when would the quantity of dna double when growing cells
S phase
2899120
briefly at M phase when the nucleus and then the cell divide in two. The process of cell division, called cell cycle, has four major parts called phases. The first part, called G phase is marked by synthesis of various enzymes that are required for DNA replication. The second part of the cell cycle is the S phase, where DNA replication produces two identical sets of chromosomes. The third part is the G phase in which a significant protein synthesis occurs, mainly involving the production of microtubules that are required during the process of division, called mitosis. The fourth phase,
Cell growth
11716076
between sister chromatids. The remaining two-thirds, or more, of homology directed repair occurs as a result of interaction between non-sister homologous chromatids. Regulation of DNA double-strand break repair pathway choice (Full Free PDF Article) Homology directed repair Homology directed repair (HDR) is a mechanism in cells to repair double strand DNA lesions. The most common form of HDR is homologous recombination. The HDR mechanism can only be used by the cell when there is a homologue piece of DNA present in the nucleus, mostly in G2 and S phase of the cell cycle. Other examples of homology-directed repair include single-strand
Homology directed repair
11716068
Homology directed repair Homology directed repair (HDR) is a mechanism in cells to repair double strand DNA lesions. The most common form of HDR is homologous recombination. The HDR mechanism can only be used by the cell when there is a homologue piece of DNA present in the nucleus, mostly in G2 and S phase of the cell cycle. Other examples of homology-directed repair include single-strand annealing and breakage-induced replication. When the homologue DNA piece is absent, another process called non-homologous end joining (NHEJ) can take place instead. HDR is important for suppressing the formation of cancer. HDR maintains genomic
Homology directed repair
9835976
double-stranded DNA helix has to be unwound to expose two single-stranded DNA templates for replication. DNA helicases are responsible for unwinding the double-stranded DNA during chromosome replication. Helicases in eukaryotic cells are remarkably complex. The catalytic core of the helicase is composed of six minichromosome maintenance (Mcm2-7) proteins, forming a hexameric ring. Away from DNA, the Mcm2-7 proteins form a single heterohexamer and are loaded in an inactive form at origins of DNA replication as a head-to-head double hexamers around double-stranded DNA. The Mcm proteins are recruited to replication origins then redistributed throughout the genomic DNA during S phase, indicative
Eukaryotic DNA replication
11143560
in PMS2 can inhibit this apoptosis. Thus, an added deficiency in PMS2 likely would be selected for in the face of the increased DNA damages when ERCC1 and/or ERCC4 (XPF) are deficient. When ERCC1 deficient Chinese hamster ovary cells were repeatedly subjected to DNA damage, of five clones derived from the surviving cells, three were mutated in Pms2. ERCC1, PMS2 double mutant Chinese hamster ovary cells, when exposed to Ultraviolet light (a DNA damaging agent), showed a 7,375-fold greater mutation frequency than wild type Chinese hamster ovary cells, and a 967-fold greater mutation frequency than the cells defective in ERCC1,
PMS2
1797351
density of the one-generation cells, but still higher than cells grown only in N DNA medium, as the original N DNA would have been split evenly among all DNA strands. The result was consistent with the semiconservative replication hypothesis. Meselson–Stahl experiment The Meselson–Stahl experiment is an experiment by Matthew Meselson and Franklin Stahl in 1958 which supported Watson and Crick's hypothesis that DNA replication was semiconservative. In semiconservative replication, when the double stranded DNA helix is replicated, each of the two new double-stranded DNA helices consisted of one strand from the original helix and one newly synthesized. It has been
Meselson–Stahl experiment
11124320
stressful conditions such as in "Helicobacter pylori"-associated gastritis. After ionizing radiation DNA-PKcs was increased in the surviving cells of oral squamous cell carcinoma tissues. The ATM protein is important in homologous recombinational repair (HRR) of DNA double strand breaks. When cancer cells are deficient in ATM the cells are "addicted" to DNA-PKcs, important in the alternative DNA repair pathway for double-strand breaks, non-homologous end joining (NHEJ). That is, in "ATM"-mutant cells, an inhibitor of DNA-PKcs causes high levels of apoptotic cell death. In "ATM" mutant cells, additional loss of DNA-PKcs leaves the cells without either major pathway (HRR and NHEJ)
DNA-PKcs
16902273
old. When 40 particular proteins were evaluated in a muscle of rats, the majority of the proteins showed significant decreases during aging from 18 months (mature rat) to 30 months (aged rat) of age. Another type of DNA damage, the double-strand break, was shown to cause cell death (loss of cells) through apoptosis. This type of DNA damage would not accumulate with age, since once a cell was lost through apoptosis, its double-strand damage would be lost with it. Thus, damaged DNA segments undermine the DNA replication machinery because these altered sequences of DNA cannot be utilized as true templates
DNA damage (naturally occurring)
5981335
plants, animals, fungi and protists. In cells that divide through mitosis, homologous recombination repairs double-strand breaks in DNA caused by ionizing radiation or DNA-damaging chemicals. Left unrepaired, these double-strand breaks can cause large-scale rearrangement of chromosomes in somatic cells, which can in turn lead to cancer. In addition to repairing DNA, homologous recombination also helps produce genetic diversity when cells divide in meiosis to become specialized gamete cells—sperm or egg cells in animals, pollen or ovules in plants, and spores in fungi. It does so by facilitating chromosomal crossover, in which regions of similar but not identical DNA are exchanged
Homologous recombination
4594070
°C for at least six months when protected from light. For longterm storage the solutions are instead frozen at −20 °C or below. The dyes bind to the minor groove of double-stranded DNA with a preference for sequences rich in adenine and thymine. Although the dyes can bind to all nucleic acids, AT-rich double-stranded DNA strands enhance fluorescence considerably. Hoechst dyes are cell-permeable and can bind to DNA in live or fixed cells. Thus, these stains are often called "supravital", meaning that live cells survive a treatment with these compounds. Cells that express specific ATP-binding cassette transporter proteins can also
Hoechst stain
3489025
damage in frequently dividing cells, because it gives rise to mutations, is a prominent cause of cancer. In contrast, DNA damage in infrequently-dividing cells is likely a prominent cause of aging. Cells cannot function if DNA damage corrupts the integrity and accessibility of essential information in the genome (but cells remain superficially functional when non-essential genes are missing or damaged). Depending on the type of damage inflicted on the DNA's double helical structure, a variety of repair strategies have evolved to restore lost information. If possible, cells use the unmodified complementary strand of the DNA or the sister chromatid as
DNA repair
16902277
based on which genes are mutated in the cells. For instance, while unirradiated cells will progress normally through the cell cycle, cells that are exposed to x-irradiation either permanently arrest (become inviable) or delay in the G2 phase before continuing to divide in mitosis, further corroborating the idea that the G2 delay is crucial for DNA repair. However, rad strains, which are deficient in DNA repair, exhibit a markedly different response. For instance, rad52 cells, which cannot repair double-stranded DNA breaks, tend to permanently arrest in G2 when exposed to even very low levels of x-irradiation, and rarely end up
DNA damage (naturally occurring)
8088499
is about 60 Å in length in eukaryotic RTs, corresponding to nearly two helical turns. When eukaryotic RT extends a conventional primer, the growing DNA/RNA double helix spirals along the cleft, and as the double helix passes the RNase H domain, the template RNA is digested to release the nascent strand of cDNA. In the case of msDNA primer extension, however, a long strand of RNA remains attached to the 3'-OH of the priming G. Although it is possible to model an RT-primer template complex which would make the 2'-OH accessible for the priming reaction, further extension of the DNA
