of DNA mechanics based on local melted or kinked regions, and they establish DNA as an active participant in the formation and function of looped regulatory complexes in vivo.
Widom, Jonathan
NSDL National Science Digital Library
This is a two-part animation. �?DNA Barcoding, Part 1,�? provides an overview of how DNA barcoding of animals can be used to identify an unknown sample or discover a new species. Cytochrome c oxidase subunit 1 (COI) is found in the mitochondria as part of the electron transport chain. The COI gene is used for DNA barcoding. Just like a barcode on an item in a grocery store identifies a product, a DNA barcode (determined by DNA sequencing) is used to identify species. Part 1 run time: 1 minute, 40 seconds. �?DNA Barcoding, Part 2�? details how small tissue samples are used for DNA barcoding, including a review of the laboratory and bioinformatics steps used in barcoding: DNA purification, polymerase chain reaction (PCR), agarose gel electrophoresis, DNA sequencing and analysis, and DNA sequence identification using the Basic Local Alignment Search Tool (BLAST) or the Barcode of Life Database (BOLD). Part 2 run time: 4 minutes, 15 seconds. Animation is closed captioned.
Patterning nanocrystals using DNA
One of the goals of nanotechnology is to enable programmed self-assembly of patterns made of various materials with nanometer-sized control. This dissertation describes the results of experiments templating arrangements of gold and semiconductor nanocrystals using 2'-deoxyribonucleic acid (DNA). Previously, simple DNA-templated linear arrangements of two and three nanocrystals structures have been made.[1] Here, we have sought to assemble larger and more complex nanostructures. Gold-DNA conjugates with 50 to 100 bases self-assembled into planned arrangements using strands of DNA containing complementary base sequences. We used two methods to increase the complexity of the arrangements: using branched synthetic doublers within the DNA covalent backbone to create discrete nanocrystal groupings, and incorporating the nanocrystals into a previously developed DNA lattice structure [2][3] that self-assembles from tiles made of DNA double-crossover molecules to create ordered nanoparticle arrays. In the first project, the introduction of a covalently-branched synthetic doubler reagent into the backbone of DNA strands created a branched DNA ''trimer.'' This DNA trimer templated various structures that contained groupings of three and four gold nanoparticles, giving promising, but inconclusive transmission electron microscopy (TEM) results. Due to the presence of a variety of possible structures in the reaction mixtures, and due to the difficulty of isolating the desired structures, the TEM and gel electrophoresis results for larger structures having four particles, and for structures containing both 5 and 10 nm gold nanoparticles were inconclusive. Better results may come from using optical detection methods, or from improved sample preparation. In the second project, we worked toward making two-dimensional ordered arrays of nanocrystals. We replicated and improved upon previous results for making DNA lattices, increasing the size of the lattices to a length greater than 20 {micro}m, and collecting atomic force microscopy (AFM) images up to 30 {micro}m. We found the lattices' requirement of divalent magnesium cations to stabilize Holliday junctions to be incompatible with the stability of charge-stabilized gold nanoparticles used for the experiments here, and gold particles added indiscriminately to the lattice surface through non-specific binding. Redesigning the lattices to avoid magnesium may improve results.
Williams, Shara Carol
NSDL National Science Digital Library
In this lesson from Science NetLinks, students will conduct activities from a module called "DNA Chips: A Genetics Lab in the Palm of Your Hand." This module is part of the National Institutes of Health Snapshots series, which focuses on a single area of biomedical research to help students understand how science, people, ethics, and history all fit together. The module for this lesson is about the DNA microarray, also known as a DNA chip.
Science Netlinks
NSDL National Science Digital Library
Students use edible models of the DNA molecule to transcribe an mRNA se- quence, then translate it into a protein. At the end of the lesson, understand that information within the DNA molecule is divided into segments called genes and learn that each gene contains the instructions for assembling a unique protein that performs a specialized function in the cell. A basic knowledge of DNA structure and function is required.
NSDL National Science Digital Library
In this activity related to plant biotechnology, learners extract DNA from fruit to investigate how it looks and feels. The procedure is similar to what scientists have to do before they can use information contained in this DNA. This lesson guide includes procedure and discussion questions to help learners reflect on the process and purpose of DNA extraction. Modifications for younger learners are included in a related PDF (see related resources).
Janice Stephens
DNA barcodes for ecology, evolution, and conservation
DNA barcodes for ecology, evolution, and conservation W. John Kress1 , Carlos Garci�a-Robledo1 10027, USA The use of DNA barcodes, which are short gene sequences taken from a standardized portion of natural systems. The suite of DNA barcode markers now applied to specific taxonomic groups of organisms
Uriarte, Maria
PCR and recombinant DNA Joan Camuas
de Barcelona #12;Topics to be covered Introduction (DNA isolation, modification enzymes) PCR DNA Koolman, Klaus-Heinrich Rohm #12;Modification enzymes in molecular biology III Major types: -T4 DNAPCR and recombinant DNA techniques Joan Camuñas Felix Ritort Group Small Biosystems Lab Universitat
Ritort, Felix
NSDL National Science Digital Library
Teachers' Domain presents this interactive, adapted from the Dolan DNA Learning Center, to help students learn about DNA Libraries, "the tools scientists use to store and reproduce genetic information that they can later access for their research." After an introduction, students can explore more about the different types of DNA libraries by clicking on any of the five DNA vectors: Yeast Artificial Chromosomes, Bacterial Artificial Chromosomes, Cosmids, Bacteriophage Lambda, and Plasmids. On the site, visitors will also find a supplemental background essay, discussion questions, and standards alignment from Teachers' Domain.
NSDL National Science Digital Library
Investigating DNA is a set of activities selected for students in a high school biology course, as well as a model for organizing and managing instruction in a high school science class. Students learn basic techniques of modern biology, the story of the discovery of DNA, and the structure and properties of DNA. They also learn to work as a team, manage their time in the classroom and lab, follow written and demonstrated procedures, and evaluate their own work. Investigating DNA includes a rationale for this approach, strategies for managing the activities, a description of each activity and a listing of resources available.
Leslie Ann Pierce (Thomas A. Edison High School REV)
Multivalent Lipid--DNA Complexes: Distinct DNA Compaction Regimes
NASA Astrophysics Data System (ADS)
Cationic liposomes (CL), while intrinsically advantageous in comparison to viruses, still have limited success for gene therapy and require more study. CL spontaneously self-assemble with DNA via counterion release, forming small particles approximately 200nm in diameter. X-ray diffraction reveals CL-DNA structures that are typically a multilamellar organization of lipids with DNA intercalated between the layers. We explore the structural properties of CL-DNA complexes formed with new multivalent lipids (Ewert et al, J. Med. Chem. 2002; 45:5023) that range from 2+ to 16+. Contrary to a simple prediction for the DNA interaxial spacing d_DNA based on a geometrical space-filling model, these lipids show dramatic DNA compaction, down to d_DNA � 25 �Variations in the membrane charge density, ? _M, lead to distinct spacing regimes. We propose that this DNA condensation is controlled by a unique locking mechanism between the DNA double helix and the large, multivalent lipid head groups. Funded by NSF DMR-0203755 and NIH GM-59288.
Evans, Heather M.; Ahmad, A.; Ewert, K.; Safinya, C. R.
The exposure of an organism to genotoxic chemicals may induce a cascade of genetic events. nitially, structural alterations to DNA are formed. ext, the DNA damage is processed and subsequently expressed in mutant gene products. inally, diseases result from the genetic damage. he ...
NSDL National Science Digital Library
This site is an excellent resource on the structure and function of DNA as well as its role in genes and chromosomes. It also covers DNA replication, RNA structure and function, RNA synthesis, the genetic code, and protein synthesis. The site includes a tutorial that tests comprehension of the covered subjects.
In just a few years, injection of plasmid DNA to elicit immune responses in vivo has developed from an interesting observation to a viable vaccine strategy. DNA vaccines have been shown to elicit both cellular and humoral immune responses and to be effective in a variety of preclinical bacterial, viral, and parasitic animal models. This review will discuss the current
Donna L. Montgomery; Jeffrey B. Ulmer; John J. Donnelly; Margaret A. Liu
Broadcast Transcript: It's a symbol of commitment. It's a memento mori. It's the DNA pendant offered by Japan's Eiwa Industry and it's two, two, two things in one. Using genetic extraction, Eiwa removes the DNA from, say, a strand of hair or a...
Hacker, Randi; Tsutsui, William
Comparative functional genomics of mammalian DNA methyltransferases
DNA methylation involves biochemical modification of DNA by addition of methyl groups onto CpG dinucleotides, and this epigenetic mechanism regulates gene expression in disease and development. Mammalian DNA methyltransferases, DNMT (DNMT1, DNMT3A and DNMT3B), together with the accessory protein DNMT3L establish specific DNA methylation patterns in the genome during gametogenesis, embryogenesis and somatic tissue development. The present study addresses the
Nelida Rodriguez-Osorio; Hongfeng Wang; Jennifer Rupinski; Susan M. Bridges; Erdogan Memili
(gene expression) DNA (DNA microarrays).
µ µ DNA . , µ . , µ . , . µ µµ µ µ (gene expression) . µ, µ µ DNA µ 100%. I. µ , µ [1]. µ µµ µ µ (gene expression. [2] M. K. Deyholos, and D. W. Galbraith, "High- Density Microarrays for Gene Expression Analysis
Athens, University of
DNA behind bars: other ways of knowing forensic DNA technologies.
This paper explores 'other' ways of knowing DNA in the field of criminal investigation. Drawing upon 26 in-depth interviews with prisoners in Austria, it illustrates how this group knows and conceptualizes DNA traces and forensic DNA technologies. These understandings and conceptualizations are both nuanced and ambiguous. While on the one hand, DNA traces and forensic DNA technologies were not treated as categorically different from other types of traces and technologies in the prisoners' accounts, they were seen as 'unique' in one respect: respondents experienced DNA traces as beyond their control because they were virtually impossible to avoid (in contrast to, for example, fingerprints). Furthermore, the scientific rigour that our interviewees assumed to underpin forensic DNA technologies rendered these technologies as impenetrable and intimidating, and as effectively challenging many offenders' expert knowledge on how to manage crime scenes and avoid convictions. Finally, due to coming 'from the inside' of the body, forensic DNA technologies were seen as 'deepening' the stigma of delinquency in many of our interviewees' bodies and selves. For our interviewees, forensic DNA technologies assumed the role of institutionalized memories of their delinquency. PMID:19569425
Prainsack, Barbara; Kitzberger, Martin
NSDL National Science Digital Library
In this activity (on pages 34-39), learners make a fairly detailed model of DNA using licorice and gumdrops. The sugar and phosphate backbone of DNA is represented by alternating red and black licorice, and the base pairs are represented by gumdrops arranged so that gumdrop colors are paired. After a pair of learners have made a DNA section, they find another team and link them up to make a model of a gene. They then split the model and "copy" it using the base pair rules from earlier, comparing their copy to the original to see if there are any differences (mutations).
University of Nebraska State Museum
, and Etsuji Tomita : A method for extracting globally structure free set of sequences, Technical Report� 1 Adleman DNA " " PCR PCR DNA DNA RNA " " " " 1 #12;PCR DNA 2 1. ([10]) DNA DNA DNA RNA RNA GFP RNA RNA RNA RNA GFP 2. DNA S S+ ([14], [15]) S+ ([17]) n (m ) S+ O(m6 n6 ) 2 #12;3. Abstract Rewriting
Hagiya, Masami
Identifying spiders through DNA barcodes
With almost 40 000 species, the spiders provide important model systems for studies of sociality, mating systems, and sexual dimorphism. However, work on this group is regularly constrained by difficulties in species identi- fication. DNA-based identification systems represent a promising approach to resolve this taxonomic impediment, but their efficacy has only been tested in a few groups. In this study,
Rowan D. H. Barrett; Paul D. N. Hebert
ERIC Educational Resources Information Center
An imaging technique that uses fluorescent dyes and allows scientists to track DNA as it moves through gels or in solution is described. The importance, opportunities, and implications of this technique are discussed. (KR)
Pennisi, Elizabeth
ERIC Educational Resources Information Center
Explains a method to enable students to understand DNA and protein synthesis using model-building and role-playing. Acquaints students with the triplet code and transcription. Includes copies of the charts used in this technique. (DDR)
Warren, Michael D.
NSDL National Science Digital Library
Teachers' Domain presents this interactive, adapted from the Dolan DNA Learning Center, with reading material and animations to help students learn the basics of DNA sequencing. The lesson is divided two parts: Sanger Sequencing and Cycle Sequencing. The processes for both techniques are covered and animations help students visualize the material presented. On the site, visitors will also find a supplemental background essay, discussion questions, and standards alignment from Teachers' Domain.
NASA Astrophysics Data System (ADS)
The forces involved in the biology of life are carefully balanced between stopping thermal fluctuations ripping our DNA apart and having bonds weak enough to allow enzymes to function. The application of recently developed techniques for measuring piconewton forces and imaging at the nanometre scale on a molecule-by-molecule basis has dramatically increased the impact of single-molecule biophysics. This article describes the most commonly used techniques for imaging and manipulating single biomolecules. Using these techniques, the mechanical properties of DNA can be investigated, for example through measurements of the forces required to stretch and unzip the DNA double helix. These properties determine the ease with which DNA can be folded into the cell nucleus and the size and complexity of the accompanying cellular machinery. Part of this cellular machinery is enzymes, which manipulate, repair and transcribe the DNA helix. Enzymatic function is increasingly being investigated at the single molecule level to give better understanding of the forces and processes involved in the genetic cycle. One of the challenges is to transfer this understanding of single molecules into living systems. Already there have been some notable successes, such as the development of techniques for gene expression through the application of mechanical forces to cells, and the imaging and control of viral infection of a cell. This understanding and control of DNA has also been used to design molecules, which can self-assemble into a range of structures.
Conroy, Rs; Danilowicz, C.
Systems toxicology is a broad-based approach to describe many of the toxicological features that occur within a living system under stress or subjected to exogenous or endogenous exposures. The ultimate goal is to capture an overview of all exposures and the ensuing biological responses of the body. The term exposome has been employed to refer to the totality of all exposures, and systems toxicology investigates how the exposome influences health effects and consequences of exposures over a lifetime. The tools to advance systems toxicology include high-throughput transcriptomics, proteomics, metabolomics, and adductomics, which is still in its infancy. A well-established methodology for the comprehensive measurement of DNA damage resulting from every day exposures is not fully developed. During the past several decades, the 32P-postlabeling technique has been employed to screen the damage to DNA induced by multiple classes of genotoxicants; however, more robust, specific, and quantitative methods have been sought to identify and quantify DNA adducts. Although triple quadrupole and ion trap mass spectrometry, particularly when using multistage scanning (LC�MSn), have shown promise in the field of DNA adductomics, it is anticipated that high-resolution and accurate-mass LC�MSn instrumentation will play a major role in assessing global DNA damage. Targeted adductomics should also benefit greatly from improved triple quadrupole technology. Once the analytical MS methods are fully mature, DNA adductomics along with other -omics tools will contribute greatly to the field of systems toxicology. PMID:24437709
Systems toxicology is a broad-based approach to describe many of the toxicological features that occur within a living system under stress or subjected to exogenous or endogenous exposures. The ultimate goal is to capture an overview of all exposures and the ensuing biological responses of the body. The term exposome has been employed to refer to the totality of all exposures, and systems toxicology investigates how the exposome influences health effects and consequences of exposures over a lifetime. The tools to advance systems toxicology include high-throughput transcriptomics, proteomics, metabolomics, and adductomics, which is still in its infancy. A well-established methodology for the comprehensive measurement of DNA damage resulting from every day exposures is not fully developed. During the past several decades, the (32)P-postlabeling technique has been employed to screen the damage to DNA induced by multiple classes of genotoxicants; however, more robust, specific, and quantitative methods have been sought to identify and quantify DNA adducts. Although triple quadrupole and ion trap mass spectrometry, particularly when using multistage scanning (LC-MS(n)), have shown promise in the field of DNA adductomics, it is anticipated that high-resolution and accurate-mass LC-MS(n) instrumentation will play a major role in assessing global DNA damage. Targeted adductomics should also benefit greatly from improved triple quadrupole technology. Once the analytical MS methods are fully mature, DNA adductomics along with other -omics tools will contribute greatly to the field of systems toxicology. PMID:24437709
Balbo, Silvia; Turesky, Robert J; Villalta, Peter W
Combustion Group Group members
2014 #12;Combustion Group Combustion Physics and Modeling Pollutants, Emissions, and Soot Formation · Coupling between reaction chemistry and soot-precursor · LES-modeling of large- scale industrial DeNOx facilities · Reduced-order modeling for process- control Research focus · Analysis of intrinsic combustion
Wang, Wei
DNA Computing Complexity Analysis Using DNA/DNA Hybridization Kinetics
DNA Computing Complexity Analysis Using DNA/DNA Hybridization Kinetics Soo�Yong Shin 1 , Eun Jeong the complexity of DNA computing. The complexity of any computational algorithm is typically measured in terms of time and space. In DNA computing, the time complexity can be measured by the total reaction time
DNA Computing Complexity Analysis Using DNA/DNA Hybridization Kinetics
DNA Computing Complexity Analysis Using DNA/DNA Hybridization Kinetics Soo-Yong Shin1 , Eun Jeong of DNA computing. The complexity of any computational algorithm is typically measured in terms of time and space. In DNA computing, the time complexity can be measured by the total reaction time
Biophysical characterization of DNA binding from single molecule force measurements
Single molecule force spectroscopy is a powerful method that uses the mechanical properties of DNA to explore DNA interactions. Here we describe how DNA stretching experiments quantitatively characterize the DNA binding of small molecules and proteins. Small molecules exhibit diverse DNA binding modes, including binding into the major and minor grooves and intercalation between base pairs of double-stranded DNA (dsDNA). Histones bind and package dsDNA, while other nuclear proteins such as high mobility group proteins bind to the backbone and bend dsDNA. Single-stranded DNA (ssDNA) binding proteins slide along dsDNA to locate and stabilize ssDNA during replication. Other proteins exhibit binding to both dsDNA and ssDNA. Nucleic acid chaperone proteins can switch rapidly between dsDNA and ssDNA binding modes, while DNA polymerases bind both forms of DNA with high affinity at distinct binding sites at the replication fork. Single molecule force measurements quantitatively characterize these DNA binding mechanisms, elucidating small molecule interactions and protein function. PMID:20576476
Chaurasiya, Kathy R.; Paramanathan, Thayaparan; McCauley, Micah J.; Williams, Mark C.
Biophysical characterization of DNA binding from single molecule force measurements
NASA Astrophysics Data System (ADS)
Single molecule force spectroscopy is a powerful method that uses the mechanical properties of DNA to explore DNA interactions. Here we describe how DNA stretching experiments quantitatively characterize the DNA binding of small molecules and proteins. Small molecules exhibit diverse DNA binding modes, including binding into the major and minor grooves and intercalation between base pairs of double-stranded DNA (dsDNA). Histones bind and package dsDNA, while other nuclear proteins such as high mobility group proteins bind to the backbone and bend dsDNA. Single-stranded DNA (ssDNA) binding proteins slide along dsDNA to locate and stabilize ssDNA during replication. Other proteins exhibit binding to both dsDNA and ssDNA. Nucleic acid chaperone proteins can switch rapidly between dsDNA and ssDNA binding modes, while DNA polymerases bind both forms of DNA with high affinity at distinct binding sites at the replication fork. Single molecule force measurements quantitatively characterize these DNA binding mechanisms, elucidating small molecule interactions and protein function.
Chaurasiya, Kathy R.; Paramanathan, Thayaparan; McCauley, Micah J.; Williams, Mark C.
Neurodegeneration-associated instability of ribosomal DNA.
