a monomer of nucleic acids is called what
nucleotides
303193
Nucleic acid Nucleic acids are the biopolymers, or small biomolecules, essential to all known forms of life. The term "nucleic acid" is the overall name for DNA and RNA. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. If the sugar is a compound ribose, the polymer is RNA (ribonucleic acid); if the sugar is derived from ribose as deoxyribose, the polymer is DNA (deoxyribonucleic acid). Nucleic acids are the most important of all biomolecules. They are found in abundance in all living things, where they
Nucleic acid
15770958
have near 100% natural abundance, while C and N have low natural abundances. For these latter two nuclei, there is the capability of isotopically enriching desired atoms within the molecules, either uniformly or in a site-specific manner. Nucleotides uniformly enriched in C and/or N can be obtained through biochemical methods, by performing polymerase chain reaction using dNTPs or NTPs derived from bacteria grown in an isotopically enriched environment. Site-specific isotope enrichment must be done through chemical synthesis of the labeled nucleoside phosphoramidite monomer and of the full strand; however these are difficult and expensive to synthesize. Because nucleic acids have
Nuclear magnetic resonance spectroscopy of nucleic acids
303363
sites on sugar molecules in adjacent nucleotides. In a double helix, the two strands are oriented in opposite directions, which permits base pairing and complementarity between the base-pairs, all which is essential for replicating or transcribing the encoded information found in DNA. Unlike in nucleic acid nucleotides, singular cyclic nucleotides are formed when the phosphate group is bound twice to the same sugar molecule, i.e., at the corners of the sugar hydroxyl groups. These individual nucleotides function in cell metabolism rather than the nucleic acid structures of long-chain molecules. Nucleic acids then are polymeric macromolecules assembled from nucleotides, the monomer-units
Nucleotide
17040975
Bridged nucleic acid Bridged nucleic acids (BNAs) are modified RNA nucleotides. They are sometimes also referred to as constrained or inaccessible RNA molecules. BNA monomers can contain a five-membered, six-membered or even a seven-membered bridged structure with a “fixed” C’-endo sugar puckering. The bridge is synthetically incorporated at the 2’, 4’-position of the ribose to afford a 2’, 4’-BNA monomer. The monomers can be incorporated into oligonucleotide polymeric structures using standard phosphoamidite chemistry. BNAs are structurally rigid oligo-nucleotides with increased binding affinities and stability. Chemical structures of BNA monomers containing a bridge at the 2’, 4’-position of the ribose to
Bridged nucleic acid
303359
Nucleotide Nucleotides are organic molecules that serve as the monomer units for forming the nucleic acid polymers deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules within all life-forms on Earth. Nucleotides are the building blocks of nucleic acids; they are composed of three subunit molecules: a nitrogenous base, a five-carbon sugar (ribose or deoxyribose), and at least one phosphate group. A nucleoside is a nitrogenous base and a 5-carbon sugar. Thus a nucleoside plus a phosphate group yields a nucleotide. Nucleotides also play a central role in metabolism at a fundamental, cellular level. They carry
Nucleotide
2163420
the functions of a living thing. Nucleic acids also have a secondary structure and tertiary structure. Primary structure is sometimes mistakenly referred to as "primary sequence". Conversely, there is no parallel concept of secondary or tertiary sequence. Nucleic acids consist of a chain of linked units called nucleotides. Each nucleotide consists of three subunits: a phosphate group and a sugar (ribose in the case of RNA, deoxyribose in DNA) make up the backbone of the nucleic acid strand, and attached to the sugar is one of a set of nucleobases. The nucleobases are important in base pairing of strands to
Nucleic acid sequence
2749441
Ribonucleotide In biochemistry, a ribonucleotide is a nucleotide containing ribose as its pentose component. It is considered a molecular precursor of nucleic acids. Nucleotides are the basic building blocks of DNA and RNA. The monomer itself from ribonucleotides forms the basic building blocks for RNA. However, the reduction of ribonucleotide, by enzyme ribonucleotide reductase (RNR), forms deoxyribonucleotide, which is the essential building block for DNA. There are several differences between DNA deoxyribonucleotides and RNA ribonucleotides. Successive nucleotides are linked together via phosphodiester bonds by 3'-5'. Ribonucleotides are also utilized in other cellular functions. These special monomers are utilized in both
Ribonucleotide
11112599
of the chain (PNA can even form a triple helix). Nucleic acid analogues are also called Xeno Nucleic Acid and represent one of the main pillars of xenobiology, the design of new-to-nature forms of life based on alternative biochemistries. Artificial nucleic acids include peptide nucleic acid (PNA), Morpholino and locked nucleic acid (LNA), as well as glycol nucleic acid (GNA) and threose nucleic acid (TNA). Each of these is distinguished from naturally occurring DNA or RNA by changes to the backbone of the molecule. In May 2014, researchers announced that they had successfully introduced two new artificial nucleotides into bacterial
Nucleic acid analogue
42881
and therefore their function. Nucleic acids, so called because of their prevalence in cellular nuclei, is the generic name of the family of biopolymers. They are complex, high-molecular-weight biochemical macromolecules that can convey genetic information in all living cells and viruses. The monomers are called nucleotides, and each consists of three components: a nitrogenous heterocyclic base (either a purine or a pyrimidine), a pentose sugar, and a phosphate group. The most common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The phosphate group and the sugar of each nucleotide bond with each other to form the backbone of
Biochemistry
15770957
crowded and difficult to interpret. Two-dimensional NMR methods are almost always used with nucleic acids. These include correlation spectroscopy (COSY) and total coherence transfer spectroscopy (TOCSY) to detect through-bond nuclear couplings, and nuclear Overhauser effect spectroscopy (NOESY) to detect couplings between nuclei that are close to each other in space. The types of NMR usually done with nucleic acids are H NMR, C NMR, N NMR, and P NMR. F NMR is also useful if nonnatural nucleotides such as 2'-fluoro-2'-deoxyadenosine are incorporated into the nucleic acid strand, as natural nucleic acids do not contain any fluorine atoms. H and P
Nuclear magnetic resonance spectroscopy of nucleic acids
10327679
a polypeptide whose sequence is determined by the template nucleic acid. Crick’s thinking behind this proposal was based on a general consideration of the chemical properties of the two classes of molecule — nucleic acids and proteins. The amino acids are characterised by having a variety of side chains which vary from being hydrophilic to hydrophobic: their individual characters reside in the very different properties these side chains have. By contrast, a nucleic acid is composed of a string of nucleotides whose sequence presents a geometrically defined surface for hydrogen bonding. This makes nucleic acids good at recognising each other,
Adaptor hypothesis
8483700