Multicopy single-stranded DNA
15065785
with relative ease indicates that we will soon have a wealth of information about where and when large changes in chromosome folding occur during development and in different diseases. Replication timing Replication timing refers to the order in which segments of DNA along the length of a chromosome are duplicated. In eukaryotic cells (cells that package their DNA within a nucleus), chromosomes consist of very long linear double-stranded DNA molecules. During the S-phase of each cell cycle (Figure 1), all of the DNA in a cell is duplicated in order to provide one copy to each of the daughter cells
Replication timing
13804211
as well as for long-term neurodegenerative diseases. DNA is damaged thousands of times during each cell cycle, and that damage must be repaired, including in cancer cells. Otherwise the cells may die due to this damage. BRCA1, BRCA2 and PALB2 are proteins that are important for the repair of double-strand DNA breaks by the error-free homologous recombinational repair, or HRR, pathway. When the gene for one of these proteins is mutated, the change can lead to errors in DNA repair that can eventually cause breast cancer. When subjected to enough damage at one time, the altered gene can cause the
PARP inhibitor
3489029
third type of DNA damage reversed by cells is certain methylation of the bases cytosine and adenine. When only one of the two strands of a double helix has a defect, the other strand can be used as a template to guide the correction of the damaged strand. In order to repair damage to one of the two paired molecules of DNA, there exist a number of excision repair mechanisms that remove the damaged nucleotide and replace it with an undamaged nucleotide complementary to that found in the undamaged DNA strand. Double-strand breaks, in which both strands in the double
DNA repair
15601640
lipid asymmetry, cytoskeleton alterations, changes in mitochondrial function, and increased concentration of cytosolic calcium. Regardless of these cellular alterations, pseudoapoptotic cells reverse these changes to resume normal cellular process. Pseudoapoptosis has also been used in some instances when describing an accelerated, drug induced apoptotic pathway by bleomycin. Cell death occurs as it would in apoptosis, but certain apoptotic mechanisms are not utilized when in the presence of bleomycin. Bleomycin (BLM) is a cytotoxic, anticancerous drug that catalyzes double-stranded breaks (DSB) and single-stranded breaks (SSB) along DNA molecules. BLM has four distinguishable molecular components that determine function, including a DNA-binding region,
Pseudoapoptosis
3489013
daughter cells after it undergoes mitosis. As a consequence, the DNA repair process is constantly active as it responds to damage in the DNA structure. When normal repair processes fail, and when cellular apoptosis does not occur, irreparable DNA damage may occur, including double-strand breaks and DNA crosslinkages (interstrand crosslinks or ICLs). This can eventually lead to malignant tumors, or cancer as per the two hit hypothesis. The rate of DNA repair is dependent on many factors, including the cell type, the age of the cell, and the extracellular environment. A cell that has accumulated a large amount of DNA
DNA repair
20530670
measured by tritiated thymidine incorporation into trichloroacetic acid (TCA) – insoluble material via salvage pathways. Thymidine incorporation measures growth based on rates of DNA synthesis, using the assumption that only growing cells can incorporate the radioactive thymidine to synthesize DNA. Weaknesses of this procedure include labeling of other molecules besides DNA when tritiated thymidine is added to a sample. In cases of carbon limitation, thymidine may also be used as a carbon source instead of as a DNA precursor. Results of thymidine incorporation experiments may be misleading when the proportion of thymidine incorporated into DNA compared to other molecules is
Bacterioplankton counting methods
13463515
which pathway will be used for repair of double strand breaks in DNA. When FEN1, Ligase III, MRE11, NBS1, PARP1 or XRCC1 are over-expressed (this occurs with FEN1 when its promoter is hypomethylated) the highly inaccurate MMEJ pathway may be favored, causing a higher rate of mutation and increased risk of cancer. Cancers are very often deficient in expression of one or more DNA repair genes, but over-expression of a DNA repair gene is less usual in cancer. For instance, at least 36 DNA repair enzymes, when mutationally defective in germ line cells, cause increased risk of cancer (hereditary cancer
Microhomology-mediated end joining
11873826
of articles from 1970 to 1977, PV Narasimh Acharya, Phd. (1924–1993) theorized and presented evidence that cells undergo "irreparable DNA damage," whereby DNA crosslinks occur when both normal cellular repair processes fail and cellular apoptosis does not occur. Specifically, Acharya noted that double-strand breaks and a "cross-linkage joining both strands at the same point is irreparable because neither strand can then serve as a template for repair. The cell will die in the next mitosis or in some rare instances, mutate." In tissues composed of non- or infrequently replicating cells, DNA damage can accumulate with age and lead either to
DNA damage theory of aging
16902278
progressing through the later stages of the cell cycle. This is because the cells cannot repair DNA damage and thus do not enter mitosis. Various other rad mutants exhibit similar responses when exposed to x-irradiation. However, the rad9 strain exhibits an entirely different effect. These cells fail to delay in the G2 phase when exposed to x-irradiation, and end up progressing through the cell cycle unperturbed, before dying. This suggests that the RAD9 gene, unlike the other RAD genes, plays a crucial role in initiating G2 arrest. To further investigate these findings, the cell cycles of double mutant strains have
DNA damage (naturally occurring)
542085
signaling system in "S. mutans" includes the Competence Stimulating Peptide (CSP) that controls genetic competence. Genetic competence is the ability of a cell to take up DNA released by another cell. Competence can lead to genetic transformation, a form of sexual interaction, favored under conditions of high cell density and/or stress where there is maximal opportunity for interaction between the competent cell and the DNA released from nearby donor cells. This system is optimally expressed when "S. mutans" cells reside in an actively growing biofilm. Biofilm grown "S. mutans" cells are genetically transformed at a rate 10- to 600-fold higher
Biofilm
3150822
when it occurs during meiosis it is an adaptation for repairing the genomic DNA which is passed on to progeny. Recombinational repair is the only repair process known which can accurately remove double-strand damages in DNA, and such damages are both common in nature and ordinarily lethal if not repaired. For instance, double-strand breaks in DNA occur about 50 times per cell cycle in human cells [see DNA damage (naturally occurring)]. Recombinational repair is prevalent from the simplest viruses to the most complex multicellular eukaryotes. It is effective against many different types of genomic damage, and in particular is highly
Evolution of sexual reproduction
16840041
designed guide RNA CRISPR/Cas9 could be used to induce double-stranded breaks at specific points within DNA sequences. It was later demonstrating that CRISPR/Cas9 could edit human cells in a dish. Although the early generation lacks the specificity of TALEN, the major advantage of this technology is the simplicity of the design. It also allows multiple sites to be targeted simultaneously, allowing the editing of multiple genes at once. CRISPR/Cpf1 is a more recently discovered system that requires a different guide RNA to create particular double-stranded breaks (leaves overhangs when cleaving the DNA) when compared to CRISPR/Cas9. Genetic engineering techniques Genetic
Genetic engineering techniques
9344571