Homologous recombination (HR)-mediated instability of the repetitively organized ribosomal DNA (rDNA) has been proposed as a mediator of cell senescence in yeast triggering the DNA damage response. High individual variability in the content of human rDNA suggests that this genomic region remained relatively unstable throughout evolution. Therefore, quantitative real-time polymerase chain reaction was used to determine the genomic content of rDNA in post mortem samples of parietal cortex from 14 young and 9 elderly individuals with no diagnosis of a chronic neurodegenerative/neurological disease. In addition, rDNA content in that brain region was compared between 10 age-matched control individuals and 10 patients with dementia with Lewy bodies (DLB) which involves neurodegeneration of the cerebral cortex. Probing rRNA-coding regions of rDNA revealed no effects of aging on the rDNA content. Elevated rDNA content was observed in DLB. Conversely, in the DLB pathology-free cerebellum, lower genomic content of rDNA was present in the DLB group. In the parietal cortex, such a DLB-associated instability of rDNA was not accompanied by any major changes of cytosine-phosphate-guanine methylation of the rDNA promoter. As increased cerebro-cortical rDNA content was previously reported in Alzheimer's disease, neurodegeneration appears to be associated with instability of rDNA. The hypothetical origins and consequences of this phenomenon are discussed including possibilities that the DNA damage-induced recombination destabilizes rDNA and that differential content of rDNA affects heterochromatin formation, gene expression and/or DNA damage response. This article is part of a Special Issue entitled: Role of the Nucleolus in Human Disease. PMID:24389328
Hallgren, Justin; Pietrzak, Maciej; Rempala, Grzegorz; Nelson, Peter T; Hetman, Michal
DNA phosphorothioate modifications influence the global transcriptional response and protect DNA from double-stranded breaks
The modification of DNA by phosphorothioate (PT) occurs when the non-bridging oxygen in the sugar-phosphate backbone of DNA is replaced with sulfur. This DNA backbone modification was recently discovered and is governed by the dndABCDE genes in a diverse group of bacteria and archaea. However, the biological function of DNA PT modifications is poorly understood. In this study, we employed the RNA-seq analysis to characterize the global transcriptional changes in response to PT modifications. Our results show that DNA without PT protection is susceptible to DNA damage caused by the dndFGHI gene products. The DNA double-stranded breaks then trigger the SOS response, cell filamentation and prophage induction. Heterologous expression of dndBCDE conferring DNA PT modifications at GPSA and GPST prevented the damage in Salmonella enterica. Our data provide insights into the physiological role of the DNA PT system. PMID:25319634
Gan, Rui; Wu, Xiaolin; He, Wei; Liu, Zhenhua; Wu, Shuangju; Chen, Chao; Chen, Si; Xiang, Qianrong; Deng, Zixin; Liang, Dequan; Chen, Shi; Wang, Lianrong
NASA Astrophysics Data System (ADS)
Immunization by genes encoding immunogens, rather than with the immunogen itself, has opened up new possibilities for vaccine research and development and offers chances for new applications and indications for future vaccines. The underlying mechanisms of antigen processing, immune presentation and regulation of immune responses raise high expectations for new and more effective prophylactic or therapeutic vaccines, particularly for vaccines against chronic or persistent infectious diseases and tumors. Our current knowledge and experience of DNA vaccination is summarized and critically reviewed with particular attention to basic immunological mechanisms, the construction of plasmids, screening for protective immunogens to be encoded by these plasmids, modes of application, pharmacokinetics, safety and immunotoxicological aspects. DNA vaccines have the potential to accelerate the research phase of new vaccines and to improve the chances of success, since finding new immunogens with the desired properties is at least technically less demanding than for conventional vaccines. However, on the way to innovative vaccine products, several hurdles have to be overcome. The efficacy of DNA vaccines in humans appears to be much less than indicated by early studies in mice. Open questions remain concerning the persistence and distribution of inoculated plasmid DNA in vivo, its potential to express antigens inappropriately, or the potentially deleterious ability to insert genes into the host cell's genome. Furthermore, the possibility of inducing immunotolerance or autoimmune diseases also needs to be investigated more thoroughly, in order to arrive at a well-founded consensus, which justifies the widespread application of DNA vaccines in a healthy population.
Gregersen, Jens-Peter
In the past two decades, ancient DNA research has progressed from the retrieval of small fragments of mitochondrial DNA from a few late Holocene specimens, to large-scale studies of ancient populations, phenotypically important nuclear loci, and even whole mitochondrial genome sequences of extinct species. However, the field is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. An improved understanding of these processes and the effects of damage on ancient DNA templates has started to provide a more robust basis for research. Recent methodological advances have included the characterization of Pleistocene mammal populations and discoveries of DNA preserved in ancient sediments. Increasingly, ancient genetic information is providing a unique means to test assumptions used in evolutionary and population genetics studies to reconstruct the past. Initial results have revealed surprisingly complex population histories, and indicate that modern phylogeographic studies may give misleading impressions about even the recent evolutionary past. With the advent and uptake of appropriate methodologies, ancient DNA is now positioned to become a powerful tool in biological research and is also evolving new and unexpected uses, such as in the search for extinct or extant life in the deep biosphere and on other planets. PMID:15875564
Willerslev, Eske; Cooper, Alan
Phase II trial of DNA methyltransferase 1 inhibition with the antisense oligonucleotide MG98 in patients with metastatic renal carcinoma: A National Cancer Institute of Canada Clinical Trials Group investigational new drug study
Summary��DNA methyltransferases (DNMTs) methylate DNA, promoting local chromatin condensation and consequent repression of gene expression.\\u000a The purpose of this two-stage phase II trial was to assess the antitumor activity of MG98, a second generation antisense oligodeoxynucleotide\\u000a inhibitor of human DNMT 1, in patients with metastatic renal carcinoma (MRC). Untreated adult patients with measurable MRC\\u000a were treated with MG98 at a
Eric Winquist; Jennifer Knox; Jean-Pierre Ayoub; Lori Wood; Nancy Wainman; Gregory K. Reid; Laura Pearce; Ajit Shah; Elizabeth Eisenhauer
Original article Ribosomal DNA and chloroplast DNA
extraction and analysis The method of total DNA extraction and analysis of cpDNA variation has been described on branches collected in winter and forced in the greenhouse later in the spring. DNA was also extracted fromOriginal article Ribosomal DNA and chloroplast DNA polymorphisms in a mixed stand of Quercus robur
Boyer, Edmond
Synthesizing human insulin using recombinant DNA, 3D animation with no audioSite: DNA Interactive (www.dnai.org)
NSDL National Science Digital Library
DNAi Location: Manipulation>Production>pieces of the puzzle>Synthesizing the DNA In order to synthesize human insulin using recombinant DNA technology, the human DNA sequence for insulin was needed. The amino acid sequence of human insulin was known. The Genentech group deduced the human DNA sequence of insulin based on its amino acid sequence. They then used the DNA nucleotides and synthesized the human DNA sequence. This sequence was then inserted into a plasmid and transformed into bacteria to produce insulin. By synthesizing the DNA sequence, the Genentech group assembled a human DNA sequence of insulin without ever having to use \\"real\\" human DNA. They thus bypassed some of the restrictions on human recombinant DNA work resulting from the Asilomar conference.
##### SAT Engine ####### _ ############ DNA ###### _
##### SAT Engine ####### _ ############ DNA ###### _ # # # #y # # #yy # # # #yy ###### DNA #################################### ############### ##################### 6 ## 10 ##### ### DNA ############### (Sakamoto et al., Science, Vol.288, pp.1223-122* *6
Hagiya, Masami
NSDL National Science Digital Library
The view of some scientists that modern humans did not descend from the Neandertals gained support when scientists from Munich, Germany analyzed DNA from a Neandertal. A news article from Archeology Online News discusses the recent research and provides links to additional news clips. This site covers one of the top ten scientific breakthroughs of 1997, compiled in the December 19, 1997 issue of Science. The top scientific breakthrough of 1997 was the cloning of a sheep, resulting in a lamb named Dolly. The nine runners up were: the Pathfinder mission to Mars, synchrotrons, biological clock genes, gamma ray bursts, Neandertal DNA, nanotubes, Europa's ocean, whole genome sequencing, and neurons.
NSDL National Science Digital Library
Fifty years ago, one of the most important landmarks in the history of science was reached when James Watson and Francis Crick discovered the double-helical structure of DNA. Developed by the Dolan DNA Learning Center at the legendary Cold Spring Harbor Laboratory, this Web site provides a host of interactive exhibits and background material about DNA, the human genome project, and the various applications that are gleaned through an intimate and detailed knowledge of human DNA specifically. From the home page, visitors can traverse an interactive timeline, complete with biographical profiles of different scientists and information about preliminary experiments that helped provide some of the fundamental groundwork leading up to the work of Watson and Crick, and which continues to the present. One other section that should not be missed is the Genome area, where visitors can explore the features of the genetic landscape, learn more about the methods used to map and sequence the entire human genome, and learn how genomes are utilized. Finally, there is a section for teachers which includes helpful learning guides and lesson builders.
ERIC Educational Resources Information Center
Describes an activity in which students reverse-translate proteins from their amino acid sequences back to their DNA sequences then assign musical notes to represent the adenine, guanine, cytosine, and thymine bases. Data is obtained from the National Institutes of Health (NIH) on the Internet. (DDR)
Miner, Carol; della Villa, Paula
ERIC Educational Resources Information Center
Presents a simulation activity that allow students to work through the exercise of DNA profiling and to grapple with some analytical and ethical questions involving a couple arranging with a surrogate mother to have a baby. Can be used to teach the principles of restriction enzyme digestion, gel electrophoresis, and probe hybridization. (MDH)
Mayo, Ellen S.; Bertino, Anthony J.
The DNA of E. coli contains 19,120 6-methyladenines and 12,045 5-methylcytosines in addition to the four regular bases and these are formed by the postreplicative action of three DNA methyltransferases. The majority of the methylated bases are formed by the Dam and Dcm methyltransferases encoded by the dam (DNA adenine methyltransferase) and dcm (DNA cytosine methyltransferase) genes. Although not essential, Dam methylation is important for strand discrimination during repair of replication errors, controlling the frequency of initiation of chromosome replication at oriC, and regulation of transcription initiation at promoters containing GATC sequences. In contrast, there is no known function for Dcm methylation although Dcm recognition sites constitute sequence motifs for Very Short Patch repair of T/G base mismatches. In certain bacteria (e.g., Vibrio cholerae, Caulobacter crescentus) adenine methylation is essential and in C. crescentus, it is important for temporal gene expression which, in turn, is required for coordinating chromosome initiation, replication and division. In practical terms, Dam and Dcm methylation can inhibit restriction enzyme cleavage; decrease transformation frequency in certain bacteria; decrease the stability of short direct repeats; are necessary for site-directed mutagenesis; and to probe eukaryotic structure and function. PMID:25405210
Marinus, M.G.; L�bner-Olesen, A.
Preclinical DNA vaccine development has continued apace during the past year, with the investigation of several new infectious and non-infectious disease targets as well as advances in our understanding of some of the basic immunologic mechanisms, such as effector cells, responsible for conferring protection. The coming year promises to be at least as exciting, as initial human clinical studies have
Jeffrey B Ulmer; Jerald C Sadoff; Margaret A Liu
NSDL National Science Digital Library
In this activity, learners create an origami model of DNA, demonstrating its double helix structure. Two templates are available as PDFs: a standard template with the base pairs already colored or a blank template where the learners have to color the four bases A, C, T and G and mark them in the correct location on the template.
Alex Bateman
Self-assembled DNA Structures for Nanoconstruction
NASA Astrophysics Data System (ADS)
In recent years, a number of research groups have begun developing nanofabrication methods based on DNA self-assembly. Here we review our recent experimental progress to utilize novel DNA nanostructures for self-assembly as well as for templates in the fabrication of functional nano-patterned materials. We have prototyped a new DNA nanostructure known as a cross structure. This nanostructure has a 4-fold symmetry which promotes its self-assembly into tetragonal 2D lattices. We have utilized the tetragonal 2D lattices as templates for highly conductive metallic nanowires and periodic 2D protein nano-arrays. We have constructed and characterized a DNA nanotube, a new self-assembling superstructure composed of DNA tiles. We have also demonstrated an aperiodic DNA lattice composed of DNA tiles assembled around a long scaffold strand; the system translates information encoded in the scaffold strand into a specific and reprogrammable barcode pattern. We have achieved metallic nanoparticle linear arrays templated on self-assembled 1D DNA arrays. We have designed and demonstrated a 2-state DNA lattice, which displays expand/contract motion switched by DNA nanoactuators. We have also achieved an autonomous DNA motor executing unidirectional motion along a linear DNA track.
Yan, Hao; Yin, Peng; Park, Sung Ha; Li, Hanying; Feng, Liping; Guan, Xiaoju; Liu, Dage; Reif, John H.; LaBean, Thomas H.
NSDL National Science Digital Library
A group theory calculator. Groups32 computes information about groups of orders 1-32; has a permutation group package; and provides a search for groups with given generators and relations. Site includes documentation as well as course handouts in PDF format.
Adleman[1] 1994 DNA Hamiltonian Path Problem , DNA
1. Adleman[1] 1994 DNA Hamiltonian Path Problem , DNA DNA [2]. DNA DNA , . , , 2 , DNA 4 . DNA 4 A(Adenine), C(Cytosine), G(Guanine), T(Thymine) 2 4 . , . 1 mole 6x10 23 DNA DNA . , . DNA NP-complete [1, 2], [2
DNA Topology: Fundamentals Sergei M Mirkin, University of Illinois at Chicago, Illinois, USA Topological characteristics of DNA and specifically DNA supercoiling influence all major DNA transactions in living cells. DNA supercoiling induces the formation of unusual secondary structure by specific DNA
Mirkin, Sergei
NSDL National Science Digital Library
The featured molecules this month come from the paper by David T. Crouse on the X-ray determination of the structure of DNA. Given that most students are aware of the double helix, it seems appropriate to back up a little and examine the components that give rise to this structure. Accordingly, the molecule collection includes: Purine and pyrimidine, structural precursors of the four bases found in DNA: cytosine (C), thymine (T), adenine (A), and guanine (G) The four corresponding deoxyribonucleosides The four deoxyribonucleotides (the nucleoside monophosphates) A two-base-pair fragment showing the AT and GC hydrogen-bonded complements Several small 24-base-pair DNA fragments polyAT, polyGC, and a random array of bases. The DNA fragments provide a good opportunity to have students explore features of the Jmol and Chime menus. Using the Jmol menu as an example (right-click on the structure to bring up the menu) students can use the measuring tools to get an idea of the length of a complete turn in the DNA, the relative widths of the major and minor grooves, and the diameter of the helix. They can use the coloring schemes to detect the various base pair combinations, and learn to read the code for the random sequence. In Chime they can use the Shapely coloring scheme for this same purpose. Exploring other aspects of the menu will allow students to present the molecules in the various forms, including ribbon and cartoon views. In RNA, thymine is replaced by uracil, and the sugar moiety has an axial hydroxyl group on the carbon atom adjacent to the base binding site (the 2? carbon). The structures of uracil and of uridine monophosphate are included in the molecule collection. Students can use the Web to download and examine more complex DNAs using a site such as the Nucleic Acid Database at Rutgers University.
DNA sequencing using fluorescence background electroblotting membrane
A method for the multiplex sequencing on DNA is disclosed which comprises the electroblotting or specific base terminated DNA fragments, which have been resolved by gel electrophoresis, onto the surface of a neutral non-aromatic polymeric microporous membrane exhibiting low background fluorescence which has been surface modified to contain amino groups. Polypropylene membranes are preferably and the introduction of amino groups is accomplished by subjecting the membrane to radio or microwave frequency plasma discharge in the presence of an aminating agent, preferably ammonia. The membrane, containing physically adsorbed DNA fragments on its surface after the electroblotting, is then treated with crosslinking means such as UV radiation or a glutaraldehyde spray to chemically bind the DNA fragments to the membrane through amino groups contained on the surface. The DNA fragments chemically bound to the membrane are subjected to hybridization probing with a tagged probe specific to the sequence of the DNA fragments. The tagging may be by either fluorophores or radioisotopes. The tagged probes hybridized to the target DNA fragments are detected and read by laser induced fluorescence detection or autoradiograms. The use of aminated low fluorescent background membranes allows the use of fluorescent detection and reading even when the available amount of DNA to be sequenced is small. The DNA bound to the membranes may be reprobed numerous times. No Drawings
Caldwell, K.D.; Chu, T.J.; Pitt, W.G.
DNA sequencing using fluorescence background electroblotting membrane
A method for the multiplex sequencing on DNA is disclosed which comprises the electroblotting or specific base terminated DNA fragments, which have been resolved by gel electrophoresis, onto the surface of a neutral non-aromatic polymeric microporous membrane exhibiting low background fluorescence which has been surface modified to contain amino groups. Polypropylene membranes are preferably and the introduction of amino groups is accomplished by subjecting the membrane to radio or microwave frequency plasma discharge in the presence of an aminating agent, preferably ammonia. The membrane, containing physically adsorbed DNA fragments on its surface after the electroblotting, is then treated with crosslinking means such as UV radiation or a glutaraldehyde spray to chemically bind the DNA fragments to the membrane through said smino groups contained on the surface thereof. The DNA fragments chemically bound to the membrane are subjected to hybridization probing with a tagged probe specific to the sequence of the DNA fragments. The tagging may be by either fluorophores or radioisotopes. The tagged probes hybridized to said target DNA fragments are detected and read by laser induced fluorescence detection or autoradiograms. The use of aminated low fluorescent background membranes allows the use of fluorescent detection and reading even when the available amount of DNA to be sequenced is small. The DNA bound to the membrances may be reprobed numerous times.
Caldwell, Karin D. (Salt Lake City, UT); Chu, Tun-Jen (Salt Lake City, UT); Pitt, William G. (Orem, UT)
Microcoding: the second step in DNA barcoding
After the process of DNA barcoding has become well advanced in a group of organisms, as it has in the economically important fungi, the question then arises as to whether shorter and literally more barcode-like DNA segments should be utilized to facilitate rapid identification and, where applicable, detection. Through appropriate software analysis of typical full-length barcodes (generally over 500 base
R. C. Summerbell; C. A. L�vesque; K. A. Seifert; M. Bovers; J. W. Fell; M. R. Diaz; T. Boekhout; G. S. de Hoog; J. A. Stalpers; P. W. Crous
Nanomechanical molecular devices made of DNA origami.
CONSPECTUS: Eight years have passed since the striking debut of the DNA origami technique ( Rothemund, P. W. K. Nature 2006 , 440 , 297 - 302 ), in which long single-stranded DNA is folded into a designed nanostructure, in either 2D or 3D, with the aid of many short staple strands. The number of proposals for new design principles for DNA origami structures seems to have already reached a peak. It is apparent that DNA origami study is now entering the second phase of creating practical applications. The development of functional nanomechanical molecular devices using the DNA origami technique is one such application attracting significant interest from researchers in the field. Nanomechanical DNA origami devices, which maintain the characteristics of DNA origami structures, have various advantages over conventional DNA nanomachines. Comparatively high assembly yield, relatively large size visible via atomic force microscopy (AFM) or transmission electron microscopy (TEM), and the capability to assemble multiple functional groups with precision using multiple staple strands are some of the advantages of the DNA origami technique for constructing sophisticated molecular devices. This Account describes the recent developments of such nanomechanical DNA origami devices and reviews the emerging target of DNA origami studies. First, simple "dynamic" DNA origami structures with transformation capability, such as DNA origami boxes and a DNA origami hatch with structure control, are briefly summarized. More elaborate nanomechanical DNA origami devices are then reviewed. The first example describes DNA origami pinching devices that can be used as "single-molecule" beacons to detect a variety of biorelated molecules, from metal ions at the size of a few tens of atomic mass number units to relatively gigantic proteins with a molecular mass greater than a hundred kilodaltons, all on a single platform. Clamshell-like DNA nanorobots equipped with logic gates can discriminate different cell lines, open their shell, and bind to their target. An intelligent DNA origami "sheath" can mimic the function of suppressors in a transcription regulation system to control the expression of a loaded gene. DNA origami "rolls" are created to construct precisely arranged plasmonic devices with metal nanoparticles. All of their functions are derived from their nanomechanical movement, which is programmable by designing the DNA sequence or by using the significant repository of technical achievements in nucleic acid chemistry. Finally, some studies on detailed structural parameters of DNA origami or their mechanical properties in nanoscale are discussed, which may be useful and inspiring for readers who intend to design new nanomechanical DNA origami devices. PMID:24772996
Kuzuya, Akinori; Ohya, Yuichi
Prognostic Significance of DNA and Histone Methylation
Nutritional Science Research Group Recently Funded Projects Prognostic Significance of DNA and Histone Methylation Principal Investigator: Piyathilake, Chandrika J Institution: University of Alabama at Birmingham NCI/DCP Program Director: Ross, Sharon
Welcome to the Five Food Groups MyPlate illustrates the five food groups that are the building blocks for a healthy diet using a familiar image � ... half your grains whole. >> See Grains Group Protein Foods Go lean with protein. >> See Protein Foods Group ...