Nucleic acid metabolism Nucleic acid metabolism is the process by which nucleic acids (DNA and RNA) are synthesized and degraded. Nucleic acids are polymers of nucleotides. Nucleotide synthesis is an anabolic mechanism generally involving the chemical reaction of phosphate, pentose sugar, and a nitrogenous base. Destruction of nucleic acid is a catabolic reaction. Additionally, parts of the nucleotides or nucleobases can be salvaged to recreate new nucleotides. Both synthesis and degradation reactions require enzymes to facilitate the event. Defects or deficiencies in these enzymes can lead to a variety of diseases. Nucleotides can be separated into purines and pyrimidines. They
Nucleic acid metabolism
97533
DNA Deoxyribonucleic acid (; DNA) is a molecule composed of two chains that coil around each other to form a double helix carrying the genetic instructions used in the growth, development, functioning and reproduction of all known living organisms and many viruses. DNA and ribonucleic acid (RNA) are nucleic acids; alongside proteins, lipids and complex carbohydrates (polysaccharides), nucleic acids are one of the four major types of macromolecules that are essential for all known forms of life. The two DNA strands are also known as polynucleotides as they are composed of simpler monomeric units called nucleotides. Each nucleotide is composed
DNA
303193
Nucleic acid Nucleic acids are the biopolymers, or small biomolecules, essential to all known forms of life. The term "nucleic acid" is the overall name for DNA and RNA. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. If the sugar is a compound ribose, the polymer is RNA (ribonucleic acid); if the sugar is derived from ribose as deoxyribose, the polymer is DNA (deoxyribonucleic acid). Nucleic acids are the most important of all biomolecules. They are found in abundance in all living things, where they
Nucleic acid
12093539
nucleic acid structure prediction. In structure prediction, the structure is determined from a known sequence, while in nucleic acid design, a sequence is generated which will form a desired structure. The structure of nucleic acids consists of a sequence of nucleotides. There are four types of nucleotides distinguished by which of the four nucleobases they contain: in DNA these are adenine (A), cytosine (C), guanine (G), and thymine (T). Nucleic acids have the property that two molecules will bind to each other to form a double helix only if the two sequences are complementary, that is, they can form matching
Nucleic acid design
2763951
Reading frame In molecular biology, a reading frame is a way of dividing the sequence of nucleotides in a nucleic acid (DNA or RNA) molecule into a set of consecutive, non-overlapping triplets. Where these triplets equate to amino acids or stop signals during translation, they are called codons. A single strand of a nucleic acid molecule has a phosphoryl end, called the 5′-end, and a hydroxyl or 3′-end. These define the 5'→3' direction. There are three reading frames that can be read in this 5'→3' direction, each beginning from a different nucleotide in a triplet. In a double stranded nucleic
Reading frame
15770955
Nuclear magnetic resonance spectroscopy of nucleic acids Nucleic acid NMR is the use of nuclear magnetic resonance spectroscopy to obtain information about the structure and dynamics of nucleic acid molecules, such as DNA or RNA. It is useful for molecules of up to 100 nucleotides, and as of 2003, nearly half of all known RNA structures had been determined by NMR spectroscopy. NMR has advantages over X-ray crystallography, which is the other method for high-resolution nucleic acid structure determination, in that the molecules are being observed in their natural solution state rather than in a crystal lattice that may affect
Nuclear magnetic resonance spectroscopy of nucleic acids
15770968
instrumentation, many detailed structural studies were reported starting in 1983. Nuclear magnetic resonance spectroscopy of nucleic acids Nucleic acid NMR is the use of nuclear magnetic resonance spectroscopy to obtain information about the structure and dynamics of nucleic acid molecules, such as DNA or RNA. It is useful for molecules of up to 100 nucleotides, and as of 2003, nearly half of all known RNA structures had been determined by NMR spectroscopy. NMR has advantages over X-ray crystallography, which is the other method for high-resolution nucleic acid structure determination, in that the molecules are being observed in their natural solution
Nuclear magnetic resonance spectroscopy of nucleic acids
2763956
be translated in a different reading frame. This is distinct from a frameshift mutation, as the nucleotide sequence (DNA or RNA) is not altered—only the frame in which it is read. Reading frame In molecular biology, a reading frame is a way of dividing the sequence of nucleotides in a nucleic acid (DNA or RNA) molecule into a set of consecutive, non-overlapping triplets. Where these triplets equate to amino acids or stop signals during translation, they are called codons. A single strand of a nucleic acid molecule has a phosphoryl end, called the 5′-end, and a hydroxyl or 3′-end. These
Reading frame
303208
peptide nucleic acid, morpholino- and locked nucleic acid, glycol nucleic acid, and threose nucleic acid. Each of these is distinguished from naturally occurring DNA or RNA by changes to the backbone of the molecules. Nucleic acid Nucleic acids are the biopolymers, or small biomolecules, essential to all known forms of life. The term "nucleic acid" is the overall name for DNA and RNA. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. If the sugar is a compound ribose, the polymer is RNA (ribonucleic acid); if
Nucleic acid
10719531
colleagues demonstrated that phosphorylated glycoaldehyde when condensed with glyceraldehyde (a product of successive formaldehyde condensations) produces phosphorylated ribose differentially, providing a plausible explanation for the origin of both the sugar ribose, and the phosphate group required to polymerize monomeric nucleotides, in modern biochemistry. Eschenmoser developed synthetic pathways for artificial nucleic acids, specifically modifying the sugar backbone of the polymer. Having developed a number of structural alternatives to the naturally occurring nucleic acids, Eschenmoser and his colleagues were able to contrast the properties of these synthetic nucleic acids with naturally occurring ones to effectively determine the properties of RNA and DNA
Albert Eschenmoser
498291
which biochemically and molecular/cellular biology form the dynamic and chaotic life bearing process of organic carbon based life forms. IMP is the "template" molecular structure for nucleotides, thus the molecular structure of extant nucleic acids. Adenine is one of the two purine nucleobases (the other being guanine) used in forming nucleotides of the nucleic acids. In DNA, adenine binds to thymine via two hydrogen bonds to assist in stabilizing the nucleic acid structures. In RNA, which is used for protein synthesis, adenine binds to uracil. Adenine forms adenosine, a nucleoside, when attached to ribose, and deoxyadenosine when attached to deoxyribose.
Adenine
7493671
Molecular beacon Molecular beacons are oligonucleotide hybridization probes that can report the presence of specific nucleic acids in homogenous solutions. The term more often used is molecular beacon probes. Molecular beacons are hairpin shaped molecules with an internally quenched fluorophore whose fluorescence is restored when they bind to a target nucleic acid sequence. This is a novel non-radioactive method for detecting specific sequences of nucleic acids. They are useful in situations where it is either not possible or desirable to isolate the probe-target hybrids from an excess of the hybridization probes. A typical molecular beacon probe is 25 nucleotides long.