Crosslinking of DNA In genetics, crosslinking of DNA occurs when various exogenous or endogenous agents react with two nucleotides of DNA, forming a covalent linkage between them. This crosslink can occur within the same strand (intrastrand) or between opposite strands of double-stranded DNA (interstrand). These adducts interfere with cellular metabolism, such as DNA replication and transcription, triggering cell death. These crosslinks can, however, be repaired through excision or recombination pathways. DNA crosslinking also has useful merit in chemotherapy and targeting cancerous cells for apoptosis , as well as in understanding how proteins interact with DNA. Many characterized crosslinking agents have
Crosslinking of DNA
97581
grow, but, when a cell divides, it must replicate the DNA in its genome so that the two daughter cells have the same genetic information as their parent. The double-stranded structure of DNA provides a simple mechanism for DNA replication. Here, the two strands are separated and then each strand's complementary DNA sequence is recreated by an enzyme called DNA polymerase. This enzyme makes the complementary strand by finding the correct base through complementary base pairing and bonding it onto the original strand. As DNA polymerases can only extend a DNA strand in a 5′ to 3′ direction, different mechanisms
DNA
17199708
When the two antibodies bind to a protein the complimentary strands will anneal and produce a double stranded piece of DNA that can then be amplified using PCR. Each pair of antibodies designed for one protein is tagged with a different DNA sequence. The DNA amplified from PCR can then be sequenced, and the protein levels quantified. In mass spectroscopy based proteomics there are three major steps needed for peptide identification: sample preparation, separation of peptides, and identification of peptides. Several groups have focused on oocytes or very early cleavage-stage cells since these cells are unusually large and provide enough
Single-cell analysis
13566589
sequenced strain was ATCC BAA-816. "Deinococcus radiodurans" has a unique quality in which it can repair both single- and double-stranded DNA. When damage is apparent to the cell, it brings it into a compartmental ring-like structure, where the DNA is repaired and then is able to fuse the nucleoids from the outside of the compartment with the damaged DNA. "D. radiodurans" is a rather large, spherical bacterium, with a diameter of 1.5 to 3.5 µm. Four cells normally stick together, forming a tetrad. The bacteria are easily cultured and do not appear to cause disease. Under controlled growth conditions, cells
Deinococcus radiodurans
3833605
or where the woman is over the age of 35 (when the risk of genetically related disorders is higher). In addition, by allowing parents to select an embryo without genetic disorders, they have the potential of saving the lives of siblings that already had similar disorders and diseases using cells from the disease free offspring. Differentiated somatic cells and ES cells use different strategies for dealing with DNA damage. For instance, human foreskin fibroblasts, one type of somatic cell, use non-homologous end joining (NHEJ), an error prone DNA repair process, as the primary pathway for repairing double-strand breaks (DSBs) during
Embryonic stem cell
9836007
helicases are double hexamers that are loaded onto double stranded DNA whereas prokaryotic helicases are single hexamers loaded onto single stranded DNA. Segregation of chromosomes is another difference between prokaryotic and eukaryotic cells. Rapidly dividing cells, such as bacteria, will often begin to segregate chromosomes that are still in the process of replication. In eukaryotic cells chromosome segregation into the daughter cells is not initiated until replication is complete in all chromosomes. Despite these differences, however, the underlying process of replication is similar for both prokaryotic and eukaryotic DNA. List of major proteins involved in eukaryotic DNA replication: Eukaryotic DNA
Eukaryotic DNA replication
97597
reproduction, when genetic recombination occurs. Chromosomal crossover is when two DNA helices break, swap a section and then rejoin. Recombination allows chromosomes to exchange genetic information and produces new combinations of genes, which increases the efficiency of natural selection and can be important in the rapid evolution of new proteins. Genetic recombination can also be involved in DNA repair, particularly in the cell's response to double-strand breaks. The most common form of chromosomal crossover is homologous recombination, where the two chromosomes involved share very similar sequences. Non-homologous recombination can be damaging to cells, as it can produce chromosomal translocations and
DNA
3381219
cells, ColE1 ori for double-stranded DNA replication, or f1 ori for single-stranded DNA replication in prokaryotes. They frequently also contain a gene for selection such as antibiotic resistance, so that the transformed cells can be identified by plating on a medium containing the antibiotic. Those cells which did not take up the cosmid would be unable to grow. Unlike plasmids, they can also be packaged in phage capsids, which allows the foreign genes to be transferred into or between cells by transduction. Plasmids become unstable after a certain amount of DNA has been inserted into them, because their increased size
Cosmid
6839960
be washed out of the cells and so not be available for re-synthesis into ATP when the kidney is rewarmed. Nuclear DNA is injured during cold storage of kidneys. Lazarus showed that single stranded DNA breaks occurred within 16 hours in hypothermically stored mice kidneys, with the injury being inhibited a little by storage in Collins' or Sacks' solutions. This nuclear injury differed from that seen in warm injury when double stranded DNA breaks occurred. Perfusion storage methods can mechanically injury the vascular endothelium of the kidney, which leads to arterial thrombosis or fibrin deposition after reimplantation. Hill noted that,
Machine perfusion
20545650
the formation of ROS by generating a superoxide anion by transferring electrons from cytosolic NADPH across the cell membrane to the extracellular molecular oxygen. This process increases the potential for leakage of electrons and free radicals from the mitochondria. The exposure to the LDIR induces electron release from the mitochondria resulting in more electrons contributing to the superoxide formation in the cells. The production of ROS in high quantity in cells results in the degradation of biomolecules such as proteins, DNA, and RNA. In one such instance the ROS are known to create double stranded and single stranded breaks in
Biological effects of radiation on the epigenome
3489040
So when a lesion is encountered, the replication fork will stall, PCNA will switch from a processive polymerase to a TLS polymerase such as Pol ι to fix the lesion, then PCNA may switch to Pol ζ to extend the mismatch, and last PCNA will switch to the processive polymerase to continue replication. Cells exposed to ionizing radiation, ultraviolet light or chemicals are prone to acquire multiple sites of bulky DNA lesions and double-strand breaks. Moreover, DNA damaging agents can damage other biomolecules such as proteins, carbohydrates, lipids, and RNA. The accumulation of damage, to be specific, double-strand breaks or
DNA repair
16365562
(MMEJ) repair of double strand breaks. It is one of 6 enzymes required for this error prone DNA repair pathway. LIG3 is upregulated in chronic myeloid leukemia, multiple myeloma, and breast cancer. Cancers are very often deficient in expression of one or more DNA repair genes, but over-expression of a DNA repair gene is less usual in cancer. For instance, at least 36 DNA repair enzymes, when mutationally defective in germ line cells, cause increased risk of cancer (hereditary cancer syndromes). (Also see DNA repair-deficiency disorder.) Similarly, at least 12 DNA repair genes have frequently been found to be epigenetically
LIG3
1945164
investigation. "In vitro," when cells approach the Hayflick limit, the time to senescence can be extended by inactivating the tumor suppressor proteins - p53 and Retinoblastoma protein (pRb). Cells that have been so-altered eventually undergo an event termed a "crisis" when the majority of the cells in the culture die. Sometimes, a cell does not stop dividing once it reaches crisis. In a typical situation, the telomeres are shortened and chromosomal integrity declines with every subsequent cell division. Exposed chromosome ends are interpreted as double-stranded breaks (DSB) in DNA; such damage is usually repaired by reattaching (religating) the broken ends