DNA encoding based feature extraction for biometric watermarking
The aim of this paper is to secure the digital code of a watermark (which is an offline handwritten signature) by using the characteristics of DNA. The watermarked image is embedded into the image as binary information and further encrypted as DNA sequences and these DNA sequences (after being grouped as tri - nucleotide sequences called codons) then attached to
Meenakshi S Arya; Nikita Jain; Jai Sisodia; Nukul Sehgal
This project is currently under contract for research through the Department of Homeland Security until 2011. The group I was responsible for studying has to remain confidential so as not to affect the current project. All dates, reference links and authors, and other distinguishing characteristics of the original group have been removed from this report. All references to the name of this group or the individual splinter groups has been changed to 'Group X'. I have been collecting texts from a variety of sources intended for the use of recruiting and radicalizing members for Group X splinter groups for the purpose of researching the motivation and intent of leaders of those groups and their influence over the likelihood of group radicalization. This work included visiting many Group X websites to find information on splinter group leaders and finding their statements to new and old members. This proved difficult because the splinter groups of Group X are united in beliefs, but differ in public opinion. They are eager to tear each other down, prove their superiority, and yet remain anonymous. After a few weeks of intense searching, a list of eight recruiting texts and eight radicalizing texts from a variety of Group X leaders were compiled.
Fields, Susannah
NASA Astrophysics Data System (ADS)
A certificate of authenticity (COA) is an inexpensive physical object with a random and unique structure S which is hard to near-exactly replicate. An inexpensive device should be able to scan object�s physical �fingerprint,� a set of features that represents S. In this paper, we explore one set of requirements that optical media such as DVDs should satisfy, to be considered as COAs. As manufacturing of such media produces inevitable errors, we use the locations and count of these errors as a �fingerprint� for each optical disc: its optical DNA. The �fingerprint� is signed using publisher�s private-key and the resulting signature is stored onto the optical medium using a post-production process. Standard DVD players with altered firmware that includes publisher�s public-key, should be able to verify the authenticity of DVDs protected with optical DNA. Our key finding is that for the proposed protocol, only DVDs with exceptional wear-and-tear characteristics would result in an inexpensive and viable anti-counterfeiting technology.
Vijaywargi, Deepak; Lewis, Dave; Kirovski, Darko
Oxidative DNA modifications are frequent in mammalian DNA and have been suggested an important mechanism in carcinogenesis, diabetes and ageing. The foundations for this suggestion are:Evidence for the importance of oxidative DNA modifications in cancer development is: high levels of oxidative lesions in cancer tissue; highly conserved and specific DNA repair systems targeting oxidative lesions; high levels of oxidative DNA
Henrik E. Poulsen
[Mitochondrial disease and mitochondrial DNA depletion syndromes].
Mitochondria is an intracellular double membrane-bound structure and it can provide energy for intracellular metabolism. The metabolism includes Krebs cycle, beta-oxidation and lipid synthesis. The density of mitochondria is different in various tissues dependent upon the demands of oxidative phosphorylation. Mitochondrial diseases can occur by defects either in mitochondrial DNA or nuclear DNA. Human mitochondrial DNA (mtDNA) encoding for 22 tRNAs, 2 rRNAs and 13 mRNAs that are translated in the mitochondria. Mitochondrial genetic diseases are most resulted from defects in the mtDNA which may be point mutations, deletions, or mitochondrial DNA depletion. These patterns of inheritance in mitochondrial diseases include sporadic, maternally inherited, or of Mendelian inheritance. Mitochondrial DNA depletion is caused by defects in the nuclear genes that are responsible for maintenance of integrity of mtDNA or deoxyribonucelotide pools and mtDNA biogenesis. The mtDNA depletion syndrome (MDS) includes the following categories: progressive external ophthalmoplegia (PEO), predominant myopathy, mitochondrial neurogastrointestinal encephalomyopathy (MNGIE), sensory-ataxic neuropathy, dysarthria, and ophthalmoplegia (SANDO) and hepato-encephalopathy. The most common tissues or organs involved in MDS and related disorders include the brain, liver and muscles. These involved genes are divided into two groups including 1) DNA polymerase gamma (POLG, POLG2) and Twinkle genes whose products function directly at the mtDNA replication fork, and 2) adenine nucleotide translocator 1, thymidine phosphorylase, thymidine kinase 2, deoxyguanosine kinase, ADP-forming succinyl-CoA synthetase ligase, MPV17 whose products supply the mitochondria with deoxyribonucleotide triphosphate pools needed for mtDNA replication, and possible mutation in the RRM2B gene. The development has provided new information about the importance of the biosynthetic pathway of the nucleotides for mtDNA replication. Further investigation on the understatanding between the nuclear and mitochondrial genomes is expected. PMID:20329599
Huang, Chin-Chang; Hsu, Chang-Huang
Energy transport in crystalline DNA composites
This work reports on the synthesis of crystalline DNA-composited films and microfibers, and details the study of thermal energy transport in them. The transient electro-thermal technique is used to characterize the thermal transport in DNA composite microfibers, and the photothermal technique is used to explore the thermal transport in the thickness direction of DNA films. Compared with microfibers, the DNA films are found to have a higher thermal transport capacity, largely due to the carefully controlled crystallization process in film synthesis. In high NaCl concentration solutions, the bond of the Na{sup +} ion and phosphate group aligns the DNA molecules with the NaCl crystal structure during crystallization. This results in significant enhancement of thermal transport in the DNA films with aligned structure.
Xu, Zaoli; Xu, Shen; Tang, Xiaoduan; Wang, Xinwei, E-mail: email@example.com [Department of Mechanical Engineering, 2010 Black Engineering Building Iowa State University, Ames, IA 50011 (United States)] [Department of Mechanical Engineering, 2010 Black Engineering Building Iowa State University, Ames, IA 50011 (United States)
DNA adsorption characteristics of hollow spherical allophane nano-particles
NASA Astrophysics Data System (ADS)
To understand the propensity of the natural allophane to adsorb the DNA molecules, the adsorption characteristics were assessed against a natural allophane, using single-stranded DNA (ss-DNA) and adenosine 5'-monophosphate (5'-AMP) as a reference molecule. The adsorption capacity of ss-DNA on AK70 exhibited one order of magnitude lower value as compared with that of 5'-AMP. The adsorption capacity of ss-DNA decreased with increasing pH due to the interaction generated between phosphate groups of ss-DNA and functional Al-OH groups on the wall perforations through deprotonation, associated with higher energy barrier for the adsorption of ss-DNA. The adsorption morphologies consisting of the individual ss-DNA with mono-layer coverage of the allophane clustered particle was successfully observed through TEM analysis.
Matsuura, Yoko; Iyoda, Fumitoshi; Hayashi, Shuhei; Arakawa, Shuichi; Okamoto, Masami; Hayashi, Hidetomo
mtDNA / Y chromosome pedigree, animated imageSite: DNA Interactive (www.dnai.org)
NSDL National Science Digital Library
DNAi location:Applications>gene genealogy>Tracing ancestries>Using genetic tools together Studies following the male lineage (using the Y chromosome) have been compared to studies following the female lineage (using mitochondrial DNA (mtDNA)). The results suggest that men and women have had different roles in the peopling of the planet and in the mixing of genes among population groups. A pedigree illustrating maternal inheritance of mtDNA and paternal inheritance of the Y chromosome.
Active DNA demethylation of the vertebrate genomes by DNA methyltransferases: deaminase, dehydroxymethylase or demethylase?
Vertebrate DNA methyltransferases (DNMTs) have been thought to primarily function to covalently add a methyl group to the 5-position of cytosine. However, recent discovery of the DNA demethylation and dehydroxymethylation activities of DNMTs in vitro suggest new routes to complete the dynamic cycle of DNA methylation-demethylation of the vertebrate genomes. The in vitro reaction conditions suggest that vertebrate DNMTs can switch from DNA methylases to DNA dehydroxymethylases under oxidative stress and to DNA demethylases in the presence of calcium ion under nonreducing conditions. These environmental parameters provide clues regarding the choices in vivo of DNMT activities utilized in different physiological systems. In particular, the nature of these parameters suggest that the DNA demethylation and dehydroxymethylation activities of the vertebrate DNMTs play essential roles in multiple biological processes including early embryo development, regulation of neuronal plasticity, tumorigenesis and hormone-regulated transcription. PMID:25111488
Wang, Keh-Yang; Chen, Chun-Chang; Shen, Che-Kun James
Abstract. In this paper we present a new type of signature for a group of persons, called a group signature, which has the following propertjes: (i) only members,of the group can sign messages; (ii) the receiver can verify that it is a valid group signaa~e, but cannot discover which gr~up member made (i) if necessary, the signature can be \\
David Chaum; Eug�ne Van Heyst
The 1998�1999 collaborative exercises and proficiency testing program on DNA typing of the Spanish and Portuguese Working Group of the International Society for Forensic Genetics (GEP-ISFG)
A total of 28 laboratories (labs) submitted results for the 1998 collaborative exercise and the proficiency testing program of the Spanish and Portuguese Working Group of the International Society for Forensic Genetics (GEP-ISFG) group. This number increased to 46 labs in 1999. Six bloodstains were submitted, each one with 200?l soaked in cotton except the sample no. 6 submitted for
Josefina G�mez; Angel Carracedo
It has been previously shown that DNA computing can solve those problems currently intractable on even the fastest electronic computers. The algorithm design for DNA computing, however, is not straightforward. A strong background in both the DNA...
Qiu, Zhiquan Frank
of Mihailova normal form concerns only free groups, it can be useful for any group G, and we will use the following natural 11 definition: Definition II.12. Let G be a group with non-trivial generators{a1,...,an}, and H be a subgroup of the direct product G... to show that the defining relators in the group ?? are mapped to the trivial element of the group ???. In all three cases we have ??(a)2 = ((1,1)?)2 = (1,1), ??(x)2 = (1,?x2) = (1,1), ??(y)2 = (?a2,?y2) = (1,1), ??(z)2 = (?a2,?z2) = (1,1), ??(x...
Muntyan, Yevgen
Rad54 Protein Stimulates Heteroduplex DNA Formation in the Synaptic Phase of DNA Strand
, Davis CA 95616, USA RAD54 is an important member of the RAD52 group of genes that carry out protein carried out the functions required for methyl methanesulfonate sulfate (MMS), UV, and DSB repair recombination using the DNA sequence of the sister chromatid or homolog to restore the DNA to its original
Kowalczykowski, Stephen C.
NASA Astrophysics Data System (ADS)
Galaxy groups can be characterized by the radius of decoupling from cosmic expansion, the radius of the caustic of second turnaround, and the velocity dispersion of galaxies within this latter radius. These parameters can be a challenge to measure, especially for small groups with few members. In this study, results are gathered pertaining to particularly well-studied groups over four decades in group mass. Scaling relations anticipated from theory are demonstrated and coefficients of the relationships are specified. There is an update of the relationship between light and mass for groups, confirming that groups with mass of a few times {{10}12}{{M}? } are the most lit up while groups with more and less mass are darker. It is demonstrated that there is an interesting one-to-one correlation between the number of dwarf satellites in a group and the group mass. There is the suggestion that small variations in the slope of the luminosity function in groups are caused by the degree of depletion of intermediate luminosity systems rather than variations in the number per unit mass of dwarfs. Finally, returning to the characteristic radii of groups, the ratio of first to second turnaround depends on the dark matter and dark energy content of the universe and a crude estimate can be made from the current observations of {{?}matter}� 0.15 in a flat topology, with a 68% probability of being less than 0.44.
Tully, R. Brent
NSDL National Science Digital Library
Today you will learn about the parts of DNA and what DNA, genes and chromosomes are. Today you will learn what DNA, genes and chromosomes are and the parts of the DNA molecule. Look at all of the websites, take whatever notes you need to. At the end of the assignment, be able to describle DNA, the parts of DNA, genes and chromosomes. Covers Biology Core Curriculum, ...
Mrs. Fomby
A method of synthesizing a desired double-stranded DNA of a predetermined length and of a predetermined sequence. Preselected sequence segments that will complete the desired double-stranded DNA are determined. Preselected segment sequences of DNA that will be used to complete the desired double-stranded DNA are provided. The preselected segment sequences of DNA are assembled to produce the desired double-stranded DNA.
Mariella, Jr., Raymond P. (Danville, CA)
DNA modifications: Another stable base in DNA
NASA Astrophysics Data System (ADS)
Oxidation of 5-methylcytosine has been proposed to mediate active and passive DNA demethylation. Tracking the history of DNA modifications has now provided the first solid evidence that 5-hydroxymethylcytosine is a stable epigenetic modification.
Brazauskas, Pijus; Kriaucionis, Skirmantas
Ancient DNA from ice age insects: proceed with caution
NASA Astrophysics Data System (ADS)
The paucity of ancient DNA (aDNA) studies in insects can be traced to the dismissal of the 1990s reports of DNA isolation from amber-entombed insects. In retrospect, amber was an obvious place to start, but it has since been demonstrated that DNA preservation is not necessarily correlated with physical preservation. The discipline of aDNA is rapidly progressing as issues regarding contamination with modern sequences and detection of DNA damage are addressed. Two major concerns in ancient DNA studies are the co-purification of DNA polymerase inhibitors and the presence of DNA lesions. Preliminary data demonstrate DNA extraction is possible from beetle remains isolated from packrat middens. Although specimens from permafrost sediments and ancient rodent middens are potential sources of aDNA, collection and curation procedures require modification to minimize contamination and optimize DNA yield. Since aDNA isolation in insects requires the complete destruction of fossil material, another consideration is the taxonomic groups that are adequately represented to justify the sacrifice of geological specimens. Although most recommended aDNA authentication procedures are easily followed, some are impossible for insect samples due to their small size, making the establishment of authentication procedures of aDNA from small samples a final consideration.
Reiss, Rebecca A.
DNA encoding a DNA repair protein
An isolated and purified DNA molecule encoding a DNA repair protein, p95, is provided, as is isolated and purified p95. Also provided are methods of detecting p95 and DNA encoding p95. The invention further provides p95 knock-out mice.
Petrini, John H.; Morgan, William Francis; Maser, Richard Scott; Carney, James Patrick
We explore the combined effect of segregation in social networks, peer effects, and the relative size of a historically disadvantaged group on the incentives to invest in market-rewarded skills and the dynamics of inequality between social groups. We identify conditions under which group inequality will persist in the absence of differences in ability, credit constraints, or labor market discrimination. Under these conditions, group inequality may be amplified even if initial group differences are negligible. Increases in social integration may destabilize an unequal state and make group equality possible, but the distributional and human capital effects of this depend on the demographic composition of the population. When the size of the initially disadvantaged group is sufficiently small, integration can lower the long-run costs of human capital investment in both groups and result in an increase the aggregate skill share. In contrast, when the initially disadvantaged group is large, integration can induce a fall in the aggregate skill share as the costs of human capital investment rise in both groups. We consider applications to concrete cases and policy implications. PMID:25554727
Bowles, Samuel; Loury, Glenn C.; Sethi, Rajiv
DNA Binding Hydroxyl Radical Probes
The hydroxyl radical is the primary mediator of DNA damage by the indirect effect of ionizing radiation. It is a powerful oxidizing agent produced by the radiolysis of water and is responsible for a significant fraction of the DNA damage associated with ionizing radiation. There is therefore an interest in the development of sensitive assays for its detection. The hydroxylation of aromatic groups to produce fluorescent products has been used for this purpose. We have examined four different chromophores which produce fluorescent products when hydroxylated. Of these, the coumarin system suffers from the fewest disadvantages. We have therefore examined its behavior when linked to a cationic peptide ligand designed to bind strongly to DNA. PMID:22125376
Tang, Vicky J; Konigsfeld, Katie M; Aguilera, Joe A; Milligan, Jamie R
Aberrant DNA methylation patterns in diabetic nephropathy
Background The aim of this study was to evaluate whether global levels of DNA methylation status were associated with albuminuria and progression of diabetic nephropathy in a case-control study of 123 patients with type 2 diabetes- 53 patients with albuminuria and 70 patients without albuminuria. Methods The 5-methyl cytosine content was assessed by reverse phase high pressure liquid chromatography (RP-HPLC) of peripheral blood mononuclear cells to determine individual global DNA methylation status in two groups. Results Global DNA methylation levels were significantly higher in patients with albuminuria compared with those in normal range of albuminuria (p?=?0.01). There were significant differences in global levels of DNA methylation in relation to albuminuria (p?=?0.028) and an interesting pattern of increasing global levels of DNA methylation in terms of albuminuria severity. In patients with micro- and macro albuminuria, we found no significant correlations between global DNA methylation levels and duration of diabetes (p?>?0.05). In both sub groups, there were not significant differences between global DNA methylation levels with good and poor glycaemic control (p?>?0.05). In addition, in patients with albuminuria, no differences in DNA methylation levels were observed between patients with and without other risk factors including age, gender, hypertension, dyslipidaemia and obesity. Conclusions These data may be helpful in further studies to develop novel biomarkers and new strategies for clinical care of patients at risk of diabetic nephropathy. PMID:25028646
newDNA-Prot: Prediction of DNA-binding proteins by employing support vector machine and a comprehensive sequence representation.
Identification of DNA-binding proteins is essential in studying cellular activities as the DNA-binding proteins play a pivotal role in gene regulation. In this study, we propose newDNA-Prot, a DNA-binding protein predictor that employs support vector machine classifier and a comprehensive feature representation. The sequence representation are categorized into 6 groups: primary sequence based, evolutionary profile based, predicted secondary structure based, predicted relative solvent accessibility based, physicochemical property based and biological function based features. The mRMR, wrapper and two-stage feature selection methods are employed for removing irrelevant features and reducing redundant features. Experiments demonstrate that the two-stage method performs better than the mRMR and wrapper methods. We also perform a statistical analysis on the selected features and results show that more than 95% of the selected features are statistically significant and they cover all 6 feature groups. The newDNA-Prot method is compared with several state of the art algorithms, including iDNA-Prot, DNAbinder and DNA-Prot. The results demonstrate that newDNA-Prot method outperforms the iDNA-Prot, DNAbinder and DNA-Prot methods. More specific, newDNA-Prot improves the runner-up method, DNA-Prot for around 10% on several evaluation measures. The proposed newDNA-Prot method is available at http://sourceforge.net/projects/newdnaprot/ PMID:25240115
Zhang, Yanping; Xu, Jun; Zheng, Wei; Zhang, Chen; Qiu, Xingye; Chen, Ke; Ruan, Jishou
Structure of the adenylation domain of an NAD +-dependent DNA ligase
Background: DNA ligases catalyse phosphodiester bond formation between adjacent bases in nicked DNA, thereby sealing the nick. A key step in the catalytic mechanism is the formation of an adenylated DNA intermediate. The adenyl group is derived from either ATP (in eucaryotes and archaea) or NAD+4 (in bacteria). This difference in cofactor specificity suggests that DNA ligase may be a
Martin R Singleton; Kjell H�kansson; David J Timson; Dale B Wigley
Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with
Optimized detection of sequence variation in heterozygous genomes using DNA microarrays-number variation detection and gene expression analysis. DNA/DNA hybridization | sequence discrimination | single- arrays by the group of Edwin Southern was the identification of DNA sequence variation (1). Early studies
Botstein, David
Molecular DNA switches and DNA chips
NASA Astrophysics Data System (ADS)
We present an assay to detect single-nucleotide polymorphisms on a chip using molecular DNA switches and isothermal rolling- circle amplification. The basic principle behind the switch is an allele-specific oligonucleotide circularization, mediated by DNA ligase. A DNA switch is closed when perfect hybridization between the probe oligonucleotide and target DNA allows ligase to covalently circularize the probe. Mismatches around the ligation site prevent probe circularization, resulting in an open switch. DNA polymerase is then used to preferentially amplify the closed switches, via rolling-circle amplification. The stringency of the molecular switches yields 102 - 103 fold discrimination between matched and mismatched sequences.
Sabanayagam, Chandran R.; Berkey, Cristin; Lavi, Uri; Cantor, Charles R.; Smith, Cassandra L.
Rapid identification of mitochondrial DNA (mtDNA) mutations in neuromuscular disorders by using surveyor strategy.