Molecular beacon
20686745
of Leeds, where she joined Astbury's laboratory. During her postgraduate studies she used X-ray diffraction to characterise biomolecules, including nucleic acids. She received her PhD in 1939. Astbury became interested in DNA, and Bell's work demonstrated it was a regular, ordered structure of nucleotides separated by 3.3 - 3.4 Å. She studied the nucleic acids in yeast, pancreases, tobacco mosaic virus and calf thymus. She recognised that the "beginnings of life are clearly associated with the interaction of proteins and nucleic acids". Bell and Astbury published an X-ray study on DNA in 1938, describing the nucleotides as a "Pile of
Florence Bell (scientist)
3459223
putty. Greek prefixes are often used to designate the number of monomer units in the oligomer, for example a tetramer being composed of four units and a hexamer of six. In biochemistry, the term oligonucleotide – or, informally, "oligo" – is used for short, single-stranded nucleic acid fragments, such as DNA or RNA, or similar fragments of analogs of nucleic acids such as peptide nucleic acid or Morpholinos. Such oligos are used in hybridization experiments (bound to glass slides or nylon membranes), as probes for in situ hybridization or in antisense experiments such as gene knockdowns. It can also refer
Oligomer
4252232
Adenosine deaminase Adenosine deaminase (also known as adenosine aminohydrolase, or ADA) is an enzyme () involved in purine metabolism. It is needed for the breakdown of adenosine from food and for the turnover of nucleic acids in tissues. Its primary function in humans is the development and maintenance of the immune system. However, the full physiological role of ADA is not yet completely understood. ADA exists in both small form (as a monomer) and large form (as a dimer-complex). In the monomer form, the enzyme is a polypeptide chain, folded into eight strands of parallel α/β barrels, which surround a
Adenosine deaminase
2076720
covalently connected along with the loss of some small molecule, most commonly water. Because they are polymerized through complex enzymatic mechanisms, none of the biopolymers' backbones are formed through the elimination of water but through the elimination of other small biological molecules. Each of these biopolymers can be characterized as either a heteropolymer, meaning it consists of more than one monomer ordered in the backbone chain, or a homopolymer, which consists of just one repeating monomer. Polypeptides and nucleic acids are very commonly heteropolymers whereas common carbohydrate macromolecules such as glycogen can be homopolymers. This is because the chemical differences
Backbone chain
297819
Biomolecular chemistry is a major category within organic chemistry which is frequently studied by biochemists. Many complex multi-functional group molecules are important in living organisms. Some are long-chain biopolymers, and these include peptides, DNA, RNA and the polysaccharides such as starches in animals and celluloses in plants. The other main classes are amino acids (monomer building blocks of peptides and proteins), carbohydrates (which includes the polysaccharides), the nucleic acids (which include DNA and RNA as polymers), and the lipids. In addition, animal biochemistry contains many small molecule intermediates which assist in energy production through the Krebs cycle, and produces isoprene,
Organic chemistry
2341382
biologically active. What is called ATP is often actually Mg-ATP. Nucleic acids have an important range of interactions with Mg. The binding of Mg to DNA and RNA stabilises structure; this can be observed in the increased melting temperature ("T") of double-stranded DNA in the presence of Mg. In addition, ribosomes contain large amounts of Mg and the stabilisation provided is essential to the complexation of this ribo-protein. A large number of enzymes involved in the biochemistry of nucleic acids bind Mg for activity, using the ion for both activation and catalysis. Finally, the autocatalysis of many ribozymes (enzymes containing
Magnesium in biology
12741
and Trp) buried in the middle of the protein, whereas hydrophilic side chains are exposed to the aqueous solvent. (Note that in biochemistry, a residue refers to a specific monomer within the polymeric chain of a polysaccharide, protein or nucleic acid.) The integral membrane proteins tend to have outer rings of exposed hydrophobic amino acids that anchor them into the lipid bilayer. In the case part-way between these two extremes, some peripheral membrane proteins have a patch of hydrophobic amino acids on their surface that locks onto the membrane. In similar fashion, proteins that have to bind to positively charged
Amino acid
11112604
analogue that lacks a 3' hydroxyl and mimics adenosine is called cordycepin. Cordycepin is an anticancer drug that targets RNA replication. Another analogue in sequencing is a nucleobase analogue, 7-deaza-GTP and is used to sequence CG rich regions, instead 7-deaza-ATP is called tubercidin, an antibiotic. RNA may be too complex to be the first nucleic acid, so before the RNA world several simpler nucleic acids that differ in the backbone, such as TNA and GNA and PNA, have been offered as candidates for the first nucleic acids. Naturally occurring bases can be divided into two classes according to their structure:
Nucleic acid analogue
11265155
code to ribosomes where it is used to make proteins. This is called translation because the protein's amino acid structure is determined by the mRNA's code. Information is hence translated from the language of nucleic acids to the language of amino acids. Some nucleic acids of RNA viruses function directly as mRNA without further modification. For this reason, these viruses are called positive-sense RNA viruses. In other RNA viruses, the RNA is a complementary copy of mRNA and these viruses rely on the cell's or their own enzyme to make mRNA. These are called negative-sense RNA viruses. In viruses made
Introduction to viruses
14460462
as programmable molecular cages. Nucleic acid structures can be made to incorporate molecules other than nucleic acids, sometimes called heteroelements, including proteins, metallic nanoparticles, quantum dots, and fullerenes. This allows the construction of materials and devices with a range of functionalities much greater than is possible with nucleic acids alone. The goal is to use the self-assembly of the nucleic acid structures to template the assembly of the nanoparticles hosted on them, controlling their position and in some cases orientation. Many of these schemes use a covalent attachment scheme, using oligonucleotides with amide or thiol functional groups as a chemical
DNA nanotechnology
984977
Polyacrylamide gel electrophoresis Polyacrylamide gel electrophoresis (PAGE) is a technique widely used in biochemistry, forensic chemistry, genetics, molecular biology and biotechnology to separate biological macromolecules, usually proteins or nucleic acids, according to their electrophoretic mobility. Electrophoretic mobility is a function of the length, conformation and charge of the molecule. Polyacrylamide gel electrophoresis is a powerful tool used to analyze RNA samples. When polyacrylamide gel is denatured after electrophoresis, it provides information on the sample composition of the RNA species. Hydration of acrylonitrile results in formation of acrylamide molecules (CHNO) by nitrile hydratase. Acrylamide monomer is in a powder state before
Polyacrylamide gel electrophoresis
4252242
mechanism of action is inhibition of adenosine deaminase. Coformycin was also described as a adenosine deaminase inhibitor but is alleged to be an antibiotic. Adenosine deaminase Adenosine deaminase (also known as adenosine aminohydrolase, or ADA) is an enzyme () involved in purine metabolism. It is needed for the breakdown of adenosine from food and for the turnover of nucleic acids in tissues. Its primary function in humans is the development and maintenance of the immune system. However, the full physiological role of ADA is not yet completely understood. ADA exists in both small form (as a monomer) and large form
Adenosine deaminase
303197
RNA (except some cells such as mature red blood cells), while viruses contain either DNA or RNA, but usually not both. The basic component of biological nucleic acids is the nucleotide, each of which contains a pentose sugar (ribose or deoxyribose), a phosphate group, and a nucleobase. Nucleic acids are also generated within the laboratory, through the use of enzymes (DNA and RNA polymerases) and by solid-phase chemical synthesis. The chemical methods also enable the generation of altered nucleic acids that are not found in nature, for example peptide nucleic acids. Nucleic acids are generally very large molecules. Indeed, DNA