Telomerase
5154534
tolerate rapidly harsh environmental fluctuations and exposure to various antimicrobial agents to survive. Transformation is a bacterial adaptation involving the transfer of DNA from one bacterium to another through the surrounding medium. Transformation is a primitive form of sexual reproduction. For a bacterium to bind, take up, and recombine exogenous DNA into its chromosome, it must enter a special physiological state termed “competence”. In "S. mutans", a peptide pheromone quorum-sensing signaling system controls genetic competence. This system functions optimally when the S. mutans cells are in crowded biofilms. "S. mutans" cells growing in a biofilm are transformed at a rate
Streptococcus mutans
13804212
death of the cells. PARP1 is a protein that is important for repairing single-strand breaks ('nicks' in the DNA). If such nicks persist unrepaired until DNA is replicated (which must precede cell division), then the replication itself can cause double strand breaks to form. Drugs that inhibit PARP1 cause multiple double strand breaks to form in this way, and in tumours with BRCA1, BRCA2 or PALB2 mutations, these double strand breaks cannot be efficiently repaired, leading to the death of the cells. Normal cells that don't replicate their DNA as often as cancer cells, and that lack any mutated BRCA1
PARP inhibitor
8893943
and the new RNA molecule to be released. Moving of the transcription bubble in the process may be seen with specialized staining techniques, spectroscopy or microscopy. This process can be seen in live bacterial cells and purified polymerase enzymes. However, in the bacterial cells, topological problems may occur during the process of transcription, but they are resolved by topoisomerase enzymes. Transcription bubble A transcription bubble is a molecular structure that is formed during the transcription of DNA when a limited portion of the DNA double strand is unwound. The Transcription bubble ranges from around 12-14 base pairs, but can be
Transcription bubble
6272702
TUNEL assay Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) is a method for detecting DNA fragmentation by labeling the 3′- hydroxyl termini in the double-strand DNA breaks generated during apoptosis. TUNEL is a method for detecting apoptotic DNA fragmentation, widely used to identify and quantify apoptotic cells, or to detect excessive DNA breakage in individual cells. The assay relies on the use of terminal deoxynucleotidyl transferase (TdT), an enzyme that catalyzes attachment of deoxynucleotides, tagged with a fluorochrome or another marker, to 3'-hydroxyl termini of DNA double strand breaks. It may also label cells having DNA damaged by other
TUNEL assay
14572535
for the success of the next step, the staining of the cells. Prior to (or during the staining step) the cells are often treated with RNase A to remove RNAs. This is important because certain dyes that stain DNA will also stain RNA, thus creating artefacts that would distort the results. An exception is the metachromatic fluorochrome acridine orange, which under the specific staining protocol can differentially stain both, RNA (generating red luminescence) and DNA (green fluorescence), or in another protocol, after removal of RNA and partial DNA denaturation, to differentially stain double-stranded DNA (green fluorescence) versus single-stranded DNA(red luminescence).
Cell cycle analysis
9344583
Because the toxicity of these drugs depends on TOP1 trapping, cellular sensitivity to these compounds depends directly on TOP1 expression levels. As a result, the function of these drugs is to serve as enzyme poisons rather than inhibitors. This can be applied to treat tumor cells by utilizing TOP 2 enzyme poisons. Crosslinking of DNA In genetics, crosslinking of DNA occurs when various exogenous or endogenous agents react with two nucleotides of DNA, forming a covalent linkage between them. This crosslink can occur within the same strand (intrastrand) or between opposite strands of double-stranded DNA (interstrand). These adducts interfere with
Crosslinking of DNA
11138468
suggest that human MRE11A is descended from prokaryotic and protist ancestral Mre11 proteins that served a role in early processes for repairing DNA damage. MRE11 has a role in microhomology-mediated end joining (MMEJ) repair of double strand breaks. It is one of 6 enzymes required for this error prone DNA repair pathway. MRE11 is over-expressed in breast cancers. Cancers are very often deficient in expression of one or more DNA repair genes, but over-expression of a DNA repair gene is less usual in cancer. For instance, at least 36 DNA repair enzymes, when mutationally defective in germ line cells, cause
MRE11A
7435841
physiological environments, topotecan is in equilibrium with its inactive carboxylate form. Topotecan's active lactone form intercalates between DNA bases in the topoisomerase-I cleavage complex. The binding of topotecan in the cleavage complex prevents topoisomerase-I from religating the nicked DNA strand after relieving the strain. This intercalation therefore traps the topoisomerase-I in the cleavage complex bound to the DNA. When the replication-fork collides with the trapped topoisomerase-I, DNA damage occurs. The unbroken DNA strand breaks and mammalian cells cannot efficiently repair these double strand breaks. The accumulation of trapped topoisomerase-I complexes is a known response to apoptotic stimuli. This disruption prevents
Topotecan
17363970
been confirmed in T cells, monocytes and B cells more than one year after transplantation. Nervana is an investigational ddRNAi construct that knocks down the expression of protein kinase C gamma (PKCγ) known to be associated with neuropathic pain and morphine tolerance. Two conserved PKCγ sequences found across all key model species and humans have been identified, and both single and double DNA cassettes designed. In vitro, expression of PKCγ was silenced by 80%. When similar ddRNAi constructs were delivered intrathecally using a lentiviral vector, pain relief in a neuropathic-rat model was demonstrated. The development of resistance to chemotherapies such
DNA-directed RNA interference
16902276
about radiation-sensitive (RAD) genes, and the effect that RAD mutations may have on the typical cellular DNA damaged-induced delay response. Specifically, the RAD9 gene plays a crucial role in detecting DNA damage and arresting the cell in G2 until the damage is repaired. Through extensive experiments, researchers have been able to illuminate the role that the RAD genes play in delaying cell division in response to DNA damage. When wild-type, growing cells are exposed to various levels of x-irradiation over a given time frame, and then analyzed with a microcolony assay, differences in the cell cycle response can be observed
DNA damage (naturally occurring)
3620046
to a negligible quantity. The inserted chromosome yields a large fragment when the homologous region is amplified. The males are distinguished as having two DNA amplicons present, while females have only a single amplicon. The kit adapted for carrying out the method includes a pair of primers to amplify the locus and optionally polymerase chain reaction reagents. LCR can be used to diagnose tuberculosis. The sequence containing protein antigen B is targeted by four oligonucleotide primers—two for the sense strand, and two for the antisense strand. The primers bind adjacent to one another, forming a segment of double stranded DNA
Amplicon
15362582
are selectively killed, and only those cells that can actively replicate DNA containing the selectable marker gene encoded by the vector are able to survive. When bacterial cells are used as host organisms, the selectable marker is usually a gene that confers resistance to an antibiotic that would otherwise kill the cells, typically ampicillin. Cells harboring the plasmid will survive when exposed to the antibiotic, while those that have failed to take up plasmid sequences will die. When mammalian cells (e.g. human or mouse cells) are used, a similar strategy is used, except that the marker gene (in this case
Molecular cloning
7145457