Mutations of mitochondrial genome are responsible for respiratory chain defects in numerous patients. We have used a strategy, based on the use of a mismatch-specific DNA endonuclease named " Surveyor Nuclease", for screening the entire mtDNA in a group of 50 patients with neuromuscular features, suggesting a respiratory chain dysfunction. We identified mtDNA mutations in 20% of patients (10/50). Among the identified mutations, four are not found in any mitochondrial database and have not been reported previously. We also confirm that mtDNA polymorphisms are frequently found in a heteroplasmic state (15 different polymorphisms were identified among which five were novel). PMID:18078792
Bannwarth, S; Procaccio, V; Rouzier, C; Fragaki, K; Poole, J; Chabrol, B; Desnuelle, C; Pouget, J; Azulay, J P; Attarian, S; Pellissier, J F; Gargus, J J; Abdenur, J E; Mozaffar, T; Calvas, P; Labauge, P; Pages, M; Wallace, D C; Lambert, J C; Paquis-Flucklinger, V
Genetic evidence for the involvement of DNA ligase IV in the DNA-PK-dependent pathway of non-homologous end joining in mammalian cells
Cells of vertebrates remove DNA double-strand breaks (DSBs) from their genome predominantly utilizing a fast, DNA-PKcs-dependent form of non- homologous end joining (D-NHEJ). Mutants with inactive DNA-PKcs remove the majority of DNA DSBs utilizing a slow, DNA-PKcs-independent pathway that does not utilize genes of the RAD52 epistasis group, is error-prone and can therefore be classified as af orm of NHEJ
Huichen Wang; Zhao-Chong Zeng; Ange R. Perrault; Xinbo Cheng; Wei Qin; George Iliakis
NSDL National Science Digital Library
This exercise involves identifying symmetry in crystals and using that information to assign crystals to crystal systems and point groups. Students examine cardboard models and wooden blocks and fill their symmetry elements into a table. Then they figure out what what crystal system and point group each sample belongs to and fill in another table.
Dexter Perkins
NSDL National Science Digital Library
In this lesson, students will explore the way fireflies are grouped in the text Ten Flashing Fireflies by Philomen Sturges. Students will represent all of the ways fireflies can be grouped so that some are in a jar and some are left to fly in the night sky.
Kathleen Brown
NSDL National Science Digital Library
Visitors can discover Professor Mark Bradley's and company's use of combinatorial chemistry to synthesize many compounds efficiently. The website features concise summaries, lists of publications, and information on the collaborators involved with the group's numerous research projects. The Research section offers brief summaries, with well-presented images and diagrams, of the group's various research interests, including Antibacterials, Pigments, and Biological Screening.
Quantitative DNA fiber mapping
The present invention relates generally to the DNA mapping and sequencing technologies. In particular, the present invention provides enhanced methods and compositions for the physical mapping and positional cloning of genomic DNA. The present invention also provides a useful analytical technique to directly map cloned DNA sequences onto individual stretched DNA molecules.
Gray, Joe W. (San Francisco, CA); Weier, Heinz-Ulrich G. (Oakland, CA)
Complexation of aluminum with DNA.
The extent of complexation of aluminum(III) with DNA (Calf thymus, Sigma type I) was estimated by means of two experimental techniques: potentiometric titration with a fluoride selective indicator electrode and dialysis followed by aluminum determination by graphite furnace AAS. Both types of experiments indicate that aluminum(III) is bound to DNA. The data are treated by assuming an ion exchange reaction with the phosphate diester groups. Using Rt to denote the concentration of these groups the values of log [AlMn-3R]/(Rt-3[AlMn-3R])[Al3+] decrease from approx. 7.6 to 5.6 when the concentration of sodium chloride is increased from 1 to 100 mM. In the pH range 4.5-5.5 the ion exchange constant increases approximately 0.5 log units. Dialysis gives lower values for the complex formation constant than potentiometry. PMID:3559548
Dyrssen, D; Haraldsson, C; Nyberg, E; Wedborg, M
Applications of a theory of sequence dependent DNA elasticity that accounts for intramolecular electrostatic forces
DNA strands that have come together to form the Watson-Crick structure, and each phosphate firstname.lastname@example.com #12;2 2 1. Introduction DNA molecules in the Watson-Crick double helical B form can often be treated of the two DNA strands that form the Watson-Crick structure, and each phosphate group bears one (negative
lthough forensic DNA testing is well established, experts sometimes disagree about the interpreta-
A lthough forensic DNA testing is well established, experts sometimes disagree about the interpreta. THOMPSON, LAURENCE D. MUELLER, AND DAN E. KRANE 12 Forensic DNA Statistics: Still Controversial In Some Group on DNA Analysis Methods (SWGDAM), a group of forensic scientists chosen by the FBI to propose
Rose, Michael R.
Recombinant DNA Technology in Apple
This review summarizes the achievements of almost 20�years of recombinant DNA technology applied\\u000a to apple, grouping the research results into the sections: developing the technology, insect resistance,\\u000a fungal disease resistance, self-incompatibility, herbicide resistance, fire blight resistance, fruit ripening,\\u000a allergens, rooting ability, and acceptance and risk assessment. The diseases fire blight, caused by Erwinia amylovora, and scab, caused by Venturia inaequalis,
Cesare Gessler; Andrea Patocchi
NSDL National Science Digital Library
DNA transformation is a naturally occurring but rare event in which DNA can be transferred into bacteria. In 1970, Morton Mandel and Akiko Higa discovered a way to make E. coli more 'competent' for transforming foreign DNA. Their calcium chloride method is widely used today to obtain high-efficiency transforming cells. This animation from Cold Spring Harbor Laboratory's Dolan DNA Learning Center presents the second part of explaining DNA transformation through a series of illustrations of the processes involved.
\\u000a Amplified detection of DNA is a central research topic in modern bioanalytical science. Electronic or optical transduction\\u000a of DNA recognition events provides readout signals for DNA biosensors. Amplification of the DNA analysis is accomplished by\\u000a the coupling of nucleic acid-functionalized enzymes or nucleic acid-functionalized nanoparticles (NP) as labels for the DNA\\u000a duplex formation. This chapter discusses the amplified amperometric analysis
Itamar Willner; Bella Shlyahovsky; Bilha Willner; Maya Zayats
Chemical methods of DNA and RNA fluorescent labeling.
Several procedures have been described for fluorescent labeling of DNA and RNA. They are based on the introduction of aldehyde groups by partial depurination of DNA or oxidation of the 3'-terminal ribonucleoside in RNA by sodium periodate. Fluorescent labels with an attached hydrazine group are efficiently coupled with the aldehyde groups and the hydrazone bonds are stabilized by reduction with sodium cyanoborohydride. Alternatively, DNA can be quantitatively split at the depurinated sites with ethylenediamine. The aldimine bond between the aldehyde group in depurinated DNA or oxidized RNA and ethylenediamine is stabilized by reduction with sodium cyanoborohydride and the primary amine group introduced at these sites is used for attachment of isothiocyanate or succinimide derivatives of fluorescent dyes. The fluorescent DNA labeling can be carried out either in solution or on a reverse phase column. These procedures provide simple, inexpensive methods of multiple DNA labeling and of introducing one fluorescent dye molecule per RNA, as well as quantitative DNA fragmentation and incorporation of one label per fragment. These methods of fluorophore attachment were shown to be efficient for use in the hybridization of labeled RNA, DNA and DNA fragments with oligonucleotide microchips. PMID:8948646
Proudnikov, D; Mirzabekov, A
The eighth volume of Advances in Viral Oncology focuses on the three major DNA virus groups with a postulated or proven tumorigenic potential: papillomaviruses, animal hepatitis viruses, and the Epstein-Bar virus. In the opening chapters, the contributors analyze the evidence that papillomaviruses and animal hepatitis viruses are involved in tumorigenesis and describe the mechanisms that trigger virus-host cell interactions. A detailed section on the Epstein-Barr virus (EBV) - comprising more than half the book - examines the transcription and mRNA processing patterns of the virus genome; the mechanisms by which EBV infects lymphoid and epithelial cells; the immunological aspects of the virus; the actions of EBV in hosts with Acquired Immune Deficiency Syndrome; and the involvement of EBV in the etiology of Burkitt's lymphoma.
Klein, G.
Identification of Phytophthora citrophthora with Cloned DNA Probes
Two different DNA fragments, one of 2.9 kilobases and the other of 5.1 kilobases, were cloned from Phytophthora citrophthora and showed no homology with DNA from plants and other related fungi. These DNA probes hybridized with DNA from 12 different P. citrophthora isolates obtained from a variety of hosts but did not hybridize with DNA from 6 P. citrophthora isolates obtained from cacao. Southern blot analysis revealed that the probes contained repetitive DNA, and restriction fragment length polymorphisms were identified among several P. citrophthora isolates. Of the isolates tested, two major groups were observed whose genetic similarity correlated with geographical distribution. One of the DNA probes was used to detect P. citrophthora growing from infected citrus roots incubated on semiselective medium. P. citrophthora was not detected by a hybridization assay of total DNA extracted directly from infected roots. Images PMID:16348140
Goodwin, P. H.; Kirkpatrick, B. C.; Duniway, J. M.
Crossing borders: the DNA of physics
NASA Astrophysics Data System (ADS)
In cell culture, the physical environment plays an important role: "Everything is everywhere, but the environment selects"[1]. The education of physicists can be viewed within this framework. The Petri dish for the reproduction of physicists is a university research group. The full professor is its DNA. The selection process of new professors - new DNA - is a determining step in creating the right culture. [1] M.W. Beijerinck and L.G.M. Baas Becking, en.wikipedia.org.
Beijerinck, H. C. W.
Nucleotide sequence of cassava latent virus DNA
Only two groups of plant viruses, the caulimoviruses1,2 and the geminiviruses3, are known to contain a genome of DNA. Unlike that of the caulimoviruses, the genome of the geminivinises is composed of single-stranded, covalently-closed circles of DNA. There is evidence that the geminiviruses, specifically bean golden mosaic virus4 and tomato golden mosaic virus5, have a genome composed of two similar-sized
John Stanley; Michael R. Gay
This group provides key consultations across NCI, developing and using statistical analysis of biological data, computer and mathematical models, and conducting research in biostatistical and epidemiological methodologies and mathematical modeling of processes.
NSDL National Science Digital Library
This is a lengthy PDF document (60 pages+) about plane groups and symmetry. It includes colorful images of each of the 17 plane groups, in several different forms. Additionally, there are some summarizing graphics that show unit cells, lattices, symmetry elements, etc. There is lots here to choose from -- I doubt that anyone will want to use all of the images. Studying plane groups is a good way to introduce crystal systems, point groups, lattices, symmetry operators, etc. All is in 2-D, but it is easy to tell students that the principles are the same in 3-D. For those who like to make changes, the PDF document was created from individual EPS files. This means that the files can be opened in Adobe Illustrator, Corel Draw, etc., and modified to fit your own needs.
Dexter Perkins
Modeling biominerals formed by apatites and DNA.
Different aspects of biominerals formed by apatite and DNA have been investigated using computer modeling tools. Firstly, the structure and stability of biominerals in which DNA molecules are embedded into hydroxyapatite and fluoroapatite nanopores have been examined by combining different molecular mechanics methods. After this, the early processes in the nucleation of hydroxyapatite at a DNA template have been investigated using molecular dynamics simulations. Results indicate that duplexes of DNA adopting a B double helix can be encapsulated inside nanopores of hydroxyapatite without undergoing significant distortions in the inter-strand hydrogen bonds and the intra-strand stacking. This ability of hydroxyapatite is practically independent of the DNA sequence, which has been attributed to the stabilizing role of the interactions between the calcium atoms of the mineral and the phosphate groups of the biomolecule. In contrast, the fluorine atoms of fluoroapatite induce pronounced structural distortions in the double helix when embedded in a pore of the same dimensions, resulting in the loss of its most relevant characteristics. On the other hand, molecular dynamics simulations have allowed us to observe the formation of calcium phosphate clusters at the surface of the B-DNA template. Electrostatic interactions between the phosphate groups of DNA and Ca(2+) have been found to essential for the formation of stable ion complexes, which were the starting point of calcium phosphate clusters by incorporating PO3(4) from the solution. PMID:24706121
Revilla-L�pez, Guillermo; Casanovas, Jordi; Bertran, Oscar; Turon, Pau; Puiggal�, Jordi; Alem�n, Carlos
DNA lesions that block DNA replication are responsible for the dnaA induction caused by DNA damage
The initiation protein DnaA of Escherichia coli regulates its own expression autogenously by binding to a 9 by consensus sequence, the dnaA box, between the promoters dnaAP1 and dnaAP2. In this study, we analysed dnaA regulation in relation to DNA damage and found dnaA expression to be inducible by DNA lesions that inhibit DNA replication. On the other hand, coding
Ariel Quifiones; Wolf-Rainer Jueterbock; Walter Messer
Binding of HIV-1 Vpr protein to the human homolog of the yeast DNA repair protein RAD23 (hHR23A) requires its xeroderma pigmentosum complementation group C binding (XPCB) domain as well as the ubiquitin-associated 2 (UBA2) domain.
The human homolog of the yeast DNA repair protein RAD23, hHR23A, has been found previously to interact with the human immunodeficiency virus, type 1 accessory protein Vpr. hHR23A is a modular protein containing an N-terminal ubiquitin-like (UBL) domain and two ubiquitin-associated domains (UBA1 and UBA2) separated by a xeroderma pigmentosum complementation group C binding (XPCB) domain. All domains are connected by flexible linkers. hHR23A binds ubiquitinated proteins and acts as a shuttling factor to the proteasome. Here, we show that hHR23A utilizes both the UBA2 and XPCB domains to form a stable complex with Vpr, linking Vpr directly to cellular DNA repair pathways and their probable exploitation by the virus. Detailed structural mapping of the Vpr contacts on hHR23A, by NMR, revealed substantial contact surfaces on the UBA2 and XPCB domains. In addition, Vpr binding disrupts an intramolecular UBL-UBA2 interaction. We also show that Lys-48-linked di-ubiquitin, when binding to UBA1, does not release the bound Vpr from the hHR23A-Vpr complex. Instead, a ternary hHR23A�Vpr�di-Ub(K48) complex is formed, indicating that Vpr does not necessarily abolish hHR23A-mediated shuttling to the proteasome. PMID:24318982
Jung, Jinwon; Byeon, In-Ja L; DeLucia, Maria; Koharudin, Leonardus M I; Ahn, Jinwoo; Gronenborn, Angela M
Even with decreasing DNA synthesis costs there remains a need for inexpensive, rapid, and reliable methods for assembling synthetic DNA into larger constructs or combinatorial libraries. Advances in cloning techniques have resulted in powerful in vitro and in vivo assembly of DNA. However, monetary and time costs have limited these approaches. Here, we report an ex vivo DNA assembly method that uses cellular lysates derived from a commonly used laboratory strain of Escherichia coli for joining double-stranded DNA with short end homologies embedded within inexpensive primers. This method concurrently shortens the time and decreases costs associated with current DNA assembly methods. PMID:25024067
Fisher, Adam B.; Canfield, Zachary B.; Hayward, Laura C.; Fong, Stephen S.; McArthur, George H.
Automata representation for Abelian groups
NASA Astrophysics Data System (ADS)
A finite automaton is one of the classic models of recognition devices, which is used to determine the type of language a string belongs to. A string is said to be recognized by a finite automaton if the automaton "reads" the string from the left to the right starting from the initial state and finishing at a final state. Another type of automata which is a counterpart of sticker systems, namely Watson-Crick automata, is finite automata which can scan the double-stranded tapes of DNA strings using the complimentary relation. The properties of groups have been extended for the recognition of finite automata over groups. In this paper, two variants of automata, modified deterministic finite automata and modified deterministic Watson-Crick automata are used in the study of Abelian groups. Moreover, the relation between finite automata diagram over Abelian groups and the Cayley table is introduced. In addition, some properties of Abelian groups are presented in terms of automata.
Fong, Wan Heng; Gan, Yee Siang; Sarmin, Nor Haniza; Turaev, Sherzod
Inherited Mendelian defects of nuclear�mitochondrial communication affecting the stability of mitochondrial DNA
The presence of mtDNA abnormalities inherited as Mendelian traits indicates the existence of mutations in nuclear genes affecting the integrity of the mitochondrial genome. Two groups of nucleus-driven abnormalities have been described: qualitative alterations of mtDNA, i.e. multiple large-scale deletions of mtDNA, and quantitative decrease of the mtDNA copy number, i.e. tissue-specific depletion of mtDNA. Autosomal dominant or recessive (adPEO),
Anna Limongelli; Valeria Tiranti
Permanent or reversible conjugation of 2?-O- or 5?-O-aminooxymethylated nucleosides with functional groups as a convenient and efficient approach to the modification of RNA and DNA sequences
2?-O-Aminooxymethyl ribonucleosides are prepared from their 3?,5?-disilylated 2?-O-phthalimidooxymethyl derivatives by treatment with NH4F in MeOH. The reaction of these novel ribonucleosides with 1-pyrenecarboxaldehyde results in the efficient formation of stable and yet reversible ribonucleoside 2?-conjugates in yields of 69�82%. Indeed, exposure of these conjugates to 0.5?M tetra-n-butylammonium fluoride (TBAF) in THF results in the cleavage of their iminoether functions to give the native ribonucleosides along with the innocuous nitrile side product. Conversely, the reaction of 5-cholesten-3-one or dansyl chloride with 2?-O-aminooxymethyl uridine provides permanent uridine 2?-conjugates, which are left essentially intact upon treatment with TBAF. Alternatively, 5?-O-aminooxymethyl thymidine is prepared by hydrazinolysis of its 3?-O-levulinyl-5?-O-phthalimidooxymethyl precursor. Pyrenylation of 5?-O-aminooxymethyl thymidine and the sensitivity of the 5?-conjugate to TBAF further exemplify the usefulness of this nucleoside for modifying DNA sequences either permanently or reversibly. Although the versatility and uniqueness of 2?-O-aminooxymethyl ribonucleosides in the preparation of modified RNA sequences is demonstrated by the single or double incorporation of a reversible pyrenylated uridine 2?-conjugate into an RNA sequence, the conjugation of 2?-O-aminooxymethyl ribonucleosides with aldehydes, including those generated from their acetals, provides reversible 2?-O-protected ribonucleosides for potential applications in the solid-phase synthesis of native RNA sequences. The synthesis of a chimeric polyuridylic acid is presented as an exemplary model. PMID:22067450
Cie?lak, Jacek; Grajkowski, Andrzej; Aus�n, Cristina; Gapeev, Alexei; Beaucage, Serge L.
Permanent or reversible conjugation of 2'-O- or 5'-O-aminooxymethylated nucleosides with functional groups as a convenient and efficient approach to the modification of RNA and DNA sequences.