Nucleic acid
3459221
Oligomer An oligomer () ("oligo-", "a few" + "-mer", "parts") is a molecular complex of chemicals that consists of a few monomer units, in contrast to a polymer, where the number of monomers is, in principle, infinite. Dimers, trimers, and tetramers are, for instance, oligomers composed of two, three, and four monomers, respectively. In biochemistry, an oligomer usually refers to a macromolecular complex formed by non-covalent bonding of a few macromolecules like proteins or nucleic acids. In this sense, a homo-oligomer would be formed by few identical molecules and by contrast, a hetero-oligomer would be made of more than one,
Oligomer
13353209
Magnet-assisted transfection Magnet-assisted transfection is a transfection method which uses magnetic interactions to deliver DNA into target cells. Nucleic acids are associated with magnetic nanoparticles, and magnetic fields drive the nucleic acid-particle complexes into target cells, where the nucleic acids are released. Nanoparticles used as carriers for nucleic acids are mostly iron oxides. These iron oxides can be generated by precipitation from acidic iron-salt solutions upon addition of appropriate bases. The magnetic nanoparticles have an approximate size of 100 nm and are additionally coated with biological polymers to allow loading of nucleic acids. Particles and nucleic acids form complexes by
Magnet-assisted transfection
5880619
Ideal chain An ideal chain (or freely-jointed chain) is the simplest model to describe polymers, such as nucleic acids and proteins. It only assumes a polymer as a random walk and neglects any kind of interactions among monomers. Although it is simple, its generality gives insight about the physics of polymers. In this model, monomers are rigid rods of a fixed length "l", and their orientation is completely independent of the orientations and positions of neighbouring monomers, to the extent that two monomers can co-exist at the same place. In some cases, the monomer has a physical interpretation, such as
Ideal chain
17177796
in terms of virus eradication, aberrant stimulation or unregulated control of the system could lead to inappropriate and / or excessive interferon output. Studies of the AGS-related proteins TREX1, the RNase H2 complex, SAMHD1 and ADAR1, suggest that an inappropriate accumulation of self-derived nucleic acids can induce type I interferon signaling. The findings of "IFIH1" mutations in the similar context implicates the aberrant sensing of nucleic acids as a cause of immune upregulation. What is the source of the nucleic acid inducing the immune disturbance in AGS? Intriguingly, it has been shown that TREX1 can metabolise reverse-transcribed HIV-1 DNA and
Aicardi–Goutières syndrome
14447302
is found in prokaryotes, while the solenoidal supercoiling is mostly seen in eukaryotes. The quaternary structure of nucleic acids is similar to that of protein quaternary structure. Although some of the concepts are not exactly the same, the quaternary structure refers to a higher-level of organization of nucleic acids. Moreover, it refers to interactions of the nucleic acids with other molecules. The most commonly seen form of higher-level organization of nucleic acids is seen in the form of chromatin which leads to its interactions with the small proteins histones. Also, the quaternary structure refers to the interactions between separate RNA
Nucleic acid structure
16583645
Spherical nucleic acid Spherical nucleic acids (SNAs) – defined as structures that are an arrangement of densely packed, highly oriented nucleic acids in a spherical geometry – were first introduced in 1996 by the Mirkin group at Northwestern University. The arrangement and orientation of one-dimensional linear nucleic acids within this three-dimensional framework results in new chemical, biological, and physical properties in the use of nucleic acids for intracellular gene regulation (though this is disputed ), molecular diagnostics, and materials synthesis applications. The first SNA consisted of 3’ alkanethiol-terminated, single-stranded oligonucleotides (short DNA sequences) covalently attached to the surface of spherical
Spherical nucleic acid
2163424
the many bases created through mutagen presence, both of them through deamination (replacement of the amine-group with a carbonyl-group). Hypoxanthine is produced from adenine, xanthine from guanine. Similarly, deamination of cytosine results in uracil. In biological systems, nucleic acids contain information which is used by a living cell to construct specific proteins. The sequence of nucleobases on a nucleic acid strand is translated by cell machinery into a sequence of amino acids making up a protein strand. Each group of three bases, called a codon, corresponds to a single amino acid, and there is a specific genetic code by which
Nucleic acid sequence
12093546
a nucleic acid duplex. This is less accurate but also much less computationally costly. Software for thermodynamic modeling of nucleic acids includes Nupack, mfold/UNAFold, and Vienna. A related approach, inverse secondary structure prediction, uses stochastic local search which improves a nucleic acid sequence by running a structure prediction algorithm and the modifying the sequence to eliminate unwanted features. Geometrical models of nucleic acids are used to predict tertiary structure. This is important because designed nucleic acid complexes usually contain multiple junction points, which introduces geometric constraints to the system. These constraints stem from the basic structure of nucleic acids, mainly
Nucleic acid design
2076718
substituent "side chains." For this reason, only proteins, carbohydrates, and nucleic acids should be considered as biological macromolecules with polymeric backbones. The character of the backbone chain depends on the type of polymerization: in step-growth polymerization, the monomer moiety becomes the backbone, and thus the backbone is typically functional. These include polythiophenes or low band gap polymers in organic semiconductors. In chain-growth polymerization, typically applied for alkenes, the backbone is not functional, but bears the functional side chains or pendant groups. The character of the backbone, i.e. its flexibility, determines the thermal properties of the polymer (such as the glass
Backbone chain
5350907
structures) forming metaphosphoric acid molecules. The simplest such compound is trimetaphosphoric acid or cyclo-triphosphoric acid having the formula HPO. Its structure is shown in the illustration. Since the ends are condensed, its formula has one less HO (water) than tripolyphosphoric acid. What are commonly called trimetaphosphates actually have a mixture of ring sizes. A general formula for such cyclic compounds is (HPO) where x = number of phosphoric units in the molecule. The hypothetical monomer monometaphosphoric acid (HPO), which would be valence isoelectronic with nitric acid, is not known to exist. When these metaphosphoric acids lose their hydrogens as H,
Phosphoric acids and phosphates
11034903
was first shown that single-stranded nucleic acids can be detected by electrophysiology measurements as they translocate through an alpha-hemolysin pore embedded in a lipid bilayer. This was an important milestone in the development of nanopore sequencing. Staphylococcus aureus alpha toxin Alpha-toxin, also known as alpha-hemolysin (Hla), is the major cytotoxic agent released by bacterium "Staphylococcus aureus" and the first identified member of the pore forming beta-barrel toxin family. This toxin consists mostly of beta-sheets (68%) with only about 10% alpha-helices. The "hla" gene on the "S. aureus" chromosome encodes the 293 residue protein monomer, which forms heptameric units on the
Staphylococcus aureus alpha toxin
15221606
biomolecules like proteins and DNA/RNA. There is some overlap of Biotechnology and Wet nanotechnology because living things are inherently bottom-up engineered and any exploitation of this by biotechnologists means they dabble in bottom-up engineering (though mostly at the level of producing macromolecules like proteins and nucleic acids from there monomer units. Wet nanotech, however, seeks to analyse living things and their components as engineering systems and aims to understand them completely to have complete control of the behavior of the system and to derive principles and methods that can be applied more broadly to bottom up manufacturing, to manipulate matter
Wet nanotechnology
6011256
Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid "Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid" was the first article published to describe the discovery of the double helix structure of DNA, using X-ray diffraction and the mathematics of a helix transform. It was published by Francis Crick and James D. Watson in the scientific journal "Nature" on pages 737–738 of its 171st volume (dated 25 April 1953). This article is often termed a "pearl" of science because it is brief and contains the answer to a fundamental mystery about living organisms. This mystery
Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid
19495335
changes and copy-number alterations. "Circulating Nucleic Acids in Plasma and Serum Congress" The early work of Stroun and Anker spurred intense investigation into the relationship of circulating nucleic acids and human conditions, such as disease, trauma, and pregnancy. For example, Lo demonstrated that fetal-specific nucleic acids could be detected in maternal peripheral blood in the late 1990s. As such, the pair organized the first global symposium dedicated to circulating nucleic acid research in 1999 held in Menthon, France. The conference was named CNAPS (Circulating Nucleic Acids in Plasma and Serum) and is held every other year to this day. In
Maurice Stroun
9726342
Nucleic acid quantitation In molecular biology, quantitation of nucleic acids is commonly performed to determine the average concentrations of DNA or RNA present in a mixture, as well as their purity. Reactions that use nucleic acids often require particular amounts and purity for optimum performance. To date, there are two main approaches used by scientists to quantitate, or establish the concentration, of nucleic acids (such as DNA or RNA) in a solution. These are spectrophotometric quantification and UV fluorescence tagging in presence of a DNA dye. One of the more commonly used practices to quantitate DNA or RNA is the
Nucleic acid quantitation
1799122
Gel electrophoresis of nucleic acids Nucleic acid electrophoresis is an analytical technique used to separate DNA or RNA fragments by size and reactivity. Nucleic acid molecules which are to be analyzed are set upon a viscous medium, the gel, where an electric field induces the nucleic acids (which are negatively charged due to their sugar-phosphate backbone) to migrate toward the anode (which is positively charged because this is an electrolytic rather than galvanic cell). The separation of these fragments is accomplished by exploiting the mobilities with which different sized molecules are able to pass through the gel. Longer molecules migrate
Gel electrophoresis of nucleic acids
19495333
to explore if other methods could be developed to not only detect the overall abundance of nucleic acids in patients with disease (and specifically cancer) but to also detect the disease-specific components of such circulating nucleic acids themselves. Unlike bacterial transformations in plants and animal cells involving clear transfer of separately identifiable nucleic acids, it was not clear how malignancy in cancer arose, although there were many competing theories. Stroun’s postulate that neoplastic malignancy was associated with the presence of tumor specific nucleic acids, led to extensive research by his group of circulating nucleic acids in cancer patients in the
Maurice Stroun
9726354
protein contamination of a DNA sample that is similar to the 260 nm/280 nm spectrophotometric version. Nucleic acid quantitation In molecular biology, quantitation of nucleic acids is commonly performed to determine the average concentrations of DNA or RNA present in a mixture, as well as their purity. Reactions that use nucleic acids often require particular amounts and purity for optimum performance. To date, there are two main approaches used by scientists to quantitate, or establish the concentration, of nucleic acids (such as DNA or RNA) in a solution. These are spectrophotometric quantification and UV fluorescence tagging in presence of a
Nucleic acid quantitation
104217
promotes denaturation of nucleic acids in order to eliminate the influence of nucleic acid shape on their electrophoretic mobility. The optical activity (absorption and scattering of light) and hydrodynamic properties (translational diffusion, sedimentation coefficients, and rotational correlation times) of formamide denatured nucleic acids are similar to those of heat-denatured nucleic acids. Therefore, depending on the desired effect, chemically denaturing DNA can provide a gentler procedure for denaturing nucleic acids than denaturation induced by heat. Studies comparing different denaturation methods such as heating, beads mill of different bead sizes, probe sonification, and chemical denaturation show that chemical denaturation can provide quicker
Denaturation (biochemistry)
1799147
Cytidine or guanosine to the electrophoresis buffer at 1 mM concentration may protect the DNA from damage. Alternatively, a blue light excitation source with a blue-excitable stain such as SYBR Green or GelGreen may be used. Gel electrophoresis research often takes advantage of software-based image analysis tools, such as ImageJ. Gel electrophoresis of nucleic acids Nucleic acid electrophoresis is an analytical technique used to separate DNA or RNA fragments by size and reactivity. Nucleic acid molecules which are to be analyzed are set upon a viscous medium, the gel, where an electric field induces the nucleic acids (which are negatively
Gel electrophoresis of nucleic acids
15770956
the molecule's structural properties. It is also possible to investigate dynamics with NMR. This comes at the cost of slightly less accurate and detailed structures than crystallography. Nucleic acid NMR uses techniques similar to those of protein NMR, but has several differences. Nucleic acids have a smaller percentage of hydrogen atoms, which are the atoms usually observed in NMR, and because nucleic acid double helices are stiff and roughly linear, they do not fold back on themselves to give "long-range" correlations. Nucleic acids also tend to have resonances distributed over a smaller range than proteins, making the spectra potentially more
Nuclear magnetic resonance spectroscopy of nucleic acids
17147297
Boom method Boom method (Boom nucleic acid extraction method) is a solid phase extraction method for isolating nucleic acid from a biological sample. This method is characterized by "absorbing the nucleic acids (NA) to the silica beads". Boom method (Boom nucleic acid extraction method) is a solid phase extraction method for "isolating nucleic acid (NA) from biological samples. Essential of this method is the use of silica beads, capable of binding the NA in the presence of a chaotropic substance according to the effect. This method is one of the most widespread methods for isolating nucleic acids from biological samples
Boom method
9726348
for nucleic acids. One A260 unit is the amount of nucleic acid contained in 1 mL and producing an OD of 1. The same conversion factors apply, and therefore, in such contexts: It is common for nucleic acid samples to be contaminated with other molecules (i.e. proteins, organic compounds, other). The secondary benefit of using spectrophotometric analysis for nucleic acid quantitation is the ability to determine sample purity using the 260 nm:280 nm calculation. The ratio of the absorbance at 260 and 280 nm (A) is used to assess the purity of nucleic acids. For pure DNA, A is widely
Nucleic acid quantitation
16724749
molecular biology. The modern synthesis was formulated before the elucidation of the double-helix structure of DNA and the establishment of molecular biology in its current status of prominence. Given what was known at the time a simple, powerful model of genetic change through undirected mutation (loosely described as "random") and natural selection, was seen as sufficient to explain evolution as observed in nature. With the discovery of the nature and roles of nucleic acids in genetics, this model prompted Francis Crick's so-called Central Dogma of Molecular Biology: "[Sequential] information cannot be transferred back from protein to either protein or nucleic
Natural genetic engineering
9645268
from two single stranded oligonucleotides. Under this assumption one can elegantly describe the thermodynamic parameters for forming double-stranded nucleic acid AB from single-stranded nucleic acids A and B. The equilibrium constant for this reaction is formula_1. According to the Van´t Hoff equation, the relation between free energy, Δ"G", and "K" is Δ"G°" = -"RT"ln "K", where "R" is the ideal gas law constant, and "T" is the kelvin temperature of the reaction. This gives, for the nucleic acid system, formula_2. The melting temperature, "T", occurs when half of the double-stranded nucleic acid has dissociated. If no additional nucleic acids are
Nucleic acid thermodynamics
932328