DNA, and DNA ligase joins the ends to make another molecule of double-stranded circular DNA. As a summary, a typical DNA rolling circle replication has five steps: Some DNA viruses replicate their genomic information in host cells via rolling circle replication. For instance, "human herpesvirus-6" (HHV-6)(hibv) expresses a set of "early genes" that are believed to be involved in this process. The long concatemers that result are subsequently cleaved between the pac-1 and pac-2 regions of HHV-6's genome by ribozymes when it is packaged into individual virions. Human Papillomavirus-16 (HPV-16) is another virus that employs rolling replication to produce progeny
Rolling circle replication
4590961
DNA and became more fluorescent when bound. This led to its use in identifying mitochondrial DNA in ultracentrifugation in 1975, the first recorded use of DAPI as a fluorescent DNA stain. Strong fluorescence when bound to DNA led to the rapid adoption of DAPI for fluorescent staining of DNA for fluorescence microscopy. Its use for detecting DNA in plant, metazoa and bacteria cells and virus particles was demonstrated in the late 1970s, and quantitative staining of DNA inside cells was demonstrated in 1977. Use of DAPI as a DNA stain for flow cytometry was also demonstrated around this time. When
DAPI
784085
Semiconservative replication Semiconservative replication describes the mechanism by which DNA is replicated in all known cells. It derives its name from the fact that this mechanism of transcription was one of three models originally proposed for DNA replication: The deciphering of the structure of DNA by Watson and Crick in 1953 suggested that each strand of the double helix would serve as a template for synthesis of a new strand. However, there was no way of knowing how the newly synthesized strands might combine with the template strands to form two double helical DNA molecules. The semiconservative model seemed most
Semiconservative replication
20545638
of DNA double strand breaks can lead to cell cycle arrest in somatic cells and cause cell death. Due to its ability to induce cell cycle arrest, ionizing radiation is used on abnormal growths in the human body such as cancer cells, in radiation therapy. Most cancer cells are fully treated with some type of radiotherapy, however some cells such as stem cell cancer cells show a reoccurrence when treated by this type of therapy. Non-ionising radiations, electromagnetic fields (EMF) such as radiofrequency (RF), or power frequency radiation have become very common in everyday life. All of these exist as
Biological effects of radiation on the epigenome
9655571
by maintaining the levels of proteins that have key roles in DNA double-strand break repair during the processes of non-homologous end joining and homologous recombination. Mutations in lamin A (LMNA) cause Hutchinson–Gilford progeria syndrome, a dramatic form of premature aging. Mouse cells deficient for maturation of prelamin A show increased DNA damage and chromosome aberrations and are more sensitive to DNA damaging agents. The inability to adequately repair DNA damages when A-type lamins are defective is likely responsible for some of the aspects of premature aging. Currently, there is no cure for laminopathies and treatment is largely symptomatic and supportive.
Laminopathy
12569910
Anti-dsDNA antibodies Anti-double stranded DNA (Anti-dsDNA) antibodies are a group of anti-nuclear antibodies (ANA) the target antigen of which is double stranded DNA. Blood tests such as enzyme-linked immunosorbent assay (ELISA) and immunofluorescence are routinely performed to detect anti-dsDNA antibodies in diagnostic laboratories. They are highly diagnostic of systemic lupus erythematosus (SLE) and are implicated in the pathogenesis of lupus nephritis. The first evidence for antinuclear antibodies arose in 1948 when Hargraves, Richmond and Morton discovered the LE cell. These abnormal cells, which are found in the bone marrow of persons who have SLE are categorised as polymorphonuclear leukocytes with
Anti-dsDNA antibodies
11590562
antipyretic and analgesic drugs are commonly prescribed. Viral disease A viral disease (or viral infection or infectious disease), occurs when an organism's body is invaded by pathogenic viruses, and infectious virus particles (virions) attach to and enter susceptible cells. Basic structural characteristics, such as genome type, virion shape and replication site, generally share the same features among virus species within the same family. There are five double-stranded DNA families: three are non enveloped (Adenoviridae, Papillomaviridae and Polyomaviridae) and two are enveloped (Herpesviridae and Poxviridae). All of the non-enveloped families have icosahedral capsids. There is one family of partly double-stranded DNA
Viral disease
11590557
Viral disease A viral disease (or viral infection or infectious disease), occurs when an organism's body is invaded by pathogenic viruses, and infectious virus particles (virions) attach to and enter susceptible cells. Basic structural characteristics, such as genome type, virion shape and replication site, generally share the same features among virus species within the same family. There are five double-stranded DNA families: three are non enveloped (Adenoviridae, Papillomaviridae and Polyomaviridae) and two are enveloped (Herpesviridae and Poxviridae). All of the non-enveloped families have icosahedral capsids. There is one family of partly double-stranded DNA viruses: Hepadnaviridae. These viruses are enveloped. There
Viral disease
19462189
cell by Tf. Most metal-based anti-tumor compounds interact strongly with DNA. Binding assays of KP1019 with the four common nucleotide bases reveal a preference for guanosine 5’-monophosphate and adenosine 5’-monophosphate. KP1019 is able to untwist and bend DNA weakly. While Pt-based compounds also target purines, KP1019’s DNA lesions may differ in quantity and strength. In tumor cells, the drug induces 15-fold lower interstrand DNA cross-linking efficiency than cisplatin. The interaction of KP1019 and its imidazole-containing analogue KP418 with DNA increases in the hypoxic environment that tumor cells are subject to. This correspondingly increased cytotoxicity as well. KP1019 and KP1339 both
KP1019
5373501
to 7 is considered Intermediate. 8 to 9 is considered High. The presence of cancer cell in small blood vessels is called vascular invasion. The presence of vascular invasion increases the probability of systemic spread. DNA analysis indicates the amount of DNA in cancer cells and how fast the cancer is growing. Cells with the normal amount of DNA are called diploid. Cells with too much or too little DNA are called aneuploid. Aneuploid cells are more likely to spread than diploid cells. DNA testings indicates the rate of growth by determining the number of cells in the synthetic phase
Invasive carcinoma of no special type
516329
pairing with guanine) would lead to formation of uracil (which would base pair with adenine) during DNA synthesis. Uracil-DNA glycosylase excises uracil bases from double-stranded DNA. This enzyme would therefore recognize and cut out both types of uracil – the one incorporated naturally, and the one formed due to cytosine deamination, which would trigger unnecessary and inappropriate repair processes. This problem is believed to have been solved in terms of evolution, i.e. by "tagging" (methylating) uracil. Methylated uracil is identical to thymine. Therefore, it is hypothesized that, over time, thymine became the DNA standard instead of uracil. Therefore, cells now
Uracil
14077279
in cells with DNA damage. Through combination of DNA damage and nuclear localization of exogenous cyclin B, they were able to determine that cells would divide even with DNA damage if the cyclin B were forced to be expressed in the nucleus. This suggests that spatial localization of cyclin B may play a role as a checkpoint of mitosis. If the cells, under normal circumstances, don’t divide when their genetic information is damaged, but will enter mitosis if endogenous cyclin B is expressed in the nucleus, it is likely that the translocation of the cyclin B to the cytoplasm is
Biochemical switches in the cell cycle
11323778
at the junction between double-stranded and single-stranded DNA. During nucleotide excision repair, several protein complexes cooperate to recognize damaged DNA and locally separate the DNA helix for a short distance on either side of the site of a site of DNA damage. The ERCC1–XPF nuclease incises the damaged DNA strand on the 5′ side of the lesion. During NER, the ERCC1 protein interacts with the XPA protein to coordinate DNA and protein binding. Mammalian cells with mutant ERCC1–XPF are moderately more sensitive than normal cells to agents (such as ionizing radiation) that cause double-stranded breaks in DNA. Particular pathways of