2'-O-Aminooxymethyl ribonucleosides are prepared from their 3',5'-disilylated 2'-O-phthalimidooxymethyl derivatives by treatment with NH(4)F in MeOH. The reaction of these novel ribonucleosides with 1-pyrenecarboxaldehyde results in the efficient formation of stable and yet reversible ribonucleoside 2'-conjugates in yields of 69-82%. Indeed, exposure of these conjugates to 0.5 M tetra-n-butylammonium fluoride (TBAF) in THF results in the cleavage of their iminoether functions to give the native ribonucleosides along with the innocuous nitrile side product. Conversely, the reaction of 5-cholesten-3-one or dansyl chloride with 2'-O-aminooxymethyl uridine provides permanent uridine 2'-conjugates, which are left essentially intact upon treatment with TBAF. Alternatively, 5'-O-aminooxymethyl thymidine is prepared by hydrazinolysis of its 3'-O-levulinyl-5'-O-phthalimidooxymethyl precursor. Pyrenylation of 5'-O-aminooxymethyl thymidine and the sensitivity of the 5'-conjugate to TBAF further exemplify the usefulness of this nucleoside for modifying DNA sequences either permanently or reversibly. Although the versatility and uniqueness of 2'-O-aminooxymethyl ribonucleosides in the preparation of modified RNA sequences is demonstrated by the single or double incorporation of a reversible pyrenylated uridine 2'-conjugate into an RNA sequence, the conjugation of 2'-O-aminooxymethyl ribonucleosides with aldehydes, including those generated from their acetals, provides reversible 2'-O-protected ribonucleosides for potential applications in the solid-phase synthesis of native RNA sequences. The synthesis of a chimeric polyuridylic acid is presented as an exemplary model. PMID:22067450
Cieslak, Jacek; Grajkowski, Andrzej; Aus�n, Cristina; Gapeev, Alexei; Beaucage, Serge L
Small Molecules, Inhibitors of DNA-PK, Targeting DNA Repair, and Beyond
Many current chemotherapies function by damaging genomic DNA in rapidly dividing cells ultimately leading to cell death. This therapeutic approach differentially targets cancer cells that generally display rapid cell division compared to normal tissue cells. However, although these treatments are initially effective in arresting tumor growth and reducing tumor burden, resistance and disease progression eventually occur. A major mechanism underlying this resistance is increased levels of cellular DNA repair. Most cells have complex mechanisms in place to repair DNA damage that occurs due to environmental exposures or normal metabolic processes. These systems, initially overwhelmed when faced with chemotherapy induced DNA damage, become more efficient under constant selective pressure and as a result chemotherapies become less effective. Thus, inhibiting DNA repair pathways using target specific small molecule inhibitors may overcome cellular resistance to DNA damaging chemotherapies. Non-homologous end joining a major mechanism for the repair of double-strand breaks (DSB) in DNA is regulated in part by the serine/threonine kinase, DNA dependent protein kinase (DNA-PK). The DNA-PK holoenzyme acts as a scaffold protein tethering broken DNA ends and recruiting other repair molecules. It also has enzymatic activity that may be involved in DNA damage signaling. Because of its� central role in repair of DSBs, DNA-PK has been the focus of a number of small molecule studies. In these studies specific DNA-PK inhibitors have shown efficacy in synergizing chemotherapies in vitro. However, compounds currently known to specifically inhibit DNA-PK are limited by poor pharmacokinetics: these compounds have poor solubility and have high metabolic lability in vivo leading to short serum half-lives. Future improvement in DNA-PK inhibition will likely be achieved by designing new molecules based on the recently reported crystallographic structure of DNA-PK. Computer based drug design will not only assist in identifying novel functional moieties to replace the metabolically labile morpholino group but will also facilitate the design of molecules to target the DNA-PKcs/Ku80 interface or one of the autophosphorylation sites. PMID:23386830
Davidson, David; Amrein, Lilian; Panasci, Lawrence; Aloyz, Raquel
MNGIE: from nuclear DNA to mitochondrial DNA
Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is a unique autosomal recessive disorder with mitochondrial DNA alterations. The disease is characterized clinically by ptosis, progressive external ophthalmoparesis, gastrointestinal dysmotility, cachexia, peripheral neuropathy, and leukoencephalopathy. Muscle biopsies typically reveal mitochondrial abnormalities including ragged-red fibers and focal cytochrome c oxidase deficiency. Analysis of mitochondrial DNA in skeletal muscle shows partial depletion, multiple deletions, or both.
Ichizo Nishino; Antonella Spinazzola; Michio Hirano
ERIC Educational Resources Information Center
This report describes an observational study of one family-grouped classroom, a system in which elementary school children remain with the same teacher for two or more years. The class was composed of junior kindergarten, senior kindergarten, and grade 1 pupils. Each child was observed over a period of one year. A detailed observation schedule,�
Young, Vivienne; Reich, Carol
ERIC Educational Resources Information Center
Research suggests that cooperative learning works best when students are first taught group-processing skills, such as leadership, decision making, communication, trust building, and conflict management. Inadequate teacher training and boring assignments can torpedo cooperative learning efforts. Administrators should reassure teachers with�
Black, Susan
STATISTICS GROUP :: WEEK #1 Jordan Webster 19 October 2011 1 #12;19 October 2011 2 19 October 2011(x|, x0) = 1 /2 2/2+(x-x0)2 divergent divergent mass of resonance Table 1: some basic info for commonly
ERIC Educational Resources Information Center
The Cantor subset of the unit interval [0, 1) is "large" in cardinality and also "large" algebraically, that is, the smallest subgroup of [0, 1) generated by the Cantor set (using addition mod 1 as the group operation) is the whole of [0, 1). In this paper, we show how to construct Cantor-like sets which are "large" in cardinality but "small"�
Mathes, Ben; Dow, Chris; Livshits, Leo
Optimal Placement of Origins for DNA Replication
DNA replication is an essential process in biology and its timing must be robust so that cells can divide properly. Random fluctuations in the formation of replication starting points, called origins, and the subsequent activation of proteins lead to variations in the replication time. We analyse these stochastic properties of DNA and derive the positions of origins corresponding to the minimum replication time. We show that under some conditions the minimization of replication time leads to the grouping of origins, and relate this to experimental data in a number of species showing origin grouping.
Jens Karschau; J. Julian Blow; Alessandro P. S. de Moura
The combination of synthetic stable branched DNA and sticky ended cohesion has led to the development of structural DNA nanotechnology over the past 30 years. The basis of this enterprise is that it is possible to construct novel DNA-based materials by combining these features in a self-assembly protocol. Thus, simple branched molecules lead directly to the construction of polyhedra whose edges consist of double helical DNA, and whose vertices correspond to the branch points. Stiffer branched motifs can be used to produce self-assembled two-dimensional and three-dimensional periodic lattices of DNA (crystals). DNA has also been used to make a variety of nanomechanical devices, including molecules that change their shapes, and molecules that can walk along a DNA sidewalk. Devices have been incorporated into two-dimensional DNA arrangements; sequence-dependent devices are driven by increases in nucleotide pairing at each step in their machine cycles. PMID:20222824
Seeman, Nadrian C.
NSDL National Science Digital Library
This resource is an animation to explain DNA replication. It is an interactive simulation activity for students. See also "Transcription and Translation Animation" to get all of the steps from DNA to protein.
McDougal Littell
NSDL National Science Digital Library
This animation adapted from Garland Science Publishing takes a close look at the DNA double helix and its individual components, describing their chemical structures and how they function together to make the DNA molecule unique.
The HPV DNA test is used to check for high-risk HPV infection in women. HPV infection around the genitals is ... warts spread when you have sex. The HPV-DNA test is generally not recommended for detecting low- ...
Most states do not have laws restricting surreptitious DNA testing. Those that do generally place restrictions only ... of states have laws that broadly restrict surreptitious DNA testing for both health and non-health-related ...
NSDL National Science Digital Library
In this activity, learners make a 3-D model of DNA using paper and toothpicks. While constructing this model, learners will explore the composition and structure of DNA. The activity also gives suggestions for alternate materials and challenges to explore.
American Museum of Natural History
Structural Organization of DNA.
ERIC Educational Resources Information Center
Explains the structural organization of DNA by providing information on the primary, secondary, tertiary, and higher organization levels of the molecule. Also includes illustrations and descriptions of sign-inversion and rotating models for supercoiling of DNA. (ML)
Banfalvi, Gaspar
DNA repair genes of mammalian cells
In the Chinese hamster ovary (CHO) cell line, various mutations affecting DNA repair have been obtained. Mutants that belong to 5 genetic complementation groups for ultraviolet (UV) sensitivity and resemble the cells from individuals having the cancer-prone genetic disorder xeroderma pigmentosum (XP) were previously identified. Each mutant is defective in the incision step of nucleotide excision repair and hypersensitive to bulky DNA lesions. These UV mutants can be divided into two subgroups; only Groups 2 and 4 are extremely sensitive to mitomycin C and other DNA cross-linking agents. The clear-cut phenotypes of the CHO mutants have allowed us to construct hybrid cells by fusion with human lymphocytes and thereby identify which human chromosomes carry genes that correct the CHO mutations. The first two mutations analyzed, UV20 (excision-repair deficient; UV Group 2) and EM9, which has a very high frequency of sister chromatid exchange (SCE), are both corrected by chromosome 19. Efforts are underway to isolate complementing repair genes by DNA-mediated gene transfer. The human gene that corrects mutant EM9 and the hamster gene that corrects UV135 (UV Group 5) have been introduced by cotransfer of genomic DNA and the dominant selectable marker gpt (guanine phosphoribosyltransferase) gene. In each case, the DNA repair function was co-selected based on resistance to 5-chlorodeoxyuridine (CldUrd) or repeated UV irradiation, respectively. The presence of a functional human repair gene in the EM9 transformants is shown by the presence of common human DNA sequences on some fragments produced by restriction enzyme cleavage. In UV135, transfer of a repair gene is indicated by a colony distribution containing jackpots and by instability of the resistant phenotype.
Thompson, L.H.; Brookman, K.W.; Salazar, E.P.; Fuscoe, J.C.; Weber, C.A.
[Analysis of 16S rDNA sequences and DNA-DNA hybridization of moderately halophilic bacteria from Xinjiang region].
Based on the previous studies on numerical taxonomy and 16S rDNA PCR-RFLP analysis, the moderately halophilic bacteria isolated from Xinjiang Region constituted a new cluster, and the phylogenetic tree was constructed by comparing with the 16S rDNA sequences of the other moderately halophilic bacteria species. In the phylogenetic tree, most of the reference strains were clustered in a group, and the similarity values of 16S rDNA sequence were above 96%. However, AI-3, Alcanivorax borkumensis and Halobacillus litoralis were clustered in another group, and the similarity value of 16S rDNA sequences between AI-3 and Alcanivorax borkumensis was 96%, and that of 16S rDNA sequences between AI-3 and Halobacillus litoralis was 99%. The results indicated that AI-3 was different from the reference strains in phylogeny. The values of DNA homology in the new cluster were more than 70%, but the value between AI-3 and Halomonas elongata was less than 50%. Thus, the strain AI-3 possibly represent a new moderately halophilic bacteria species. PMID:12557387
Zeng, Jing; Dou, Yuetan; Wang, Lei; Yang, Susheng
DNA profiling of sugarcane genotypes using randomly amplified polymorphic DNA.
DNA profiles of 40 sugarcane genotypes were constructed with 30 RAPD markers. Sugarcane genotypes of both Saccharum officinarum and S. barberi were included in this study. Multiple alleles were detected from each RAPD; there was a high level of polymorphism. On average, 7.93 alleles were produced per primer, giving a total of 238 alleles. The genetic distances between these genotypes were assessed with the POPGENE DNA sequence analysis software. A dendrogram was constructed from these data; cultivated species of sugarcane formed clusters with S. barberi genotypes. The 40 genotypes were clustered into two main groups; genetic distances ranged from 20.29 to 64.66%. These RAPD fingerprints will help sugarcane breeders to evaluate the efficiency of current conventional breeding methods and will help characterize the genetic pedigree of commercial sugarcane varieties. These data will also be valuable for conservation and utilization of the genetic resources in germplasm collections. PMID:20391332
Tabasum, S; Khan, F A; Nawaz, S; Iqbal, M Z; Saeed, A
DNA modification by methyltransferases
Enzymatic methylation of DNA plays important roles in both prokaryotes and eukaryotes. Structural study of the Hhal DNA methyltransferase has provided considerable insight into the chemistry of C5-cytosine methylation. The DNA-protein complex reveals a substrate cytosine flipped out of the double helix during the reaction, and a novel two-loop DNA-binding motif used for both sequence recognition and flipping the base.
Xiaodong Cheng
NSDL National Science Digital Library
Two sequencing techniques were developed independently in the 1970s. The method developed by Fred Sanger used chemically altered 'dideoxy' bases to terminate newly synthesized DNA fragments at specific bases (either A, C, T, or G). These fragments are then size-separated, and the DNA sequence can be read. This animation from Cold Spring Harbor Laboratory's Dolan DNA Learning Center presents early DNA sequencing through a series of illustrations of the processes involved.
The terms recombinant DNA technology, DNA cloning, molecular cloning, or gene\\u000a cloning all refer to use of molecular techniques to select a specific sequence or sequences of DNA from an organism and transfer\\u000a it into another organism to code for or alter specific traits. Thus, recombinant DNA technology provides a powerful molecular\\u000a tool that enables scientists to engineer sequences of
Pedro J. Chedrese
Murine monoclonal anti-DNA autoantibodies bind to endogenous bacteria.
Several bacterial species (including Streptococcus faecalis, Bacillus cereus, Staphylococcus aureus, and Escherichia coli) were tested for their ability to react with monoclonal anti-DNA antibodies that were derived from MRL-lpr/lpr mice. S. faecalis reacted with 8/15 of such antibodies. The binding was unaffected by DNase, but it was competitively inhibited by DNA. F(ab')2 fragments of the monoclonal antibodies reacted with the bacteria, but Fc fragments did not. Phospholipids extracted from the bacterial cells were able to bind to three representative anti-DNA antibodies that also bound to whole bacteria. The results suggest that bacterial phospholipids might provide an immunogenic stimulus for the production of antibodies that cross-react with DNA. We propose that some anti-DNA auto-antibodies and anti-bacterial antibodies evolve from a restricted group of antibodies with high avidity for the phosphodiester groups that occur in DNA and bacterial cells walls. PMID:3874226
Carroll, P; Stafford, D; Schwartz, R S; Stollar, B D
Meta-DNA: synthetic biology via DNA nanostructures and
Meta-DNA: synthetic biology via DNA nanostructures and hybridization reactions Harish Chandran1 of DNA manipulations achieved by protein enzymes be simulated via simple DNA hybridization chemistry? In this work, we develop a biochemical system which we call meta-DNA (abbreviated as mDNA), based on strands
Reif, John H.
DNA microarray technologies for measuring proteinDNA interactions
DNA microarray technologies for measuring proteinDNA interactions Martha L Bulyk DNA approach to analyse the in vitro binding of proteins directly to double-stranded DNA microarrays (protein specificities. Recent advances in DNA microarray synthesis technologies have facilitated the definition of DNA
Bulyk, Martha L.
Recombinational DNA Repair in Bacteria
Recombinational DNA Repair in Bacteria: Postreplication Kevin P Rice,University of Wisconsin Recombinational DNA repair represents the primary function for homologous DNA recombination in bacteria. Most of genetic diversity, primarily during conjugation, homologous DNA recombination in bacteria is now
Cox, Michael M.
ERIC Educational Resources Information Center
Explores the meaning of DNA. Discusses histories of DNA, literature on DNA, the contributions of Max Delbruck and Barbara McClintock, life, views of control, current research, and the language of DNA. Contains 24 references. (JRH)
Flannery, Maura C.
NSDL National Science Digital Library
This animation takes the students through a tour of a typical human cell, moving from larger to smaller cell structures (i.e., from nucleus to chromosomes to DNA strands and their bases). It briefly describes some of these structures and describes how DNA strands are constructed. This animation can be used as an introduction to the study of chromosomes and DNA.
Dexter Pratt (AAAS; Science Netlinks)
The paper presents the principles of bio molecular computation (BMC) and several algorithms for DNA (deoxyribonucleic acid) steganography and cryptography: One-Time-Pad (OTP), DNA XOR OTP and DNA chromosomes indexing. It represents a synthesis of our work in the field, sustained by former referred publications. Experimental results obtained using Matlab Bioinformatics Toolbox and conclusions are ending the work.
Monica BORDA; Olga TORNEA
Just like disk or RAM, DNA and RNA can store vast amounts of information, and just like data stored in digital media, DNA data can be easily copied or tampered with. However, unlike in the digital realm, there are no techniques for watermarking, annotating, or encrypting information in DNA and RNA. The ability to catalogue genes, place checksums, watermark, and
Boris Shimanovsky; Jessica Feng; Miodrag Potkonjak
DNA replication in thermophiles
DNA replication enzymes in the thermophilic Archaea have previously attracted attention due to their obvious use in methods such as PCR. The proofreading ability of the Pyrococcus furiosus DNA polymerase has resulted in a commercially successful product (Pfu polymerase). One of the many notable features of the Archaea is the fact that their DNA processing enzymes appear on the whole
A. I. Majern�k; E. R. Jenkinson; J. P. J. Chong
NSDL National Science Digital Library
This laboratory exercise is designed to show learners how DNA can easily be extracted from onion cells using simple materials. Use this experiment to supplement any unit on genetics and to demonstrate how scientists study DNA. Adult supervision is recommended. This resource guide includes tips and suggestions for instructors as well as other DNA extraction experiments and a chart for learners to answer questions.
Lana Hays
NSDL National Science Digital Library
This laboratory exercise is designed to show learners how DNA can easily be extracted from yeast using simple materials. Use this experiment to supplement any unit on genetics and to demonstrate how scientists study DNA. Adult supervision is recommended. This resource guide includes tips and suggestions for instructors as well as other DNA extraction experiments and a chart for learners to answer questions.
Lana Hays
NSDL National Science Digital Library
This laboratory exercise is designed to show learners how DNA can easily be extracted from wheat germ using simple materials. Use this experiment to supplement any unit on genetics and to demonstrate how scientists study DNA. Adult supervision is recommended. This resource guide includes tips and suggestions for instructors as well as other DNA extraction experiments and a chart for learners to answer questions.
Lana Hays
NASA Technical Reports Server (NTRS)
The problem with the shortage of under represented groups in science and engineering is absolutely crucial, especially considering that U.S. will experience a shortage of 560,000 science and engineering personnel by the year 2010. Most studies by the National Science Foundation also concluded that projected shortages cannot be alleviated without significant increases in the involvement of Blacks, Hispanics, Native Americans, handicapped persons, and women.
Peters, David A.
NASA Astrophysics Data System (ADS)
Not long after EDWIN HUBBLE established that galaxies are `island universes' similar to our home galaxy, the MILKY WAY, he realized that a few of these external galaxies are considerably closer to us than any others. In 1936 he first coined the term `Local Group' in his famous book The Realm of the Nebulae to identify our nearest galactic neighbors. More than 60 yr later, the galaxies of the Loca...
Mateo, M.; Murdin, P.
Evaluation of DNAstable for DNA storage at ambient temperature.
Preserving DNA is important for validation of prospective and retrospective analyses, requiring many expensive types of equipment (e.g., freezers and back-up generators) and energy. While freezing is the most common method for storing extracted DNA evidence or well-characterized DNA samples for validation studies, DNAstable (Biomatrica), a commercially available medium for room temperature storage of DNA extracts was evaluated in this study. Two groups of samples consisting of different DNA quantities were investigated, one ranging from 20 to 400 ng (group 1) and the other one ranging from 1.4 to 20 ng (group 2). The DNA samples with and without DNAstable were stored at four different temperatures [?25 �C (room temperature), -20 �C, 37 �C or 50 �C]. DNA degradation over several months was monitored by SYBR Green-based qPCR assays and by PCR amplification of the core CODIS STR markers for group 1 and 2 DNA samples, respectively. For the time points tested in this study (up to 365 days), the findings indicate that the -20 �C controls and the DNAstable protected samples at room temperature provided similar DNA recoveries that were higher compared to the unprotected controls kept at RT, 37 �C or 50 �C. These results suggest that DNAstable can protect DNA samples with effectiveness similar to that of the traditional -20 �C freezing method. In addition, extrapolations from accelerated aging experiments conducted at high temperatures support that DNAstable is an effective technology for preserving purified DNA at room temperature with a larger protective impact on DNA samples of low quantity (<20 ng). PMID:24315605
Howlett, Susanne E; Castillo, Hilda S; Gioeni, Lora J; Robertson, James M; Donfack, Joseph
Repeated DNA sequences and species relatedness in the genus Equisetum
The kinetics with which DNA reassociates and the thermal stability of rapidly reassociating (repetitive) DNA sequences have been monitored for six species in the genusEquisetum. Using the kinetic complexity for each of two repeated DNA sequence components as the basis for comparison, species in the subgenusEquisetum (E. arvense, E. fluviatile andE. telmateia) form one group and species in the subgenusHippochaete
Arnold J. Bendich; Robert S. Anderson
Syndromes associated with mitochondrial DNA depletion
Mitochondrial dysfunction accounts for a large group of inherited metabolic disorders most of which are due to a dysfunctional mitochondrial respiratory chain (MRC) and, consequently, deficient energy production. MRC function depends on the coordinated expression of both nuclear (nDNA) and mitochondrial (mtDNA) genomes. Thus, mitochondrial diseases can be caused by genetic defects in either the mitochondrial or the nuclear genome, or in the cross-talk between the two. This impaired cross-talk gives rise to so-called nuclear-mitochondrial intergenomic communication disorders, which result in loss or instability of the mitochondrial genome and, in turn, impaired maintenance of qualitative and quantitative mtDNA integrity. In children, most MRC disorders are associated with nuclear gene defects rather than alterations in the mtDNA itself. The mitochondrial DNA depletion syndromes (MDSs) are a clinically heterogeneous group of disorders with an autosomal recessive pattern of transmission that have onset in infancy or early childhood and are characterized by a reduced number of copies of mtDNA in affected tissues and organs. The MDSs can be divided into least four clinical presentations: hepatocerebral, myopathic, encephalomyopathic and neurogastrointestinal. The focus of this review is to offer an overview of these syndromes, listing the clinical phenotypes, together with their relative frequency, mutational spectrum, and possible insights for improving diagnostic strategies. PMID:24708634
Fern spore extracts can damage DNA.