is encapsulated, it is then called a satellite virus. Prions, named for their description as ""pr"oteinaceous and "in"fectious particles", lack any detectable (as of 2002) nucleic acids or virus-like particles. They resist inactivation procedures that normally affect nucleic acids. Virus classification Virus classification is the process of naming viruses and placing them into a taxonomic system. Similar to the classification systems used for cellular organisms, virus classification is the subject of ongoing debate and proposals. This is mainly due to the pseudo-living nature of viruses, which is to say they are non-living particles with some chemical characteristics similar to those
Virus classification
8549144
company using heavier isotopes of carbon (C13) and hydrogen (deuterium) to stabilize essential compounds like amino acids, nucleic acids and lipids to target age-related diseases. Cantor held positions at Columbia University and the University of California, Berkeley. Cantor’s laboratory at Boston University has developed methods for separating large DNA molecules, for studying structural relationships in complex proteins and nucleic acids, and for sensitive detection of proteins and nucleic acids in a variety of settings. Professor Cantor has been director of the Department of Energy Human Genome Project and Chairman of the Department of Biomedical Engineering at Boston University. Cantor is
Charles Cantor
12551594
peptide nucleic acids are capable of forming duplex structures with individual DNA- and RNA-strands and are, therefore, not only called DNA-analog, but also they are considered as candidates for the first genetic material on Earth. The corresponding diamino acids such as 2,3-diaminopropanoic acid were detected in the Murchison meteorite and in a simulated comet. Diamino acid In chemistry, a diamino acid, also called a diamino carboxylic acid, is a molecule containing at least one carboxyl and two amine functional groups. Diamino acids belong to the class of amino acids. Asparagine, glutamine and lysine are proteinaceous diamino acids which are components
Diamino acid
13353213
synergistic effects in transfection efficiency can arise from the possible combination of lipofection and magnet-assisted transfection. In future, this technology might be also an alternative strategy to the currently used viral and non-viral vectors in gene-therapy and gene transfer. Magnet-assisted transfection Magnet-assisted transfection is a transfection method which uses magnetic interactions to deliver DNA into target cells. Nucleic acids are associated with magnetic nanoparticles, and magnetic fields drive the nucleic acid-particle complexes into target cells, where the nucleic acids are released. Nanoparticles used as carriers for nucleic acids are mostly iron oxides. These iron oxides can be generated by precipitation
Magnet-assisted transfection
6659422
obtain nucleic acid samples, the cell must be lysed and the nucleic acids separated from all other cell materials. Phenol is a useful compound for breaking down superfluous cell materials that would otherwise contaminate the nucleic acid sample. There are two reasons why phenol makes such an effective purifier for nucleic acid samples. The first is that it is a non-polar compound. Because nucleic acids are highly polar, they do not dissolve in the presence of phenol. The second is that phenol has a density of 1.07 g/cm, which is higher than the density of water (1.00 g/cm). Thus, when
Phenol extraction
9520888
called a capsid, and nucleic acid (either RNA or DNA). The capsid's main function is to protect the nucleic acid. Mutagenesis of viral capsids is a well-established technique that permits the alteration of the capsid surface. Such alterations can include changing the charge or attaching specific ligands to the capsid surface via their chemical interactions with surface molecules or amino acids. Viral capsids have been shown to allow the attachment of small peptides (<30 amino acids) onto their surface. Furthermore, heterologous expression of CCMV in yeast allows large-scale production of wild-type or genetically modified CCMV capsids. These capsids can either
Cowpea chlorotic mottle virus
12551593
Diamino acid In chemistry, a diamino acid, also called a diamino carboxylic acid, is a molecule containing at least one carboxyl and two amine functional groups. Diamino acids belong to the class of amino acids. Asparagine, glutamine and lysine are proteinaceous diamino acids which are components of proteins. These three diamino acids are coded by codons of the genetic material and belong therefore to the cationic amino acids. Ornithine and 2,6-diaminopimelic acid are non-proteinaceous diamino acids. In biochemistry, diamino acids are of particular interest. Diamino acids are used for the synthesis of specific peptide nucleic acids, such as daPNA. Artificial
Diamino acid
5962044
dye (fluorochrome) is acridine orange. Under certain conditions it stains single-stranded nucleic acids fluorescing red (red luminescence) while when interacts with double stranded nucleic acids gives green fluorescence. Metachromasia Metachromasia (var. metachromasy) is a characteristical change in the color of staining carried out in biological tissues, exhibited by certain dyes when they bind to particular substances present in these tissues, called chromotropes. For example, toluidine blue becomes dark blue (with a colour range from blue-red dependent on glycosaminoglycan content) when bound to cartilage. Other widely used metachromatic stains are the haematological Giemsa and May-Grunwald stains that also contain thiazine dyes.
Metachromasia
10327678
in a specific sequence, that sequence being determined by the nucleotide sequence of the nucleic acid (DNA or RNA) template. Crick proposed that each amino acid is first attached to its own specific “adaptor” piece of nucleic acid (in an enzyme-catalysed reaction). The order of assembly of the amino acids is then determined by a specific recognition between the adaptor and the nucleic acid which is serving as the informational template. In this way the amino acids could be lined up by the template in a specific order. Coupling between adjacent amino acids would then lead to the synthesis of
Adaptor hypothesis
12657814
such as rifampin, act upon DNA-dependent RNA polymerase. Antifolates act primarily as inhibitors of both RNA and DNA, and are often grouped with nucleic acid inhibitors in textbooks. However, they also act indirectly as protein synthesis inhibitors (because tetrahydrofolate is also involved in the synthesis of amino acids serine and methionine), so they are sometimes considered as their own category, antimetabolites. However, the term "antimetabolite", when used literally, can apply to many different classes of drugs. Nucleic acid inhibitor A nucleic acid inhibitor is a type of antibacterial that acts by inhibiting the production of nucleic acids. There are two
Nucleic acid inhibitor
9726350
not true — it takes a relatively large amount of protein contamination to significantly affect the 260:280 ratio in a nucleic acid solution. 260:280 ratio has high sensitivity for nucleic acid contamination in protein: 260:230 ratio lacks sensitivity for protein contamination in nucleic acids (table shown for RNA, 100% DNA is approximately 1.8): This difference is due to the much higher mass attenuation coefficient nucleic acids have at 260 nm and 280 nm, compared to that of proteins. Because of this, even for relatively high concentrations of protein, the protein contributes relatively little to the 260 and 280 absorbance. While
Nucleic acid quantitation
146628
molecular biologist and played a crucial role in research related to revealing the helical structure of DNA. He is widely known for the use of the term "central dogma" to summarize the idea that once information is transferred from nucleic acids (DNA or RNA) to proteins, it cannot flow back to nucleic acids. In other words, the final step in the flow of information from nucleic acids to proteins is irreversible. During the remainder of his career, he held the post of J.W. Kieckhefer Distinguished Research Professor at the Salk Institute for Biological Studies in La Jolla, California. His later
Francis Crick
13202818
Nucleic acid structure determination Structure probing of nucleic acids is the process by which biochemical techniques are used to determine nucleic acid structure. This analysis can be used to define the patterns which can infer the molecular structure, experimental analysis of molecular structure and function, and further understanding on development of smaller molecules for further biological research. Structure probing analysis can be done through many different methods, which include chemical probing, hydroxyl radical probing, SHAPE, nucleotide analog interference mapping (NAIM), and in-line probing. x-ray crystallography is not common for nucleic acids alone, since neither DNA nor RNA readily form crystals.