ERCC4
11141145
the junction between double-stranded and single-stranded DNA. During nucleotide excision repair, several protein complexes cooperate to recognize damaged DNA and locally separate the DNA helix for a short distance on either side of the site of a DNA damage. The ERCC1–XPF nuclease incises the damaged DNA strand on the 5′ side of the lesion. During NER, the ERCC1 protein interacts with the XPA protein to coordinate DNA and protein binding. Mammalian cells with mutant ERCC1–XPF are moderately more sensitive than normal cells to agents (such as ionizing radiation) that cause double-stranded breaks in DNA. Particular pathways of both homologous recombination
ERCC1
13804214
cells that are low in oxygen (e.g. in fast growing tumors) are sensitive to PARP inhibitors. Started Phase III: Started Phase II: Started Phase I: Currently Discontinued: Experimental: The main function of radiotherapy is to produce DNA strand breaks, causing severe DNA damage and leading to cell death. Radiotherapy has the potential to kill 100% of any targeted cells, but the dose required to do so would cause unacceptable side effects to healthy tissue. Radiotherapy therefore can only be given up to a certain level of radiation exposure. Combining radiation therapy with PARP inhibitors offers promise, since the inhibitors would
PARP inhibitor
9414833
originates a sporophyte composed of a foot, seta, and capsule, where thousands of haploid spores are produced by meiosis. "P. patens" is an excellent model in which to analyze repair of DNA damages in plants by the homologous recombination pathway. Failure to repair double-strand breaks and other DNA damages in somatic cells by homologous recombination can lead to cell dysfunction or death, and when failure occurs during meiosis, it can cause loss of gametes. The genome sequence of "P. patens" has revealed the presence of numerous genes that encode proteins necessary for repair of DNA damages by homologous recombination and
Physcomitrella patens
2453324
sister chromatid. In the nucleus of many types of normal cells, the BRCA1 protein interacts with RAD51 during repair of DNA double-strand breaks. These breaks can be caused by natural radiation or other exposures, but also occur when chromosomes exchange genetic material (homologous recombination, e.g., "crossing over" during meiosis). The BRCA2 protein, which has a function similar to that of BRCA1, also interacts with the RAD51 protein. By influencing DNA damage repair, these three proteins play a role in maintaining the stability of the human genome. BRCA1 is also involved in another type of DNA repair, termed mismatch repair. BRCA1
BRCA1
4564025
and LH in males will not increase the rate of spermatogenesis. However, with age, the rate of production will decrease, even when the amount of hormone that is secreted is constant; this is due to higher rates of degeneration of germ cells during meiotic prophase. In the following table, ploidy, copy number and chromosome/chromatid counts listed are for a single cell, generally prior to DNA synthesis and division (in G if applicable). Primary spermatocytes are arrested after DNA synthesis and prior to division. Spermatocytes regularly overcome double-strand breaks and other DNA damages in the prophase stage of meiosis. These damages
Spermatocyte
9314418
new embryo with 23 pairs of chromosomes, half from each parent. Mating and resultant mate choice result in sexual selection. In normal cell division (mitosis) is possible when the double helix separates, and a complement of each separated half is made, resulting in two identical double helices in one cell, with each occupying one of the two new daughter cells created when the cell divides. Chromosomes all contain DNA made up of four nucleotides, abbreviated C (cytosine), G (guanine), A (adenine), or T (thymine), which line up in a particular sequence and make a long string. There are two strings
Introduction to genetics
16365559
now evident that the DNA ligase III-alpha/XRCC1 complex enables cells that either lack or have reduced DNA ligase I activity to complete DNA replication. Given the biochemical and cell biology studies linking the DNA ligase III-alpha/XRCC1 complex with excision repair and the repair of DNA single strand breaks, it was surprising that the cells lacking nuclear DNA ligase III-alpha did not exhibit significantly increased sensitivity to DNA damaging agent. These studies suggest that there is significant functional redundancy between DNA ligase I and DNA ligase III-alpha in these nuclear DNA repair pathways. In mammalian cells, most DNA double strand breaks
LIG3
10851061
fluid and put through the flow cytometer. Cells are sent one at a time through a laser beam and the light scatter is measured by a detector. Cells or their components can be labeled with fluorescent markers so that they emit different wavelengths of light in response to the laser, allowing for additional data collection. For quantitative cell cycle analysis, cells are usually fixed with ethanol and stained with DNA-binding dyes like propidium iodide, Hoechst 33342, DAPI, 7-Aminoactinomysin D, Mithramycin, DRAQ5, or TO-PRO-3, allowing for determination of phase by DNA quantity. However, if these cells have been fixed, they are
Cell synchronization
4871984
and MBD4 are strictly specific for double-stranded DNA. TDG can remove thymine glycol when present opposite guanine, as well as derivatives of U with modifications at carbon 5. Current evidence suggests that, in human cells, TDG and SMUG1 are the major enzymes responsible for the repair of the U:G mispairs caused by spontaneous cytosine deamination, whereas uracil arising in DNA through dU misincorporation is mainly dealt with by UNG. MBD4 is thought to correct T:G mismatches that arise from deamination of 5-methylcytosine to thymine in CpG sites. MBD4 mutant mice develop normally and do not show increased cancer susceptibility or
DNA glycosylase
2725897
they cut, while others, including restriction enzymes, are very sequence-specific. Some cleave only double-stranded DNA; others are specific for single-stranded molecules; and still others are active toward both. DNase enzymes can be inhaled using a nebuliser by cystic fibrosis sufferers. DNase enzymes help because white blood cells accumulate in the mucus, and, when they break down, they release DNA, which adds to the 'stickiness' of the mucus. DNase enzymes break down the DNA, and the mucus is much easier to clear from the lungs. Intrapleural tissue plasminogen activator (tPA) combined with deoxyribonuclease has been shown to increase pleural drainage, decrease
Deoxyribonuclease
11918292
cells cannot divide indefinitely as after a few cycles of cell division the cells stop expressing an enzyme telomerase. The genetic material, in the form of deoxyribonucleic acid (DNA), continues to shorten with each cell division, and cells eventually stop dividing when they sense that their DNA is critically shortened. However, this enzyme in "youthful" cells replaces these lost bits (nucleotides) of DNA, thus making almost unlimited cycles of cell division possible. It is believed that the above-mentioned tissues have a constitutional elevated expression of telomerase. When ultimately many cells are produced by a single cell, "clonal expansion" is said
Clone (cell biology)
11124321
for repair of DNA double-strand breaks. Elevated DNA-PKcs expression is found in a large fraction (40% to 90%) of some cancers (the remaining fraction of cancers often has reduced or absent expression of DNA-PKcs). The elevation of DNA-PKcs is thought to reflect the induction of a compensatory DNA repair capability, due to the genome instability in these cancers. (As indicated in the article Genome instability, such genome instability may be due to deficiencies in other DNA repair genes present in the cancers.) Elevated DNA-PKcs is thought to be "beneficial to the tumor cells", though it would be at the expense
DNA-PKcs
2088527
If this uneven division occurs in meiosis I, then none of the daughter cells will have proper chromosomal distribution and severe effects can ensue, including Down’s syndrome. Unequal division can also occur during the second meiotic division. Nondisjunction which occurs at this stage can result in normal daughter cells and deformed cells. While the main function of homologous chromosomes is their use in nuclear division, they are also used in repairing double-strand breaks of DNA. These double-stranded breaks may occur in replicating DNA and are most often the result of interaction of DNA with naturally occurring damaging molecules such as