The carcinogenicity of the vegetative tissues of bracken fern (Pteridium) has long been established. More recently, the carcinogenic effects of the spores of bracken have also been recognized. Both vegetative tissues and spores of bracken can induce adducts in DNA in animal tissues, but the possible genotoxic or carcinogenic effects of spores from fern species other than bracken are unknown. The single-cell gel electrophoresis ('comet') assay was used to investigate whether fern spores can cause DNA damage in vitro. Extracts of spores from six fern species were administered to cultured human premyeloid leukaemia (K562) cells. Spore extracts of five fern species: Anemia phyllitidis, Dicksonia antarctica, Pteridium aquilinum, Pteris vittata and Sadleria pallida, induced significantly more DNA strand breaks than those in the control groups. Only in one species, Osmunda regalis, was the effect no different from that in the control groups. Using extracts from A. phyllitidis and P. vittata, the extent of DNA damage was increased by increasing the original dose 10 times, whereas an experiment in which exposure times were varied suggested that the highest levels of strand breaks appear after 2 h exposure. Simultaneous incubation with human S9 liver enzyme mix ablated the damaging effect of the extracts. Our data show that fern spore extracts can cause DNA damage in human cells in vitro. Considering the strong correlation between DNA damage and carcinogenic events, the observations made in this report may well have some implications for human health. PMID:10883670
Sim�n, S E; Povey, A C; Ward, T H; Margison, G P; Sheffield, E
DNAzymes in DNA Nanomachines and DNA Analysis
NASA Astrophysics Data System (ADS)
This chapter discusses our efforts in using DNAzymes in DNA nano-machines and DNA analysis systems. 10-23 DNAzymes can cleave specific phos-phodiester bonds in RNA. We use them to construct an autonomous DNA-RNA chimera nanomotor, which constantly extracts chemical energy from RNA substrates and transduces the energy into a mechanical motion: cycles of contraction and extension. The motor's motion can be reversibly turned on and off by a DNA analogue (brake) of the RNA substrate. Addition and removal of the brake stops and restarts, respectively, the motor's motion. Furthermore, when the RNA substrates are preorganized into a one-dimensional track, a DNAzyme can continuously move along the track so long as there are substrates available ahead. Based on a similar mechanism, a novel DNA detection system has been developed. A target DNA activates a DNAzyme to cleave RNA-containing molecular beacons (MB), which generates an enhanced fluorescence signal. A following work integrates two steps of signal amplifications: a rolling-circle amplification (RCA) to synthesize multiple copies of DNAzymes, and the DNAzymes catalyze a chemical reaction to generate a colorimetric signal. This method allows detection of DNA analytes whose concentration is as low as 1 pM.
He, Yu; Tian, Ye; Chen, Yi; Mao, Chengde
NSDL National Science Digital Library
The universality of the genetic code has allowed DNA isolated from a specific organism to be transferred and incorporated in another organism, transforming bacterial, yeast, plant, and animal cells. This transformation ability is the essence of recombinant DNA technology. Recombinant DNA has been used to make medically useful proteins that would otherwise have been difficult to obtain in necessary amounts, or to engineer plants to be herbicide or insect resistant. The following activity, which focuses on mapping DNA using restriction enzymes, can help students gain a better understanding about DNA and its manipulation. The activity is designed for high school and college biology students.
Isabel Chagas
An automated DNA sequencing apparatus having a reactor for providing at least two series of DNA products formed from a single primer and a DNA strand, each DNA product of a series differing in molecular weight and having a chain terminating agent at one end; separating means for separating the DNA products to form a series bands, the intensity of substantially all nearby bands in a different series being different, band reading means for determining the position an This invention was made with government support including a grant from the U.S. Public Health Service, contract number AI-06045. The U.S. government has certain rights in the invention.
Tabor, Stanley (Cambridge, MA); Richardson, Charles C. (Chestnut Hill, MA)
Heterobifunctional modification of DNA for conjugation to solid surfaces
Many biosensors, DNA arrays, and next-generation DNA sequencing technologies need common methods for end modification of random DNA sequences generated from a sample of DNA. Surface immobilization of chemically modified DNA is often the first step in creating appropriate sensing platforms. We describe a simple technique for efficient heterobifunctional modification of arbitrary double-stranded DNA fragments with chosen chemical groups. The modification requires the use of short (10�20 base pairs) synthetic adaptors having desired terminal functional groups and installs known sequences, which can be used for hybridization of primers in the sequencing-by-synthesis approaches. The method, based on ligation under optimized conditions, is selective and provides high yields of the target heterobifunctional DNA product. An additional two-step procedure can be applied to select further for the desired bifunctionalized product using PCR amplification with a chemically modified primer. Both functional groups in the modified DNA are chemically active and can be used in surface immobilization of the DNA strands to create the surface of a biosensor or sequencing chip. PMID:20422158
Lim, Hana I.; Oliver, Piercen M.; Marzillier, Jutta; Vezenov, Dmitri V.
Nanomaterials and nanoclusters based on DNA modulation.
Besides the inherent chirality, DNA is enriched by nitrogen and oxygen functional groups that are preferential to coordinate with transition metal ions, and its self-assembled structures, including the G-quadruplex, the i-motif, and the conventional Watson-Crick duplex, etc., can be adjusted via different base pairings. Recently biotemplating on the basis of DNA self-assembly has been considered as an attractive method to construct switchable nanomaterials, to direct crystal growth and to design enantioselective selectors/catalysts. This review briefly covers the recent progress relevant to DNA modulated nano/subnano materials. The long-term goal of this area of research is to explore novel promisingly environmental-benign approaches to construct switchable nanomachines, nano/subnano clusters and enantioselective recognition platforms respectively, through DNA-based modulation. PMID:24832072
Fu, Yan; Wang, Xian; Zhang, Jinli; Li, Wei
Reproductive & Cardiovascular Disease Research Group
NSDL National Science Digital Library
The Reproductive & Cardiovascular Disease Research Group is "based in the Department of Biochemistry and Immunology at St. George's, University of London." The Group's "research interests include a number of areas concerned with reproductive and cardiovascular diseases such as trophoblast biology, nitric oxide and apoptosis, with particular emphasis on the role of these subjects in diseases of pregnancy such as pre-eclampsia." This website contains descriptions of protocols commonly utilized by the Research Group such as DNA laddering, Comet Assay, Immunoprecipitation, and Caspase Assay, to name a few. This site also contains informative sections concerning Nitric Oxide, Apoptosis, and Trophoblasts. The website includes a list of publications, and email addresses of group members as well.
Dash, Phil.
The evaporation kinetics of droplets containing DNA was studied, as a function of DNA concentration. Drops containing very low DNA concentrations dried by maintaining a constant base, whereas those with high concentration dried with a constant contact angle. To understand this phenomenon, the distribution of the DNA inside the droplet was measured using confocal microscopy. The results indicated that the DNA was condensed mostly on the surface of the droplets. In the case of high concentration droplets, it formed a shell, whereas isolated islands were found for droplets of low DNA concentrations. Rheologic results indicate the formation of a hydro gel in the low concentration drops, whereas phase separation between the self-assembled DNA structures and the water phase occurred at higher concentration. PMID:16800691
Fang, Xiaohua; Li, Bingquan; Petersen, Eric; Seo, Young-Soo; Samuilov, Vladimir A; Chen, Yong; Sokolov, Jonathan C; Shew, Chwen-Yang; Rafailovich, Miriam H
We study the electronic properties of DNA by way of a tight-binding model applied to four particular DNA sequences. The charge transfer properties are presented in terms of localization lengths (crudely speaking, the length over which electrons travel). Various types of disorder, including random potentials, are employed to account for different real environments. We have performed calculations on poly(dG)-poly(dC), telomeric-DNA, random-ATGC DNA, and ?-DNA. We find that random and ?-DNA have localization lengths allowing for electron motion among a few dozen basepairs only. A novel enhancement of localization lengths is observed at particular energies for an increasing binary backbone disorder. We comment on the possible biological relevance of sequence-dependent charge transfer in DNA. PMID:16040753
Klotsa, Daphne; R�mer, Rudolf A.; Turner, Matthew S.
Polyplexes of poly(methylaminophosphazene): energetics of DNA melting.
The interaction of DNA with a synthetic biocompatible and biodegradable cationic polymer, poly(methylaminophosphazene) hydrochloride (PMAP�HCl), was investigated by high-sensitivity differential scanning calorimetry under conditions of strong and weak electrostatic interactions of the macroions. Thermodynamic parameters of the DNA double-helix melting were determined as a function of pH and the PMAP�HCl/DNA weight ratio. PMAP�HCL was shown to reveal two functions with respect to DNA: the polyelectrolyte function and the donor-acceptor one. The first function stabilizes the helical conformation of DNA, and the second one destabilizes it. The stabilizing effect of PMAP�HCl is of entropic origin, related to a displacement of mobile counterions from the DNA's nearest surroundings by the poly(methylaminophosphazene) charged groups. The donor-acceptor function of poly(methylaminophosphazene) dominates when its electrostatic interaction with DNA is either saturated (in the complex coacervate phase at high poly(methylaminophosphazene) concentrations) or completely suppressed (in a salt medium when the polycation carries a small charge). Under these conditions, poly(methylaminophosphazene) destabilizes DNA. It preferentially binds to the DNA coil form likely via the formation of multiple labile hydrogen bonds with the donor-acceptor groups of DNA. PMID:21830752
Burova, Tatiana V; Grinberg, Natalia V; Tur, Dzidra R; Papkov, Vladimir S; Dubovik, Alexander S; Grinberg, Valerij Y; Khokhlov, Alexei R
DNA BARCODING Limitations of mitochondrial gene barcoding in Octocorallia
DNA BARCODING Limitations of mitochondrial gene barcoding in Octocorallia CATHERINE S. MCFADDEN and other mitochondrial genes will be ineffective DNA barcodes for anthozoan cnidarians has not been well of mitochondrial gene barcoding in the sub-class Octocorallia, a large, diverse, and ecologically important group
Benayahu, Yehuda
Technology Transfer Automated Retrieval System (TEKTRAN)
Methylation of DNA occurs at cytosines within CpG (cytosine-guanine) dinucleotides and is one of several epigenetic mechanisms that serve to establish and maintain tissue-specific patterns of gene expression. The methyl groups transferred in mammalian DNA methylation reactions are ultimately derived...
Character-based DNA barcoding allows discrimination of genera, species
Character-based DNA barcoding allows discrimination of genera, species and populations in Odonata J. Currently, phenetic approaches and tree-building methods have been used to define species boundaries taxonomic groups cannot be determined. As an alternative, DNA barcoding approaches can be `character based
DeSalle, Rob
Escherichia coli DnaB helicase-DnaC protein complex: allosteric effects of the nucleotides on the nucleic acid binding and the kinetic mechanism of NTP hydrolysis. 3.
Allosteric interactions between the DNA- and NTP-binding sites of the Escherichia coli DnaB helicase engaged in the DnaB-DnaC complex and the mechanism of NTP hydrolysis by the complex have been examined using the fluorescence titration, analytical ultracentrifugation, and rapid quench-flow technique. Surprisingly, the ssDNA affinity of the DnaB-DnaC complex is independent of the structure of the phosphate group of the cofactor bound to the helicase. Thus, the DnaC protein eliminates the antagonistic allosteric effect of NTP and NDP on the ssDNA affinity of the enzyme. The protein changes the engagement of the DNA-binding subsites of the helicase in interactions with the nucleic acid, depending on the structure of the phosphate group of the present nucleotide cofactor and profoundly affects the structure of the bound DNA. Moreover, the ssDNA affinity of the helicase in the DnaB-DnaC complex is under the control of the nucleotide-binding site of the DnaC protein. The protein does not affect the NTP hydrolysis mechanism of the helicase. Nevertheless, the rate of the chemical step is diminished in the DnaB-DnaC complex. In the tertiary DnaB-DnaC-ssDNA complex, the ssDNA changes the internal dynamics between intermediates of the pyrimidine cofactor, in a manner independent of the base composition of the DNA, while the hydrolysis step of the purine cofactor is specifically stimulated by the homoadenosine ssDNA. The significance of these results for functional activities of the DnaB-DnaC complex is discussed. PMID:19432487
Roychowdhury, Anasuya; Szymanski, Michal R; Jezewska, Maria J; Bujalowski, Wlodzimierz
DNA: structure, dense phases, charges, interactions
DNA: structure, dense phases, charges, interactions #12;Outline 1. DNA: structure, charges, dense phases 2. Counterion and DNA condensation 3. ES DNA-DNA interactions 4. DNA toroidal structures 5. Interactions of real DNA helices 6. DNA-DNA ES recognition 7. DNA melting in aggregates 8. Azimuthal
Potsdam, Universit�t
AID APE1 DNA DNA Jiangliang Xu ( ) AID APE1 DNA DNA Proceedings of the National APE1 APE1 CSR 25%DNA AID SHM APE1 #12; APE1 APE1 APE1 CSR AID SHM cMyc APEAID DNA APE1 CSR S DNA 3D APE1 DNA DNA DNA Ku80 APE1 S DNA APE1 AID Top1 DNA APE1 DNA CSR
Takada, Shoji
mtDNA Variation in Caste Populations of Andhra Pradesh, India.
Various anthropological analyses have documented extensive regional variation among populations on the subcontinent of India using morphological, protein, blood group, and nuclear DNA polymorphisms. These patterns are the ...
Bamshad, Michael; Fraley, Alexander E.; Crawford, Michael H.; Cann, Rebecca L.; Busi, Baskara R.; Naidu, J. M.; Jorde, Lynn B.
Conformational changes of the phenyl and naphthyl isocyanate-DNA adducts during DNA replication and by minor groove binding molecules
DNA lesions produced by aromatic isocyanates have an extra bulky group on the nucleotide bases, with the capability of forming stacking interaction within a DNA helix. In this work, we investigated the conformation of the 2?-deoxyadenosine and 2?-deoxycytidine derivatives tethering a phenyl or naphthyl group, introduced in a DNA duplex. The chemical modification experiments using KMnO4 and 1-cyclohexyl-3 -(2-morpholinoethyl) carbodiimide metho-p-toluenesulfonate have shown that the 2?-deoxycytidine lesions form the base pair with guanine while the 2?-deoxyadenosine lesions have less ability of forming the base pair with thymine in solution. Nevertheless, the kinetic analysis shows that these DNA lesions are compatible with DNA ligase and DNA polymerase reactions, as much as natural DNA bases. We suggest that the adduct lesions have a capability of adopting dual conformations, depending on the difference in their interaction energies between stacking of the attached aromatic group and base pairing through hydrogen bonds. It is also presented that the attached aromatic groups change their orientation by interacting with the minor groove binding netropsin, distamycin and synthetic polyamide. The nucleotide derivatives would be useful for enhancing the phenotypic diversity of DNA molecules and for exploring new non-natural nucleotides. PMID:23873956
Nakano, Shu-ichi; Uotani, Yuuki; Sato, Yuichi; Oka, Hirohito; Fujii, Masayuki; Sugimoto, Naoki
Molecular biology - Methylation talk between histones and DNA�
The addition of methyl groups to DNA or histones is a way to directly or indirectly silence gene expression. Although the two events are conceivably connected, they have always been studied separately. In his Perspective, ...
Bird, Adrian P
Original Article Using DNA to Test the Utility of
-tailed deer (Odocoileus hemionus sitkensis) during a 3-year study (2006�2008) in 3 watersheds in southeast The Wildlife Society. KEY WORDS Alaska, DNA, fecal pellets, Odocoileus hemionus sitkensis, pellet-group counts
Ickert-Bond, Steffi
Low-Dose Formaldehyde Delays DNA Damage Recognition and DNA Excision Repair in Human Cells
Objective Formaldehyde is still widely employed as a universal crosslinking agent, preservative and disinfectant, despite its proven carcinogenicity in occupationally exposed workers. Therefore, it is of paramount importance to understand the possible impact of low-dose formaldehyde exposures in the general population. Due to the concomitant occurrence of multiple indoor and outdoor toxicants, we tested how formaldehyde, at micromolar concentrations, interferes with general DNA damage recognition and excision processes that remove some of the most frequently inflicted DNA lesions. Methodology/Principal Findings The overall mobility of the DNA damage sensors UV-DDB (ultraviolet-damaged DNA-binding) and XPC (xeroderma pigmentosum group C) was analyzed by assessing real-time protein dynamics in the nucleus of cultured human cells exposed to non-cytotoxic (<100 ?M) formaldehyde concentrations. The DNA lesion-specific recruitment of these damage sensors was tested by monitoring their accumulation at local irradiation spots. DNA repair activity was determined in host-cell reactivation assays and, more directly, by measuring the excision of DNA lesions from chromosomes. Taken together, these assays demonstrated that formaldehyde obstructs the rapid nuclear trafficking of DNA damage sensors and, consequently, slows down their relocation to DNA damage sites thus delaying the excision repair of target lesions. A concentration-dependent effect relationship established a threshold concentration of as low as 25 micromolar for the inhibition of DNA excision repair. Conclusions/Significance A main implication of the retarded repair activity is that low-dose formaldehyde may exert an adjuvant role in carcinogenesis by impeding the excision of multiple mutagenic base lesions. In view of this generally disruptive effect on DNA repair, we propose that formaldehyde exposures in the general population should be further decreased to help reducing cancer risks. PMID:24722772
Luch, Andreas; Frey, Flurina C. Clement; Meier, Regula; Fei, Jia; Naegeli, Hanspeter
Handbook on Group Counseling and Group Guidance.
ERIC Educational Resources Information Center
This handbook was developed to provide useful information to help the school counselor identify and apply appropriate methods to "reach" every student. The first section presents an overview of group counseling. It focuses on group counseling, group dynamics, benefits of group counseling, group development, issues in group counseling, group�
Houston Independent School District, TX.
DNA Isolation and Amplification from Cacti
The cacti family is a morphologically heterogeneous group comprising 100 genera and about 1500 species (Hernandez and Barcenas, 1996). With the exception of one genus, all members of this family are native to America (Hernandez and Barcenas, 1996). There are three subfamilies, Opuntioideae, Cactoideae, and Pereskioideae (Gibson and Nobel, 1986). DNA isolation from cacti is notoriously difficult because they contain
Marlene de la Cruz; Fabiola Ramirez; Hector Hernandez
DNA Barcodes for Nearctic Auchenorrhyncha (Insecta: Hemiptera)
Background Many studies have shown the suitability of sequence variation in the 5? region of the mitochondrial cytochrome c oxidase I (COI) gene as a DNA barcode for the identification of species in a wide range of animal groups. We examined 471 species in 147 genera of Hemiptera: Auchenorrhyncha drawn from specimens in the Canadian National Collection of Insects to assess the effectiveness of DNA barcoding in this group. Methodology/Principal Findings Analysis of the COI gene revealed less than 2% intra-specific divergence in 93% of the taxa examined, while minimum interspecific distances exceeded 2% in 70% of congeneric species pairs. Although most species are characterized by a distinct sequence cluster, sequences for members of many groups of closely related species either shared sequences or showed close similarity, with 25% of species separated from their nearest neighbor by less than 1%. Conclusions/Significance This study, although preliminary, provides DNA barcodes for about 8% of the species of this hemipteran suborder found in North America north of Mexico. Barcodes can enable the identification of many species of Auchenorrhyncha, but members of some species groups cannot be discriminated. Future use of DNA barcodes in regulatory, pest management, and environmental applications will be possible as the barcode library for Auchenorrhyncha expands to include more species and broader geographic coverage. PMID:25004106
Foottit, Robert G.; Maw, Eric; Hebert, P. D. N.
Before the routine use of DNA profiling, blood typing was an important forensic tool. However, blood typing was not very discriminating. For example, roughly 30% of the United States population has type A-positive blood. Therefore, if A-positive blood were found at a crime scene, it could have come from 30% of the population. DNA profiling has a much better ability for discrimination. Forensic laboratories no longer routinely determine blood type. If blood is found at a crime scene, DNA profiling is performed. From Jeffrey's discovery of DNA fingerprinting to the development of PCR of STRs to the formation of DNA databases, our knowledge of DNA and DNA profiling have expanded greatly. Also, the applications for which we use DNA profiling have increased. DNA profiling is not just used for criminal case work, but it has expanded to encompass paternity testing, disaster victim identification, monitoring bone marrow transplants, detecting fetal cells in a mother's blood, tracing human history, and a multitude of other areas. The future of DNA profiling looks expansive with the development of newer instrumentation and techniques. PMID:22693781
McDonald, Jessica; Lehman, Donald C
lambda DNA Fingerprinting Simulation
NSDL National Science Digital Library
The purpose of this lab activity is to demonstrate (through simulation) how DNA fingerprinting (or DNA profiling) might be used to solve a crime. Learners perform restriction digests on DNA samples from four individuals, and then search for similarities between the individuals by running the restriction fragments on an electrophoresis gel. This activity does not do a true DNA fingerprint. It simulates two of the three steps of DNA fingerprinting: restriction of DNA sample and separation by electrophoresis. This activity does not make use of the third step, the radioactive probes. In order to make DNA fingerprinting affordable, lambda DNA is used instead of plasmids. This means that the instructor has to switch the labels on the samples given to the learners. What is labeled DNA is actually the different restriction enzymes and what is labeled restriction enzyme is the lambda DNA. Although there is some deception on the part of the instructor, learners are able to do a restriction digest that simulates a crime scene which adds interest for the learner.