Nucleic acid structure determination
19495337
research into circulating nucleic acids. In 2005, Stroun’s semi-forgotten pioneering work in circulating nucleic acids was later acknowledged in a compilation of scientists that gave rise to various groundbreaking fields. Maurice Stroun currently serves as an advisor to Guardant Health, a company that has commercialized a comprehensive liquid biopsy based on circulating DNA in peripheral blood. Maurice Stroun Maurice Stroun (born September 3, 1926) is a researcher and professor at the University of Geneva in the Department of Plant Biochemistry and Physiology. He is known for first hypothesizing and demonstrating the existence of disease-specific circulating nucleic acids as well as
Maurice Stroun
303205
groups joined by ester bonds. These two strands run in opposite directions to each other and are, therefore, anti-parallel. Attached to each sugar is one of four types of molecules called nucleobases (informally, bases). It is the sequence of these four nucleobases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA in a process called transcription. Within cells DNA is organized into long structures called chromosomes. During cell division these
Nucleic acid
3723010
a 3-D model for a protein of unknown structure from experimental structures of evolutionarily-related proteins, called a protein family. Protein structure Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers specifically polypeptides formed from sequences of amino acids, the monomers of the polymer. A single amino acid monomer may also be called a residue indicating a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions, in which the amino acids lose one water molecule per reaction in order to attach to one another with a peptide bond. By convention,
Protein structure
2648781
is an iron-binding site. The amino acids which bind the iron ion to the transferrin are identical for both lobes; two tyrosines, one histidine, and one aspartic acid. For the iron ion to bind, an anion is required, preferably carbonate (). Transferrin also has a transferrin iron-bound receptor; it is a disulfide-linked homodimer. In humans, each monomer consists of 760 amino acids. It enables ligand bonding to the transferrin, as each monomer can bind to one or two atoms of iron. Each monomer consists of three domains: the protease, the helical, and the apical domains. The shape of a transferrin
Transferrin
303196
and the biotechnology and pharmaceutical industries. The term "nucleic acid" is the overall name for DNA and RNA, members of a family of biopolymers, and is synonymous with "polynucleotide". Nucleic acids were named for their initial discovery within the nucleus, and for the presence of phosphate groups (related to phosphoric acid). Although first discovered within the nucleus of eukaryotic cells, nucleic acids are now known to be found in all life forms including within bacteria, archaea, mitochondria, chloroplasts, viruses, and viroids. (note: there is debate as to whether viruses are living or non-living). All living cells contain both DNA and
Nucleic acid
3722985
Protein structure Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers specifically polypeptides formed from sequences of amino acids, the monomers of the polymer. A single amino acid monomer may also be called a residue indicating a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions, in which the amino acids lose one water molecule per reaction in order to attach to one another with a peptide bond. By convention, a chain under 30 amino acids is often identified as a peptide, rather than a protein. To be able
Protein structure
348346
replaced by RNA only later. On the other hand, the discovery in 2009 that activated pyrimidine ribonucleotides can be synthesized under plausible prebiotic conditions suggests that it is premature to dismiss the RNA-first scenarios. Suggestions for 'simple' "pre-RNA" nucleic acids have included peptide nucleic acid (PNA), threose nucleic acid (TNA) or glycol nucleic acid (GNA). Despite their structural simplicity and possession of properties comparable with RNA, the chemically plausible generation of "simpler" nucleic acids under prebiotic conditions has yet to be demonstrated. RNA enzymes, or ribozymes, are found in today's DNA-based life and could be examples of living fossils. Ribozymes
RNA world
4862661
Heteroduplex A heteroduplex is a double-stranded (duplex) molecule of nucleic acid originated through the genetic recombination of single complementary strands derived from "different" sources, such as from different homologous chromosomes or even from different organisms. One such example is the heteroduplex DNA strand formed in hybridization processes, usually for biochemistry-based phylogenetic analyses. Another is the heteroduplexes formed when non-natural analogs of nucleic acids are used to bind with nucleic acids; these heteroduplexes result from performing antisense techniques using single-stranded peptide nucleic acid, 2'-O-methyl phosphorothioate or Morpholino oligos to bind with RNA. In meiosis, the process of crossing-over occurs between non-sister
Heteroduplex
18624823
oligonucleotides. Hybridization assay A hybridization assay comprises any form of quantifiable hybridization "i.e." the quantitative annealing of two complementary strands of nucleic acids, known as nucleic acid hybridization. In the context of biochemistry and drug development, a hybridization assay is a type of Ligand Binding Assay (LBA) used to quantify nucleic acids in biological matrices. Hybridization assays can be in solution or on a solid support such as 96-well plates or labelled beads. Hybridization assays involve labelled nucleic acid probes to identify related DNA or RNA molecules (i.e. with significantly high degree of sequence similarity) within a complex mixture of
Hybridization assay
18624814
Hybridization assay A hybridization assay comprises any form of quantifiable hybridization "i.e." the quantitative annealing of two complementary strands of nucleic acids, known as nucleic acid hybridization. In the context of biochemistry and drug development, a hybridization assay is a type of Ligand Binding Assay (LBA) used to quantify nucleic acids in biological matrices. Hybridization assays can be in solution or on a solid support such as 96-well plates or labelled beads. Hybridization assays involve labelled nucleic acid probes to identify related DNA or RNA molecules (i.e. with significantly high degree of sequence similarity) within a complex mixture of unlabelled
Hybridization assay
10261750
nucleic acids by amplifying a nucleic acid molecule with the enzyme DNA polymerase. Conventional PCR is based on the theory that amplification is exponential. Therefore, nucleic acids may be quantified by comparing the number of amplification cycles and amount of PCR end-product to those of a reference sample. However, many factors complicate this calculation, creating uncertainties and inaccuracies. These factors include the following: initial amplification cycles may not be exponential; PCR amplification eventually plateaus after an uncertain number of cycles; and low initial concentrations of target nucleic acid molecules may not amplify to detectable levels. However, the most significant limitation
Digital polymerase chain reaction
348247
RNA has led to many important biological discoveries and numerous Nobel Prizes. Nucleic acids were discovered in 1868 by Friedrich Miescher, who called the material 'nuclein' since it was found in the nucleus. It was later discovered that prokaryotic cells, which do not have a nucleus, also contain nucleic acids. The role of RNA in protein synthesis was suspected already in 1939. Severo Ochoa won the 1959 Nobel Prize in Medicine (shared with Arthur Kornberg) after he discovered an enzyme that can synthesize RNA in the laboratory. However, the enzyme discovered by Ochoa (polynucleotide phosphorylase) was later shown to be
RNA
1799127
in techniques such as DNA foot printing, EMSA and other DNA-protein interaction techniques. The measurement and analysis are mostly done with a specialized gel analysis software. Capillary electrophoresis results are typically displayed in a trace view called an electropherogram. A number of factors can affect the migration of nucleic acids: the dimension of the gel pores, the voltage used, the ionic strength of the buffer, and the concentration intercalating dye such as ethidium bromide if used during electrophoresis. The gel sieves the DNA by the size of the DNA molecule whereby smaller molecules travel faster. Double-stranded DNA moves at a
Gel electrophoresis of nucleic acids
5156641
the exception of ribozymes, nucleic acid molecules within cells primarily serve as storage of genetic information due to its ability to form complementary base pairs, which allows for high-fidelity copying and transfer of genetic information. In contrast, nucleic acid molecules are more limited in their catalytic ability, in comparison to protein enzymes, to just three types of interactions: hydrogen bonding, pi stacking, and metal-ion coordination. This is due to the limited number of functional groups of the nucleic acid monomers: while proteins are built from up to twenty different amino acids with various functional groups, nucleic acids are built from