Homologous chromosome
2032311
mutations. In addition, faulty repair of these accumulated DNA damages may give rise to epigenetic alterations or epimutations. While a mutation or epimutation in a DNA repair gene, itself, would not confer a selective advantage, such a repair defect may be carried along as a passenger in a cell when the cell acquires an additional mutation/epimutation that does provide a proliferative advantage. Such cells, with both proliferative advantages and one or more DNA repair defects (causing a very high mutation rate), likely give rise to the high frequency of total genome mutations seen in carcinomas. In somatic cells, deficiencies in
Carcinoma
15065775
Replication timing Replication timing refers to the order in which segments of DNA along the length of a chromosome are duplicated. In eukaryotic cells (cells that package their DNA within a nucleus), chromosomes consist of very long linear double-stranded DNA molecules. During the S-phase of each cell cycle (Figure 1), all of the DNA in a cell is duplicated in order to provide one copy to each of the daughter cells after the next cell division. The process of duplicating DNA is called DNA replication, and it takes place by first unwinding the duplex DNA molecule, starting at many locations
Replication timing
2999703
Y chromosome in one of the first embryonic cell divisions. These mosaics can then be used to analyze such things as courtship behavior, female sexual attraction, and the autonomy or non-autonomy of particular genes. Genetic mosaics can also be created through mitotic recombination. Such mosaics were originally created by irradiating flies heterozygous for a particular allele with X-rays, inducing double-strand DNA breaks which, when repaired, could result in a cell homozygous for one of the two alleles. After further rounds of replication, this cell would result in a patch, or "clone" of cells mutant for the allele being studied. More
Mosaic (genetics)
188445
RNA and various enzymes, including reverse transcriptase, integrase, ribonuclease, and protease, are injected into the cell. During the microtubule-based transport to the nucleus, the viral single-strand RNA genome is transcribed into double-strand DNA, which is then integrated into a host chromosome. HIV can infect dendritic cells (DCs) by this CD4-CCR5 route, but another route using mannose-specific C-type lectin receptors such as DC-SIGN can also be used. DCs are one of the first cells encountered by the virus during sexual transmission. They are currently thought to play an important role by transmitting HIV to T cells when the virus is captured
HIV
4081047
glow brightly when they attached to the DNA double helix. When rhodium complexes were attached to the DNA, they would attract the electron causing the glow, and "turn off" the effect. During her time at Columbia, Barton obtained two patents for this method of analyzing DNA structure. In 1989, Barton moved to Caltech, where her research has focused on charge transport in DNA. By using specially-designed chiral metal complexes as probes of DNA she has been able to study how DNA is damaged and repaired. In DNA-based diagnostic tests, complexes are used to determine whether electrons can flow across the
Jacqueline Barton
199588
from cosmic rays and solar wind, are normally absorbed by Earth's atmosphere. When they interact in sufficient quantity, their effect is visible to the naked eye in a phenomenon called an aurora. Outside Earth's atmosphere, crews are exposed to about 1 millisievert each day, which is about a year of natural exposure on Earth. This results in a higher risk of cancer for astronauts. Radiation can penetrate living tissue and damage the DNA and chromosomes of lymphocytes. These cells are central to the immune system, and so any damage to them could contribute to the lower immunity experienced by astronauts.
International Space Station
3712258
study membrane biology, including the uptake of macromolecules and viruses . These are also used in somaclonal variation. Protoplasts are widely used for DNA transformation (for making genetically modified organisms), since the cell wall would otherwise block the passage of DNA into the cell. In the case of plant cells, protoplasts may be regenerated into whole plants first by growing into a group of plant cells that develops into a callus and then by regeneration of shoots (caulogenesis) from the callus using plant tissue culture methods. Growth of protoplasts into callus and regeneration of shoots requires the proper balance of
Protoplast
182101
the House of Representatives. Within certain regulatory limits, and subject to the effect of state legislation, therapeutic cloning is now legal in some parts of Australia. Canadian law prohibits the following: cloning humans, cloning stem cells, growing human embryos for research purposes, and buying or selling of embryos, sperm, eggs or other human reproductive material. It also bans making changes to human DNA that would pass from one generation to the next, including use of animal DNA in humans. Surrogate mothers are legally allowed, as is donation of sperm or eggs for reproductive purposes. Human embryos and stem cells are
Human cloning
7392698
mammalian target of rapamycin, and more. SIRT1, SIRT6 and SIRT7 proteins are employed in DNA repair. SIRT1 protein promotes homologous recombination in human cells and is involved in recombinational repair of DNA breaks. SIRT6 is a chromatin-associated protein and in mammalian cells is required for base excision repair of DNA damage. SIRT6 deficiency in mice leads to a degenerative aging-like phenotype. In addition, SIRT6 promotes the repair of DNA double-strand breaks. Furthermore, over-expression of SIRT6 can stimulate homologous recombinational repair. SIRT7 knockout mice display features of premature aging. SIRT7 protein is required for repair of double-strand breaks by non-homologous end
Sirtuin
3412877
other antimetabolite anti-cancer drugs, it acts by disrupting the DNA replication process of dividing cancer cells in the body. Hydroxyurea selectively inhibits ribonucleoside diphosphate reductase, an enzyme required to convert ribonucleoside diphosphates into deoxyribonucleoside diphosphates, thereby preventing cells from leaving the G1/S phase of the cell cycle. This agent also exhibits radiosensitizing activity by maintaining cells in the radiation-sensitive G1 phase and interfering with DNA repair. Biochemical research has explored its role as a DNA replication inhibitor which causes deoxyribonucleotide depletion and results in DNA double strand breaks near replication forks (see DNA repair). Repair of DNA damaged by chemicals
Hydroxycarbamide
8843688
strand hypothesis has proven difficult. After Cairns first proposed the immortal DNA strand mechanism, the theory has undergone several refinements. In 2002, he proposed that in addition to using immortal DNA strand mechanisms to segregate DNA, when the immortal DNA strands of adult stem cells undergo damage, they will choose to die (apoptose) rather than use DNA repair mechanisms that are normally used in non-stem cells. Emmanuel David Tannenbaum and James Sherley developed a quantitative model describing how repair of point mutations might differ in adult stem cells. They found that in adult stem cells, repair was most efficient if
Immortal DNA strand hypothesis
784087
37 °C, the rate of strand elongation was 749 nucleotides per second. The mutation rate per base pair per round of replication during phage T4 DNA synthesis is . Thus semiconservative DNA replication is both rapid and accurate. Semiconservative replication Semiconservative replication describes the mechanism by which DNA is replicated in all known cells. It derives its name from the fact that this mechanism of transcription was one of three models originally proposed for DNA replication: The deciphering of the structure of DNA by Watson and Crick in 1953 suggested that each strand of the double helix would serve as
Semiconservative replication
20409856
false-positives. In contrast, in linear amplification, the errors would appear randomly at different locations in the amplicons to be easily filtered out. Genomic DNA is randomly fragmented and tagged by Tn5 transposon insertion containing T7 promoter sequence, and the resulting DNA fragments are linearly amplified into RNAs by T7 in vitro transcription. Following reverse transcription and second strand synthesis, double-stranded DNA amplicons are formed representing the linear amplification product of the original genomic DNA, which is suitable for DNA library preparation and sequencing. 1. Cell lysis. Single cells are placed into PCR tubes containing lysis buffer by mouth pipetting, flow