Thomas J. Conley
Using optical tweezers to study protein-DNA interactions
NASA Astrophysics Data System (ADS)
Mechanical manipulation of single DNA molecules can provide novel information about protein-DNA interactions. Here we review two examples studied by our group. First, we have studied the forced unraveling of nucleosomes assembled on heterogeneous DNA using core histones, the histone chaperone NAP-1, and ATP-dependent chromatin assembly and remodeling factor (ACF). We measure abrupt events releasing ~55 to 95 base pairs of DNA, which are attributable to non-equilibrium unraveling of individual nucleosomes. Wide variations observed in the unraveling force and sudden DNA re-wrapping events may have an important regulatory influence on DNA directed biochemical processes. Second, we have studied the mechanics and dynamics of single DNA looping and cleavage by "two-site" restriction enzymes. Cleavage is measured as a function of DNA tension, incubation time, and enzyme concentration, distinguishing enzymes that require DNA looping from ones that do not. Forced disruption of fixed DNA loops formed in the absence of Mg2+ is observed, allowing the distribution of number of loops, loop length, and disruption force to be measured as a function of time, DNA tension, and ionic conditions.
Smith, Douglas E.; Gemmen, Gregory J.; Millin, Rachel; Rickgauer, John P.; Schweitzer, Allan L.; Fuller, Derek N.
Detection and quantitation of single nucleotide polymorphisms, DNA sequence variations, DNA mutations, DNA damage and DNA mismatches
DNA mutation binding proteins alone and as chimeric proteins with nucleases are used with solid supports to detect DNA sequence variations, DNA mutations and single nucleotide polymorphisms. The solid supports may be flow cytometry beads, DNA chips, glass slides or DNA dips sticks. DNA molecules are coupled to solid supports to form DNA-support complexes. Labeled DNA is used with unlabeled DNA mutation binding proteins such at TthMutS to detect DNA sequence variations, DNA mutations and single nucleotide length polymorphisms by binding which gives an increase in signal. Unlabeled DNA is utilized with labeled chimeras to detect DNA sequence variations, DNA mutations and single nucleotide length polymorphisms by nuclease activity of the chimera which gives a decrease in signal.
McCutchen-Maloney, Sandra L. (Pleasanton, CA)
NASA Technical Reports Server (NTRS)
As a starting point, the group defined a primary goal of maintaining in flight a level of systemic oxygen transport capacity comparable to each individual's preflight upright baseline. The goal of maintaining capacity at preflight levels would seem to be a reasonable objective for several different reasons, including the maintenance of good health in general and the preservation of sufficient cardiovascular reserve capacity to meet operational demands. It is also important not to introduce confounding variables in whatever other physiological studies are being performed. A change in the level of fitness is likely to be a significant confounding variable in the study of many organ systems. The principal component of the in-flight cardiovascular exercise program should be large-muscle activity such as treadmill exercise. It is desirable that at least one session per week be monitored to assure maintenance of proper functional levels and to provide guidance for any adjustments of the exercise prescription. Appropriate measurements include evaluation of the heart-rate/workload or the heart-rate/oxygen-uptake relationship. Respiratory gas analysis is helpful by providing better opportunities to document relative workload levels from analysis of the interrelationships among VO2, VCO2, and ventilation. The committee felt that there is no clear evidence that any particular in-flight exercise regimen is protective against orthostatic hypotension during the early readaptation phase. Some group members suggested that maintenance of the lower body muscle mass and muscle tone may be helpful. There is also evidence that late in-flight interventions to reexpand blood volume to preflight levels are helpful in preventing or minimizing postflight orthostatic hypotension.
Blomqvist, Gunnar
Stepwise functionalization of ZnO nanotips with DNA.
A surface functionalization methodology for the development of ZnO nanotips biosensors that can be integrated with microelectronics was developed. Two types of long chain carboxylic acids linkers were employed for the functionalization of 0.5 mum thick MOCVD-grown ZnO nanotip films with single-stranded DNA (ssDNA), followed by hybridization with complementary ssDNA tagged with fluorescein. The ZnO functionalization strategy was developed for the fabrication of ZnO nanotips-linker-biomolecule films integrated with bulk acoustic wave (BAW) biosensors, and it involved three main steps. First, 16-(2-pyridyldithiol)hexadecanoic acid or N-(15-carboxypentadecanoyloxy)succinimide, both bifunctional C16 carboxylic acids, were bound to ZnO nanotip films through the COOH group, leaving at the opposite end of the alkyl chain a thiol group protected as a 2-pyridyl disulfide, or a carboxylic group protected as a N-succinimide, respectively. In the second step, ssDNA was covalently linked to each type of ZnO-linker film: the 2-pyridyl disulfide end group was substituted with 16 bases 5'-thiol-modified DNA (SH-ssDNA), and the N-succinimide ester end group was substituted with 16 bases 5'-amino-modified DNA (NH(2)-ssDNA). In the third step, the DNA-functionalized ZnO nanotip films were hybridized with complementary 5'-fluorescein ssDNA. The surface-modified ZnO nanotip films were characterized after each step by FT-IR-ATR, fluorescence emission spectroscopy, and fluorescence microscopy. This functionalization approach allows sequential reactions on the surface and, in principle, can be extended to numerous other molecules and biomolecules. PMID:19199718
Taratula, Olena; Galoppini, Elena; Mendelsohn, Richard; Reyes, Pavel Ivanoff; Zhang, Zheng; Duan, Ziqing; Zhong, Jian; Lu, Yicheng
A search for specificity in DNA-drug interactions.
The GRID force field and a principal component analysis have been used in order to predict the interactions of small chemical groups with all 64 different triplet sequences of B-DNA. Factors that favor binding to guanine-cytosine base pairs have been identified, and a dictionary of ligand groups and their locations is presented as a guide to the design of specific DNA ligands. PMID:7918250
Cruciani, G; Goodford, P J
Crosslinking of DNA repair and replication proteins to DNA in cells treated with 6-thioguanine and UVA
The DNA of patients taking immunosuppressive and anti-inflammatory thiopurines contains 6-thioguanine (6-TG) and their skin is hypersensitive to ultraviolet A (UVA) radiation. DNA 6-TG absorbs UVA and generates reactive oxygen species that damage DNA and proteins. Here, we show that the DNA damage includes covalent DNA�protein crosslinks. An oligonucleotide containing a single 6-TG is photochemically crosslinked to cysteine-containing oligopeptides by low doses of UVA. Crosslinking is significantly more efficient if guanine sulphonate (GSO3)�an oxidized 6-TG and a previously identified UVA photoproduct�replaces 6-TG, suggesting that GSO3 is an important reaction intermediate. Crosslinking occurs via oligopeptide sulphydryl and free amino groups. The oligonucleotide�oligopeptide adducts are heat stable but are partially reversed by reducing treatments. UVA irradiation of human cells containing DNA 6-TG induces extensive heat- and reducing agent-resistant covalent DNA�protein crosslinks and diminishes the recovery of some DNA repair and replication proteins from nuclear extracts. DNA�protein crosslinked material has an altered buoyant density and can be purified by banding in cesium chloride (CsCl) gradients. PCNA, the MSH2 mismatch repair protein and the XPA nucleotide excision repair (NER) factor are among the proteins detectable in the DNA-crosslinked material. These findings suggest that the 6-TG/UVA combination might compromise DNA repair by sequestering essential proteins. PMID:21398635
Gueranger, Quentin; Kia, Azadeh; Frith, David; Karran, Peter
Persistence of cccDNA during the natural history of chronic hepatitis B and decline during adefovir dipivoxil therapy 1 1 In addition to the Adefovir Dipivoxil cccDNA Study Group investigators, the authors thank the study site personnel and patients who participated in this study; Huiling Yang, Manuel Tsiang, Anant Jain, Craig James, Rick Fallis, John Fry, and Michael Wulfsohn of Gilead Sciences for their support and advice during this study; Hans Will and Maura Dandri for critical review of this manuscript; and Brian Sutton and Jennifer Elder of Inveresk (Cary, North Carolina) for advice and independent validation of statistical analyses. P.M. represents the Adefovir Dipivoxil cccDNA Study Group, which also includes the following clinical investigators: Peter Buggisch (Universit�tskrankenhaus Hamburg-Eppendorf, Germany); Ian Kronberg (Western Hospital, Melbourne, Australia); William Sievert (Monash University and Medical Centre, Melbourne, Australia); Stanislas Pol (H�pital Necker, Pa
Background & Aims: Hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) is a unique episomal replicative intermediate responsible for persistent infection of hepatocytes. Technical constraints have hampered the direct study of cccDNA maintenance and clearance mechanisms in patients. The aim of this study was to develop a sensitive and specific assay for quantifying cccDNA in biopsy samples from chronic
Scott Bowden; Stephen Locarnini; Karsten Wursthorn; Jorg Petersen; George Lau; Christian Trepo; Patrick Marcellin; Zachary Goodman; William E. Delaney; Shelly Xiong; Carol L. Brosgart; Craig S. Gibbs; Fabien Zoulim
NSDL National Science Digital Library
This site offers four interactive modules that investigate the applications of DNA science to improve medicine and society. The modules focus on forensic analysis, such as DNA fingerprinting, solving the mystery of Anastasia Romanov, and using DNA to determine human origins, as well as using DNA to advance human health. Each module is subdivided into additional parts. These parts include videos of scientists, computer simulations, and tutorials. One tutorial covers The Innocence Project,a non-profit legal clinic that uses DNA evidence to help convicted criminals prove their innocence. In one simulation, visitors can match DNA samples between a convicted criminal and those collected from the scene of the crime. Copyright 2005 Eisenhower National Clearinghouse
Dolan DNA Learning Center. Cold Spring Harbor Laboratory
NSDL National Science Digital Library
This four-part, interactive module treats teachers to a direct look at the people involved in breaking the mystery behind the code of life. The modules are arranged by topics that focus on how the structure of DNA was determined, how DNA is copied, how DNA is read, and how DNA is controlled. Each module is subdivided into additional parts. These parts include images of scientists who contributed to the history of DNA discoveries. By clicking on the images, teachers are taken to a new window to watch short videos by or about the scientists. Teachers can also click on links to computer simulations, such as an activity to create a model of DNA using cardboard cutouts, just as James Watson did. Copyright 2005 Eisenhower National Clearinghouse
Dolan DNA Learning Center. Cold Spring Harbor Laboratory
NSDL National Science Digital Library
By building their own DNA model in this OLogy activity, kids learn about the unique genetic code that's found in every cell of their bodies. The activity begins with a brief look at how all living things are made of cells, and that what makes them unique is DNA. Then, using toothpicks, colored paper, and other common supplies, students create a 3-D model of DNA and "do the DNA twist" to make it look like a double spiral. Interspersed throughout the activity are kid-friendly descriptions of the discovery of DNA and where it's found. The experiment ends with additional challenges for students, such as making a DNA mobile with pipe cleaners or some other flexible material.
DNA BARCODING Mitochondrial DNA barcoding detects some species that
DNA BARCODING Mitochondrial DNA barcoding detects some species that are real, and some; Nymphalidae) difficult to determine. We use mitochondrial DNA (mtDNA) barcoding, nuclear sequences. Although earlier biosystematic studies based on morphology described only four species, mtDNA barcoding
Dasmahapatra, Kanchon
Preparation of Plasmid DNA Preparation of PCR DNA
Abstract Preparation of Plasmid DNA Preparation of PCR DNA Design of DNA Chip Methods, the appropriate DNA has been extracted and amplified before being spotted on a microarray chip. This experiment Polymerase Chain Reaction. Although PCR is a very acceptable method for obtaining large quantities of DNA
Campbell, A. Malcolm
Electrochemical DNA Hybridization Detection Using DNA Dohyoung Kwon,a
Full Paper Electrochemical DNA Hybridization Detection Using DNA Cleavage Dohyoung Kwon,a Kyuwon method for detection of DNA hybridization using enzymatic cleavage. The strategy is based on that S1 nuclease is able to specifically cleave only single strand DNA, but not double strand DNA. The capture
Kwak, Juhyoun
DNA repair in Chromobacterium violaceum.
Chromobacterium violaceum is a Gram-negative beta-proteobacterium that inhabits a variety of ecosystems in tropical and subtropical regions, including the water and banks of the Negro River in the Brazilian Amazon. This bacterium has been the subject of extensive study over the last three decades, due to its biotechnological properties, including the characteristic violacein pigment, which has antimicrobial and anti-tumoral activities. C. violaceum promotes the solubilization of gold in a mercury-free process, and has been used in the synthesis of homopolyesters suitable for the production of biodegradable polymers. The complete genome sequence of this organism has been completed by the Brazilian National Genome Project Consortium. The aim of our group was to study the DNA repair genes in this organism, due to their importance in the maintenance of genomic integrity. We identified DNA repair genes involved in different pathways in C. violaceum through a similarity search against known sequences deposited in databases. The phylogenetic analyses were done using programs of the PHILYP package. This analysis revealed various metabolic pathways, including photoreactivation, base excision repair, nucleotide excision repair, mismatch repair, recombinational repair, and the SOS system. The similarity between the C. violaceum sequences and those of Neisserie miningitidis and Ralstonia solanacearum was greater than that between the C. violaceum and Escherichia coli sequences. The peculiarities found in the C. violaceum genome were the absence of LexA, some horizontal transfer events and a large number of repair genes involved with alkyl and oxidative DNA damage. PMID:15100997
Duarte, F�bio Teixeira; Carvalho, Fab�ola Marques de; Bezerra e Silva, Uaska; Scortecci, K�tia Castanho; Blaha, Carlos Alfredo Galindo; Agnez-Lima, Lucymara Fassarella; Batistuzzo de Medeiros, Silvia Regina
(2) DNA O(n^5) Quorum-Sensing Lux
- 1 - ( ) ( ) DNA RNA DNA RNA DNA DNA 2 DNA #12;- 2 - 17 6 (1) (2) DNA O(n^5) (3) Quorum-Sensing Lux (4) (5) LMNtal ambient LMNtal (1) (2) DNA (3) DNA (4) DNA (5) DNA (1) DNA ANP-96 (Precision System Science ) (2) RTRACS DNA RTRACS (3) in vivo in vivo (4) DNA trans cis 1/10 (5) DNA-PNA DNA DNA DNA DNA DNA
Hagiya, Masami
NSDL National Science Digital Library
Many students find studying DNA difficult because it is so small that the concepts are quite abstract. This lab enables students to work with DNA concretely by easily isolating chromosomal DNA using the same basic tools and methods that scientists use. The lab is a good introduction to using pipets and to using the metric system. If the chemistry of the solutions is taught it is also a great practical application.
BEGIN:VCARD VERSION:2.1 FN:Kate Dollard N:Dollard; Kate ORG:Cambridge Rindge and Latin REV:2005-04-12 END:VCARD
NSDL National Science Digital Library
This virtual lab from the Genetic Science Learning Center at the University of Utah provides a simple overview of DNA extraction, including what it's used for, illustrations, and an activity using cheek cells and laboratory equipment to isolate DNA. The lab is followed by a classroom activity that allows students and teachers to Extract DNA from Anything Living, using household items like spinach but not little sister's big toe.
NSDL National Science Digital Library
This laboratory exercise is designed to show learners how DNA can be extracted from a chunk of thymus (sweetbread) or liver. This experiment requires the use of a centrifuge (not included in cost of materials). Use this experiment to supplement any unit on genetics and to demonstrate how scientists study DNA. Adult supervision is recommended. This resource guide includes tips and suggestions for instructors as well as other DNA extraction experiments and a chart for learners to answer questions.
Lana Hays
The base sequence in nucleic acids encodes substantial structural and functional information into the biopolymer. This encoded information provides the basis for the tailoring and assembly of DNA machines. A DNA machine is defined as a molecular device that exhibits the following fundamental features. (1) It performs a fuel-driven mechanical process that mimics macroscopic machines. (2) The mechanical process requires an energy input, "fuel." (3) The mechanical operation is accompanied by an energy consumption process that leads to "waste products." (4) The cyclic operation of the DNA devices, involves the use of "fuel" and "anti-fuel" ingredients. A variety of DNA-based machines are described, including the construction of "tweezers," "walkers," "robots," "cranes," "transporters," "springs," "gears," and interlocked cyclic DNA structures acting as reconfigurable catenanes, rotaxanes, and rotors. Different "fuels", such as nucleic acid strands, pH (H?/OH?), metal ions, and light, are used to trigger the mechanical functions of the DNA devices. The operation of the devices in solution and on surfaces is described, and a variety of optical, electrical, and photoelectrochemical methods to follow the operations of the DNA machines are presented. We further address the possible applications of DNA machines and the future perspectives of molecular DNA devices. These include the application of DNA machines as functional structures for the construction of logic gates and computing, for the programmed organization of metallic nanoparticle structures and the control of plasmonic properties, and for controlling chemical transformations by DNA machines. We further discuss the future applications of DNA machines for intracellular sensing, controlling intracellular metabolic pathways, and the use of the functional nanostructures for drug delivery and medical applications. PMID:24647836
Wang, Fuan; Willner, Bilha; Willner, Itamar
DNA methylation patterns provide insight into epigenetic regulation in the Pacific oyster (Crassostrea gigas)
BACKGROUND: DNA methylation is an epigenetic mechanism with important regulatory functions in animals. While the mechanism itself is evolutionarily ancient, the distribution and function of DNA methylation is diverse both within and among phylogenetic groups. Although DNA methylation has been well studied in mammals, there are limited data on invertebrates, particularly molluscs. Here we characterize the distribution and investigate potential
Mackenzie R Gavery; Steven B Roberts
DNA as a Binary Code: How the Physical Structure of Nucleotide Bases Carries Information
NSDL National Science Digital Library
The DNA triplet code also functions as a binary code. Because double-ring compounds cannot bind to double-ring compounds in the DNA code, the sequence of bases classified simply as purines or pyrimidines can encode for smaller groups of possible amino acids. This is an intuitive approach to teaching the DNA code.
Gary McCallister
DNA Modification Methylase Activity of Escherichia coli Restriction Endonucleases K and P
The highly purified restriction endonucleases of E. coli K and coliphage P1 transfer methyl groups from S-adenosylmethionine to adenine residues of unmodified DNA. Incubation of unmodified DNA with endonucleases K or P and S-adenosylmethionine renders the DNA resistant to restriction. The enzymes, therefore, have both restriction endonuclease and modification methylase activities.
Allan Haberman; Janet Heywood; Matthew Meselson
Analysis of Oral Papillomas, Leukoplakias, and Invasive Carcinomas for Human Papillomavirus Type Related DNA
Five papillomas, five leukoplakias, and six carcinomas were investigated for the presence of papillomavirus group-specific antigens and viral DNA. Viral proteins were identified with genus-specific papillomavirus antibodies. Cloned human papillomavirus (HPV) 11 and 16 DNA were used as probes in Southern blot hybridization at conditions of different stringency in order to determine viral DNA. Four of five papillomas, four of
Thomas L�ning; Hans Ikenberg; J�rgen Becker; Lutz Gissmann; Ilsetraut Hoepfer; Harald zur Hausen
BAYESIAN MODELS FOR DNA SEQUENCING Nicholas M. Haan and Simon J. Godsill
BAYESIAN MODELS FOR DNA SEQUENCING Nicholas M. Haan and Simon J. Godsill Signal Processing Group for the objective in- corporation of information. In this paper, we develop a Bayesian model for DNA sequencing- cuss the use of the Bayesian paradigm for rigorous inference from DNA sequencing data where
Godsill, Simon
SEQUENTIAL METHODS FOR DNA SEQUENCING Nicholas M. Haan and Simon J. Godsill
SEQUENTIAL METHODS FOR DNA SEQUENCING Nicholas M. Haan and Simon J. Godsill Signal Processing Group for determining the letters of our genetic code, known as DNA sequencing, currently depend on clever use to encode the genetic information within each of us. For our purposes, DNA can be thought of as a sequence
Godsill, Simon
DNA as a Binary Code: How the Physical Structure of Nucleotide Bases Carries Information
ERIC Educational Resources Information Center
The DNA triplet code also functions as a binary code. Because double-ring compounds cannot bind to double-ring compounds in the DNA code, the sequence of bases classified simply as purines or pyrimidines can encode for smaller groups of possible amino acids. This is an intuitive approach to teaching the DNA code. (Contains 6 figures.)