Deoxyribozyme
4223532
occur in most Northern European and North American populations. Gay and bi-sexual men are more susceptible to infection (through still unknown routes of sexual transmission) whereas the virus is transmitted through non-sexual routes in developing countries. KSHV is a herpesvirus, and is a large double-stranded DNA virus with a protein covering that packages its nucleic acids, called the capsid, which is then surrounded by an amorphous protein layer called the tegument, and finally enclosed in a lipid envelope derived in part from the cell membrane. KSHV has a genome which is approximately 165,000 nucleic acid bases in length. KSHV is
Kaposi's sarcoma-associated herpesvirus
16583647
to understand and exploit this elegant recognition motif. The recognition abilities of nucleic acids are enhanced when arranged in a spherical geometry, which allows for polyvalent interactions. This polyvalency, along with the high density and degree of orientation described above, helps to explain why a three-dimensional nucleic acid structure composed of linear, one-dimensional nucleic acids exhibits different properties than its lower-dimensional constituents (Fig. 2). Two decades of research on SNAs have revealed that they combine properties from the inorganic core and the nucleic acid shell. The inorganic nanoparticle core (in addition to gold, silver, iron oxide, silica, and semiconductor materials
Spherical nucleic acid
2163425
each possible combination of three bases corresponds to a specific amino acid. The central dogma of molecular biology outlines the mechanism by which proteins are constructed using information contained in nucleic acids. DNA is transcribed into mRNA molecules, which travels to the ribosome where the mRNA is used as a template for the construction of the protein strand. Since nucleic acids can bind to molecules with complementary sequences, there is a distinction between "sense" sequences which code for proteins, and the complementary "antisense" sequence which is by itself nonfunctional, but can bind to the sense strand. DNA sequencing is the
Nucleic acid sequence
4135736
RiboGreen RiboGreen is a proprietary fluorescent dye that is used in the detection and quantification of nucleic acids, including both RNA and DNA. It is synthesized and marketed by Molecular Probes/Invitrogen (a division of Life Technologies, now part of Thermo Fisher Scientific) of Eugene, Oregon, United States. In its free form, RiboGreen exhibits little fluorescence and possesses a negligible absorbance signature. When bound to nucleic acids, the dye fluoresces with an intensity that, according to the manufacturer, is several orders of magnitude greater than the unbound form. The fluorescence can be detected by a sensor and the nucleic acid can
RiboGreen
9726343
use of spectrophotometric analysis using a spectrophotometer. A spectrophotometer is able to determine the average concentrations of the nucleic acids DNA or RNA present in a mixture, as well as their purity. Spectrophotometric analysis is based on the principles that nucleic acids absorb ultraviolet light in a specific pattern. In the case of DNA and RNA, a sample is exposed to ultraviolet light at a wavelength of 260 nanometres (nm) and a photo-detector measures the light that passes through the sample. Some of the ultraviolet light will pass through and some will be absorbed by the DNA / RNA. The
Nucleic acid quantitation
29097
of each antibody is an immunoglobulin (Ig) monomer (containing only one Ig unit); secreted antibodies can also be dimeric with two Ig units as with IgA, tetrameric with four Ig units like teleost fish IgM, or pentameric with five Ig units, like mammalian IgM. The Ig monomer is a "Y"-shaped molecule that consists of four polypeptide chains; two identical "heavy chains" and two identical "light chains" connected by disulfide bonds. Each chain is composed of structural domains called immunoglobulin domains. These domains contain about 70–110 amino acids and are classified into different categories (for example, variable or IgV, and constant
Antibody
2582043
a significant barrier, as the helicase is able to destabilize the nucleic acids, unwinding the double-helix at a constant rate, regardless of the nucleic acid sequence. In active helicases, formula_10 is approximately equal to formula_11. Another way to view the active helicase is its ability to directly destabilize the replication fork to promote unwinding. Active helicases show similar behavior when acting on both double-strand nucleic acids, dsNA, or ssNA, in regards to the rates of unwinding and rates of translocation, where in both systems formula_10 and formula_11 are approximately equal. These two categories of helicases may also be modelled as
Helicase
4252757
being used as extensions to template DNA strands, XNA activity has been tested for use as genetic catalysts. Although proteins are the most common components of cellular enzymatic activity, nucleic acids are also used in the cell to catalyze reactions. A 2015 study found several different kinds of XNA, most notably FANA (2'-fluoroarabino nucleic acids), as well as HNA, CeNA and ANA (arabino nucleic acids) could be used to cleave RNA during post-transcriptional RNA processing acting as XNA enzymes, hence the name XNAzymes. FANA XNAzymes also showed the ability to ligate DNA, RNA and XNA substrates. Although XNAzyme studies are
Xenobiology
5858574
stacking interactions with RNA. Lysine residues in the helical portion of RNA-binding proteins help to stabilize interactions with nucleic acids. This nucleic acid binding is strengthened by electrostatic attraction between the positive lysine side chains and the negative nucleic acid phosphate backbones. Additionally, it is possible to model RNPs computationally. Although computational methods of deducing RNP structures are less accurate than experimental methods, they provide a rough model of the structure which allows for predictions of the identity of significant amino acids and nucleotide residues. Such information helps in understanding the overall function the RNP.'RNP' can also refer to ribonucleoprotein
Nucleoprotein
4327368
Tautomer Tautomers () are constitutional isomers of organic compounds that readily interconvert. This reaction commonly results in the relocation of a proton. Tautomerism is for example relevant to the behavior of amino acids and nucleic acids, two of the fundamental building blocks of life. The concept of tautomerizations is called tautomerism. The chemical reaction interconverting the two is called tautomerization. Tautomerization is pervasive in organic chemistry. It is typically associated with polar molecules and ions containing functional groups that are at least weakly acidic. Most common tautomers exist in pairs, which means that the proton is located at one of
Tautomer
17527876
biopsy. For example, because cell-free nucleic acids exist in human plasma, a simple blood sample can be enough to sample genetic information from tumours, transplants or an unborn fetus. Many, but not all, molecular diagnostics methods based on nucleic acids detection use polymerase chain reaction (PCR) to vastly increase the number of nucleic acid molecules, thereby amplifying the target sequence(s) in the patient sample. PCR is a method that a template DNA is amplified using synthetic primers, a DNA polymerase, and dNTPs. The mixture is cycled between at least 2 temperatures: a high temperature for denaturing double-stranded DNA into single-stranded
Molecular diagnostics
1799123
more slowly because they experience more resistance within the gel. Because the size of the molecule affects its mobility, smaller fragments end up nearer to the anode than longer ones in a given period. After some time, the voltage is removed and the fragmentation gradient is analyzed. For larger separations between similar sized fragments, either the voltage or run time can be increased. Extended runs across a low voltage gel yield the most accurate resolution. Voltage is, however, not the sole factor in determining electrophoresis of nucleic acids. The nucleic acid to be separated can be prepared in several ways
Gel electrophoresis of nucleic acids
11143601
exploited to modulate the pharmacological properties of nucleic acids and/or for nucleic acid delivery to target cells Recently, DMBT1-derived peptides have been successfully harnessed for siRNA intracellular delivery. DMBT1 has been shown to interact with Surfactant protein D. DMBT1-derived peptides also interacts with nucleic acids. DMBT1 Deleted in malignant brain tumors 1 protein is a protein that in humans is encoded by the "DMBT1" gene. Loss of sequences from human chromosome 10q has been associated with the progression of human cancers. The gene DMBT1 was originally isolated based on its deletion in a medulloblastoma cell line. DMBT1 is expressed with
DMBT1