LIANTI
9835868
Prokaryotic DNA replication Prokaryotic DNA replication is the process by which a prokaryote duplicates its DNA into another copy that is passed on to daughter cells. Although it is often studied in the model organism "E. coli", other bacteria show many similarities. Replication is bi-directional and originates at a single origin of replication (OriC). It consists of three steps: Initiation, elongation, and termination. All cells must finish DNA replication before they can proceed for cell division. Media conditions that support fast growth in bacteria also couples with shorter inter-initiation time in them, i.e. the doubling time in fast growing cells
Prokaryotic DNA replication
8843682
adult stem cells to be labeled during their formation. These long-term cells were demonstrated to be actively cycling, as demonstrated by incorporation and release of BrdU. Since these cells were cycling but continued to contain the BrdU label in their DNA, the researchers reasoned that they must be segregating their DNA using an immortal DNA strand mechanism. Joshua Merok "et al." from the lab of James Sherley engineered mammalian cells with an inducible p53 gene that controls asymmetric divisions. BrdU pulse/chase experiments with these cells demonstrated that chromosomes segregated non-randomly only when the cells were induced to divide asymmetrically like
Immortal DNA strand hypothesis
2868917
within cancer cells could lead to increased apoptosis due to high accumulation of DNA damage. One such inhibitor of histone acetyltransferases is called garcinol. This compound is found within the rinds of the garcinia indica fruit, otherwise known as mangosteen. To explore the effects of garcinol on histone acetyltransferases, researchers used HeLa cells. The cells underwent irradiation, creating double-strand breaks within the DNA, and garcinol was introduced into the cells to see if it influenced the DNA damage response. If garcinol is successful at inhibiting the process of non-homologous end joining, a DNA repair mechanism that shows preference in fixing
Histone acetyltransferase
12426388
archaea, "Halobacterium volcanii" forms cytoplasmic bridges between cells that appear to be used for transfer of DNA from one cell to another. Another archaeon, "Sulfolobus solfataricus", transfers DNA between cells by direct contact. Frols et al. found that exposure of "S. solfataricus" to DNA damaging agents induces cellular aggregation, and suggested that cellular aggregation may enhance DNA transfer among cells to provide increased repair of damaged DNA via homologous recombination. While prokaryotes are considered strictly unicellular, most can form stable aggregate communities. When such communities are encased in a stabilizing polymer matrix ("slime"), they may be called "biofilms". Cells in
Prokaryote
9557984
biological importance of phosphates is as a component of nucleotides, which serve as energy storage within cells (ATP) or when linked together, form the nucleic acids DNA and RNA. The double helix of our DNA is only possible because of the phosphate ester bridge that binds the helix. Besides making biomolecules, phosphorus is also found in bone and the enamel of mammalian teeth, whose strength is derived from calcium phosphate in the form of Hydroxylapatite. It is also found in the exoskeleton of insects, and phospholipids (found in all biological membranes). It also functions as a buffering agent in maintaining
Phosphorus cycle
17248086
Zeocin Zeocin is a formulation of phleomycin D1, a glycopeptide antibiotic and one of the phleomycins from "Streptomyces verticillus" belonging to the bleomycin family of antibiotics. It is a broad-spectrum antibiotic that is effective against most bacteria, filamentous fungi, yeast, plant, and animal cells. It causes cell death by intercalating into DNA and inducing double stranded breaks of the DNA. Zeocin is blue in colour due to the presence of copper ion Cu. The copper-chelated form of zeocin is inactive. When zeocin enters a cell, the Cu is reduced to Cu and then removed, and zeocin becomes activated and can
Zeocin
13566595
final step, there is crossover by means of RecA-dependent homologous recombination. "D. radiodurans" is capable of genetic transformation, a process by which DNA derived from one cell can be taken up by another cell and integrated into the recipient genome by homologous recombination. When DNA damages (e.g. pyrimidine dimers) are introduced into donor DNA by UV irradiation, the recipient cells efficiently repair the damages in the transforming DNA as they do in cellular DNA when the cells themselves are irradiated. Michael Daly has suggested the bacterium uses manganese complexes as antioxidants to protect itself against radiation damage. In 2007 his
Deinococcus radiodurans
1797344
Meselson–Stahl experiment The Meselson–Stahl experiment is an experiment by Matthew Meselson and Franklin Stahl in 1958 which supported Watson and Crick's hypothesis that DNA replication was semiconservative. In semiconservative replication, when the double stranded DNA helix is replicated, each of the two new double-stranded DNA helices consisted of one strand from the original helix and one newly synthesized. It has been called "the most beautiful experiment in biology." Meselson and Stahl decided the best way to tag the parent DNA would be to change one of the atoms in the parent DNA molecule. Since nitrogen is found in the nitrogenous
Meselson–Stahl experiment
10195512
hyperactivation induces pan-nuclear phosphorylation of histone H2AX among all the chromatin. H2AX phosphorylation is the signal, which allows double-strand break repair proteins (from NHEJ and homologous recombination pathways) to form DNA repair complexes selectively on DNA double-strand breaks. Dbait-dependent unspecific phosphorylation of H2AX results in inefficient double strand break recognition and repair. Most of the anticancer therapies act by induction of DNA damage (chemotherapy and radiation therapy). DNA breaks are the most lethal damage for cells, as one single double-strand break if unrepaired is sufficient to lead to cell death. "Dbait" enhances the efficacy of the DNA damaging agents as
SiDNA
19495332
is related to the uptake by cells of spontaneously released bacterial DNA, thus suggesting the existence of circulating DNA. In view of the malignant transformations obtained with DNA, the oncogenic (cancer-causing) role of circulating DNA is postulated." In the late 1970s, building on the discovery of circulating DNA in human blood by Mandel and Metais, Leon and his collaborators developed a radioimmunoassay for measuring nanogram quantities of nucleic acids in serum. This technique enabled them to observe that cancer patients tended to possess a greater quantity of circulating DNA in serum (on average) than their healthy counterparts. This led Stroun
Maurice Stroun
547384
other before being purified from the solution. Each method of extraction works well in the laboratory, but an analyst typically selects their preferred method based on factors such as the cost, the time involved, the quantity of DNA yielded, and the quality of DNA yielded. After the DNA is extracted from the sample, it can be analyzed, whether it be RFLP analysis or quantification and PCR analysis. The first methods for finding out genetics used for DNA profiling involved RFLP analysis. DNA is collected from cells and cut into small pieces using a restriction enzyme (a restriction digest). This generates
DNA profiling
17266475
all cases, cells lack the ability to repair double-stranded DNA breaks, making these compounds especially effective for treating tumor cells. The free radical mechanism to treat certain types of cancers extends beyond enediynes. Tirapazamine generates a free radical under anoxic conditions instead of the trigger mechanism of an enediyne. The free radical then continues on to cleave DNA in a similar manner to 1,4-didehydrobenzene in order to treat cancerous cells. It is currently in Phase III trials. Free radical damage to DNA Free radical damage to DNA can occur as a result of exposure to ionizing radiation or to radiomimetic
Free radical damage to DNA