McCallister, Gary
ThefirstreportofthepossibleexistenceofDNA, homologoustomitochondrialDNA(mtDNA)but
of functional mitochondrial genes from mitochondrion to nucleus. One of the underlying causes of this process is thought to be a `gene transfer ratchet'14. Because the rate of DNA transfer from mitochondrion to nucleus is thought to be much greater than in the reverse direction17, a net movement of genes from mitochondrion
Bensasson, Douda
During this year we performed two major projects: I. We developed a detailed theoretical model which complements our experiments on surface DNA electrophoresis. We found that it was possible to enhance the separation of DNA chains by imposing a chemical nanoscale pattern on the surface. This approach utilized the surface interaction effect of the DNA chains with the substrate and is a refinement to our previous method in which DNA chains were separated on homogeneous flat surfaces. By introducing the nano-patterns on the surface, the conformational changes of DNA chains of different lengths can be amplified, which results in the different friction strengths with the substrate surface. Our results also show that, when compared to the DNA electrophoresis performed on homogeneous flat surfaces, nanopatterned surfaces offer a larger window in choosing different surface interactions to achieve separation. II. In collaboration with a large international manufacturer of skin care products we also embarked on a project involving photo toxicity of titanium dioxide nanoparticles, which are a key ingredient in sunscreen and cosmetic lotions. The results clearly implicated the nanoparticles in catalyzing damage to chromosomal DNA. We then used this knowledge to develop a polymer/anti-oxidant coating which prevented the photocatalytic reaction on DNA while still retaining the UV absorptive properties of the nanoparticles. The standard gel electrophoresis was not sufficient in determining the extent of the DNA damage. The conclusions of this study were based predominantly on analysis obtained with the surface electrophoresis method.
NSDL National Science Digital Library
Making DNA Jewelry Models is a portion of a unit on molecular genetics. Using the directions for this hands-on activity/lab helps students construct a model of DNA to learn DNA structure and decode it to better understand protein synthesis. They also have an actual badge of their DNA literacy to wear or use. Whether a key ring, earrings, bracelet, or necklace, students from fourth grade through adult can do and enjoy this activity. (Even visually impaired students made a model using larger beads.)
BEGIN:VCARD VERSION:2.1 FN:Catherine Sheils Ross N:Sheils Ross; Catherine ORG:Berkley High School (retired-6/98) REV:2005-04-09 END:VCARD
NASA Astrophysics Data System (ADS)
DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve it analytically in the case of identical binding. We uncover a switchlike transition between looped and unlooped phases and identify the key parameters that control this transition. Our results establish the basis for the quantitative understanding of fundamental cellular processes like DNA recombination, gene silencing, and telomere maintenance.
Vilar, Jose M. G.; Saiz, Leonor
DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve it analytically in the case of identical binding. We uncover a switch-like transition between looped and unlooped phases and identify the key parameters that control this transition. Our results establish the basis for the quantitative understanding of fundamental cellular processes like DNA recombination, gene silencing, and telomere maintenance.
Jose M. G. Vilar; Leonor Saiz
NSDL National Science Digital Library
The Southwest Center for Microsystems Education is a Regional Advanced Technology Education Center funded in part by the National Science Foundation. These resources provide an overview on the topic of DNA. Users will learn the role of DNA as genetic material, the molecular components of DNA and the structure and replication of DNA. A comprehensive PowerPoint presentation is included along with instructor and participant guides. Visitors are encouraged to create an account and log in in order to access the full set of resources.
DNA sequence recognition by bispyrazinonaphthalimides antitumor agents.
Bifunctional DNA intercalating agents have long attracted considerable attention as anticancer agents. One of the lead compounds in this category is the dimeric antitumor drug elinafide, composed of two tricyclic naphthalimide chromophores separated by an aminoalkyl linker chain optimally designed to permit bisintercalation of the drug into DNA. In an effort to optimize the DNA recognition capacity, different series of elinafide analogues have been prepared by extending the surface of the planar drug chromophore which is important for DNA sequence recognition. We report here a detailed investigation of the DNA sequence preference of three tetracyclic monomeric or dimeric pyrazinonaphthalimide derivatives. Melting temperature measurements and surface plasmon resonance (SPR) studies indicate that the dimerization of the tetracyclic planar chromophore considerably augments the affinity of the drug for DNA, polynucleotides, or hairpin oligonucleotides and promotes selective interaction with G.C sites. The (CH(2))(2)NH(CH(2))(3)NH(CH(2))(2) connector stabilizes the drug-DNA complexes. The methylation of the two nitrogen atoms of this linker chain reduces the binding affinity and increases the dissociation rates of the drug-DNA complexes by a factor of 10. DNase I footprinting experiments were used to investigate the sequence selectivity of the drugs, demonstrating highly preferential binding to G.C-rich sequences. It also served to select a high-affinity site encompassing the sequence 5'-GACGGCCAG which was then introduced into a biotin-labeled hairpin oligonucleotide to accurately measure the binding parameters by SPR. The affinity constant of the unmethylated dimer for this sequence is 500 times higher than that of the monomer compound and approximately 10 times higher than that of the methylated dimer. The DNA groove accessibility was also probed with three related oligonucleotides carrying G --> c(7)G, G --> I, and C --> M substitutions. The level of drug binding to the two hairpin oligonucleotides containing 7-deazaguanine (c(7)G) or 5-methylcytosine (M) residues is unchanged or only slightly reduced compared to that of the unmodified target. In contrast, incorporation of inosine (I) residues considerably decreases the extent of drug binding or even abolishes the interaction as is the case with the monomer. The pyrazinonaphthalimide derivatives are thus much more sensitive to the deletion of the exocyclic guanine 2-amino group exposed in the minor groove of the duplex than to the modification of the major groove elements. The complementary SPR footprinting methodology combining site selection and quantitative DNA affinity analysis constitutes a reliable method for dissecting the DNA sequence selectivity profile of reversible DNA binding small molecules. PMID:14529286
Carrasco, Carolina; Joubert, Alexandra; Tardy, Christelle; Maestre, Nicolas; Cacho, Monica; Bra�a, Miguel F; Bailly, Christian
In the 1960s, I developed methods for directly visualizing DNA and DNA-protein complexes using an electron microscope. This made it possible to examine the shape of DNA and to visualize proteins as they fold and loop DNA. Early applications included the first visualization of true nucleosomes and linkers and the demonstration that repeating tracts of adenines can cause a curvature in DNA. The binding of DNA repair proteins, including p53 and BRCA2, has been visualized at three- and four-way junctions in DNA. The trombone model of DNA replication was directly verified, and the looping of DNA at telomeres was discovered. PMID:24005675
Griffith, Jack D.
DNA Timeline: A Scavenger Hunt
NSDL National Science Digital Library
This is a DNA timeline to illustrate the discovery of DNA. There is also some resources to get a brief understanding of DNA, then a song to reinforce your learning of DNA. Print out this worksheet to use while reading the DNA timeline website. Worksheet DNA timeline worksheet to print This is the website to use while filling out the DNA timeline worksheet. DNA timeline website writeInsertLink('projectBody','DNA timeline website'); After accessing this page, you need to go to 'timeline' to begin the assignment. Print this worksheet Finding the Structure: pieces of the ...
Mrs. Clemons
SUMMARY: By catalyzing the joining of breaks in the phosphodiester backbone of duplex DNA, DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. Three related classes of ATP-dependent DNA ligase are readily apparent in eukaryotic cells. Enzymes of each class comprise catalytic and non-catalytic domains together with additional domains of varying function. DNA
Ina V Martin; Stuart A MacNeill
Restriction Enzymes and DNA Fingerprinting
NSDL National Science Digital Library
The discovery of restriction enzymes and their applications in DNA analysis has proven to be essential for biologists and chemists. This lesson focuses on restriction enzymes and their applications to DNA analysis and DNA fingerprinting. Use this lesson and its associated activity in conjunction with biology lessons on DNA analysis and DNA replication.
National Science Foundation GK-12 and Research Experience for Teachers (RET) Programs,
Intercalation of antitumor drug doxorubicin and its analogue by DNA duplex: structural features and biological implications.
The intercalation of antitumor drug doxorubicin (DOX) and its analogue N-(trifluoroacetyl) doxorubicin (FDOX) with DNA duplex was investigated, using FTIR, CD, fluorescence spectroscopic methods and molecular modeling. Both DOX and FDOX were intercalated into DNA duplex with the free binding energy of -4.99 kcal for DOX-DNA and -4.92 kcal for FDOX-DNA adducts and the presence of H-bonding network between doxorubicin NH2 group and cytosine-19. Spectroscopic results showed FDOX forms more stable complexes than DOX with KDOX-DNA=2.5(� 0.5)� 10(4)M(-1) and KFDOX-DNA=3.4(� 0.7)� 10(4)M(-1). The number of drug molecules bound per DNA (n) was 1.2 for DOX and 0.6 for FDOX. Major alterations of DNA structure were observed by DOX intercalation with a partial B to A-DNA transition, while no DNA conformational changes occurred upon FDOX interaction. This study further confirms the importance of unmodified daunosamine amino group for optimal interactions with DNA. The results of in vitro MTT assay carried out on SKC01 colon carcinoma corroborate the observed DNA interactions. Such DNA structural changes can be related to doxorubicin antitumor activity, which prevents DNA duplication. PMID:24560949
Agudelo, Daniel; Bourassa, Philippe; B�rub�, Gervais; Tajmir-Riahi, Heidar-Ali
A new structural insight into XPA�DNA interactions
XPA (xeroderma pigmentosum group A) protein is an essential factor for NER (nucleotide excision repair) which is believed to be involved in DNA damage recognition/verification, NER factor recruiting and stabilization of repair intermediates. Past studies on the structure of XPA have focused primarily on XPA interaction with damaged DNA. However, how XPA interacts with other DNA structures remains unknown though recent evidence suggest that these structures could be important for its roles in both NER and non-NER activities. Previously, we reported that XPA recognizes undamaged DNA ds/ssDNA (double-strand/single-strandDNA) junctions with a binding affinity much higher than its ability to bind bulky DNA damage. To understand how this interaction occurs biochemically we implemented a structural determination of the interaction using a MS-based protein footprinting method and limited proteolysis. By monitoring surface accessibility of XPA lysines to NHS-biotin modification in the free protein and the DNA junction-bound complex we show that XPA physically interacts with the DNA junctions via two lysines, K168 and K179, located in the previously known XPA(98�219) DBD (DNA-binding domain). Importantly, we also uncovered new lysine residues, outside of the known DBD, involved in the binding. We found that residues K221, K222, K224 and K236�in the C-terminal domain are involved in DNA binding. Limited proteolysis analysis of XPA�DNA interactions further confirmed this observation. Structural modelling with these data suggests a clamp-like DBD for the XPA binding to ds/ssDNA junctions. Our results provide a novel structure-function view of XPA�DNA junction interactions. PMID:25385088
Hilton, Benjamin; Shkriabai, Nick; Musich, Phillip�R.; Kvaratskhelia, Mamuka; Shell, Steven; Zou, Yue
[Study on the interaction of cordycepin and DNA].
The absorbance, fluorescence and Scatchard plots methods as well as the effect of phosphate group on the fluorescence intensity of the cordycepin-DNA-EB system were used to study the interaction of the antitumor compound cordycepin and DNA. It is obvious tiat there is hyperchromic effect and hypochromic effect with slight red shift on the subtracted UV spectrum. It proves that the adenine base of cordycepin can be inserted into the double-helix of DNA. The results of the fluorescence intensity that decreases after increases with a little blue shift on the fluorescence spectrum also proved this. At the same time the phosphate can affect the cordycepin-DNA-EB system. Finally that the result depended on the Scatchard equation indicates that cordycepin reacts electrostatically on phosphate backbone of DNA. There also exists an intercalation into the double-helix of DNA. PMID:15766091
Peng, Jun-feng; Ling, Jian-ya; Zhang, Han-xing; Zhang, Chang-kai
African Mitochondrial DNA Subhaplogroups and Peripheral Neuropathy during Antiretroviral Therapy
Susceptibility to peripheral neuropathy during antiretroviral therapy with nucleoside reverse transcriptase inhibitors (NRTIs) was previously associated with a European mitochondrial DNA (mtDNA) haplogroup among non-Hispanic white persons. To determine if NRTI-associated peripheral neuropathy was related to mtDNA variation in non-Hispanic black persons, we sequenced mtDNA of participants from AIDS Clinical Trials Group study 384. Of 156 non-Hispanic blacks with genomic data, 51 (33%) developed peripheral neuropathy. In a multivariate model, African mtDNA subhaplogroup L1c was an independent predictor of peripheral neuropathy (OR=3.7, 95% CI 1.1-12.0). An African mtDNA subhaplogroup is for the first time implicated in susceptibility to NRTI-associated toxicity. PMID:20402593
Canter, Jeffrey A.; Robbins, Gregory K.; Selph, Doug; Clifford, David B.; Kallianpur, Asha R.; Shafer, Robert; Levy, Shawn; Murdock, Deborah G.; Ritchie, Marylyn D.; Haas, David W.; Hulgan, Todd
DNA methyltransferase 1 mutations and mitochondrial pathology: is mtDNA methylated?
Autosomal dominant cerebellar ataxia-deafness and narcolepsy (ADCA-DN) and Hereditary sensory neuropathy with dementia and hearing loss (HSN1E) are two rare, overlapping neurodegenerative syndromes that have been recently linked to allelic dominant pathogenic mutations in the DNMT1 gene, coding for DNA (cytosine-5)-methyltransferase 1 (DNMT1). DNMT1 is the enzyme responsible for maintaining the nuclear genome methylation patterns during the DNA replication and repair, thus regulating gene expression. The mutations responsible for ADCA-DN and HSN1E affect the replication foci targeting sequence domain, which regulates DNMT1 binding to chromatin. DNMT1 dysfunction is anticipated to lead to a global alteration of the DNA methylation pattern with predictable downstream consequences on gene expression. Interestingly, ADCA-DN and HSN1E phenotypes share some clinical features typical of mitochondrial diseases, such as optic atrophy, peripheral neuropathy, and deafness, and some biochemical evidence of mitochondrial dysfunction. The recent discovery of a mitochondrial isoform of DNMT1 and its proposed role in methylating mitochondrial DNA (mtDNA) suggests that DNMT1 mutations may directly affect mtDNA and mitochondrial physiology. On the basis of this latter finding the link between DNMT1 abnormal activity and mitochondrial dysfunction in ADCA-DN and HSN1E appears intuitive, however, mtDNA methylation remains highly debated. In the last years several groups demonstrated the presence of 5-methylcytosine in mtDNA by different approaches, but, on the other end, the opposite evidence that mtDNA is not methylated has also been published. Since over 1500 mitochondrial proteins are encoded by the nuclear genome, the altered methylation of these genes may well have a critical role in leading to the mitochondrial impairment observed in ADCA-DN and HSN1E. Thus, many open questions still remain unanswered, such as why mtDNA should be methylated, and how this process is regulated and executed?
Maresca, Alessandra; Zaffagnini, Mirko; Caporali, Leonardo; Carelli, Valerio; Zanna, Claudia
In vitro supplementation with deoxynucleoside monophosphates rescues mitochondrial DNA depletion
Mitochondrial DNA depletion syndromes are a genetically heterogeneous group of often severe diseases, characterized by reduced cellular mitochondrial DNA content. Investigation of potential therapeutic strategies for mitochondrial DNA depletion syndromes will be dependent on good model systems. We have previously suggested that myotubes may be the optimal model system for such studies. Here we firstly validate this technique in a diverse range of cells of patients with mitochondrial DNA depletion syndromes, showing contrasting effects in cell lines from genetically and phenotypically differing patients. Secondly, we developed a putative therapeutic approach using variable combinations of deoxynucleoside monophosphates in different types of mitochondrial DNA depletion syndromes, showing near normalization of mitochondrial DNA content in many cases. Furthermore, we used nucleoside reverse transcriptase inhibitors to precisely titrate mtDNA depletion in vitro. In this manner we can unmask a physiological defect in mitochondrial depletion syndrome cell lines which is also ameliorated by deoxynucleoside monophosphate supplementation. Finally, we have extended this model to study fibroblasts after myogenic transdifferentiation by MyoD transfection, which similar to primary myotubes also showed deoxynucleoside monophosphate responsive mitochondrial DNA depletion in vitro, thus providing a more convenient method for deriving future models of mitochondrial DNA depletion. Our results suggest that using different combinations of deoxynucleoside monophosphates depending on the primary gene defect and molecular mechanism may be a possible therapeutic approach for many patients with mitochondrial DNA depletion syndromes and is worthy of further clinical investigation. PMID:22608879
Bulst, Stefanie; Holinski-Feder, Elke; Payne, Brendan; Abicht, Angela; Krause, Sabine; Lochm�ller, Hanns; Chinnery, Patrick F.; Walter, Maggie C.; Horvath, Rita
Influence of killing method on Lepidoptera DNA barcode recovery.
The global DNA barcoding initiative has revolutionized the field of biodiversity research. Such large-scale sequencing projects require the collection of large numbers of specimens, which need to be killed and preserved in a way that is both DNA-friendly and which will keep voucher specimens in good condition for later study. Factors such as time since collection, correct storage (exposure to free water and heat) and DNA extraction protocol are known to play a role in the success of downstream molecular applications. Limited data are available on the most efficient, DNA-friendly protocol for killing. In this study, we evaluate the quality of DNA barcode (cytochrome oxidase I) sequences amplified from DNA extracted from specimens collected using three different killing methods (ethyl acetate, cyanide and freezing). Previous studies have suggested that chemicals, such as ethyl acetate and formaldehyde, degraded DNA and as such may not be appropriate for the collection of insects for DNA-based research. All Lepidoptera collected produced DNA barcodes of good quality, and our study found no clear difference in nucleotide signal strength, probability of incorrect base calling and phylogenetic utility among the three different treatment groups. Our findings suggest that ethyl acetate, cyanide and freezing can all be used to collect specimens for DNA analysis. PMID:25229871
Willows-Munro, Sandi; Schoeman, M Corrie
Molecular characterization of races and vegetative compatibility groups in Fusarium oxysporum f. sp. vasinfectum.
Restriction fragment length polymorphism (RFLP) and vegetative compatibility analyses were undertaken to assess genetic relationships among 52 isolates of Fusarium oxysporum f. sp. vasinfectum of worldwide origin and representing race A, 3, or 4 on cotton plants. Ten distinct vegetative compatibility groups (VCGs) were obtained, and isolates belonging to distinct races were never in the same VCG. Race A isolates were separated into eight VCGs, whereas isolates of race 3 were classified into a single VCG (0113), as were those of race 4 (0114). Ribosomal and mitochondrial DNA (rDNA and mtDNA) RFLPs separated four rDNA haplotypes and seven mtDNA haplotypes. Race A isolates displayed the most polymorphism, with three rDNA haplotypes and four mtDNA haplotypes; race 4 isolates formed a single rDNA group but exhibited three mtDNA haplotypes, while race 3 isolates had unique rDNA and mtDNA haplotypes. Two mtDNA molecules with distinct sizes were identified; the first (45-kb mtDNA) was found in all race A isolates and seven race 4 isolates, and the second (55-kb mtDNA) was found in all race 3 isolates and in two isolates of race 4. These two mtDNA molecules were closely related to mtDNAs of F. oxysporum isolates belonging to other formae speciales (conglutinans, lycopersici, matthioli, and raphani). Isolates within a VCG shared the same rDNA and mtDNA haplotypes, with the exception of VCG0114, in which three distinct mtDNA haplotypes were observed. Genetic relationships among isolates inferred from rDNA or mtDNA site restriction data were different, and there was not a strict correlation between race and RFLPs.(ABSTRACT TRUNCATED AT 250 WORDS) Images PMID:7993090
Fernandez, D; Assigbese, K; Dubois, M P; Geiger, J P