query: single stranded nucleic acid that consists of nucleotides that contain ribose sugar

pos: Nucleic acid 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

pos: Nucleic acid 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

pos: Nucleotide 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

pos: Nucleic acid 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

pos: L-Ribonucleic acid aptamer L-Ribonucleic acid aptamer An -ribonucleic acid aptamer (-RNA aptamer, trade name Spiegelmer) is an RNA-like molecule built from -ribose units. It is an artificial oligonucleotide named for being a mirror image of natural oligonucleotides. -RNA aptamers are a form of aptamers. Due to their -nucleotides, they are highly resistant to degradation by nucleases. -RNA aptamers are considered potential drugs and are currently being tested in clinical trials. -RNA aptamers, built using -ribose, are the enantiomers of natural oligonucleotides, which are made with -ribose. Nucleic acid aptamers, including -RNA aptamers, contain adenosine monophosphate, guanosine monophosphate, cytidine monophosphate, uridine monophosphate, a phosphate

pos: Biochemistry 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

pos: Black queen cell virus It has a linear, single-stranded, positive sense RNA genome encased in an icosahedral capsid (described above). Viruses with icosahedral symmetry have triangulation numbers, which describe the faces in terms of the number of facets (smaller triangles inside the faces) each contains. BQCV is a pseudo-T=3 capsid, meaning that it is mathematically a T=1 capsid, but the way the capsid is structured makes it look like T=3. The genome of this virus contains 8550 nucleotides and it is polyadenylated. Nucleotides "are organic molecules that serve as the monomer units for forming the nucleic acid polymers deoxyribonucleic acid(DNA) and ribonucleic acid (RNA)".

pos: Backbone chain sugar) which contains a linkage that is "alpha" to glucose and "beta" to fructose. Generally, carbohydrates which our bodies break down are "alpha"-linked (example: glycogen) and those which have structural function are "beta"-linked (example: cellulose). Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are of great importance because they code for the production of all cellular proteins. They are made up of monomers called nucleotides which consist of an organic base: A, G, C and T or U, a pentose sugar, and a phosphate group. They have backbones in which the 3’ carbon of the ribose sugar is connected to the

pos: Nucleic acid hybridization Nucleic acid hybridization In molecular biology, hybridization (or hybridisation) is a phenomenon in which single-stranded deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) molecules anneal to complementary DNA or RNA. Though a double-stranded DNA sequence is generally stable under physiological conditions, changing these conditions in the laboratory (generally by raising the surrounding temperature) will cause the molecules to separate into single strands. These strands are complementary to each other but may also be complementary to other sequences present in their surroundings. Lowering the surrounding temperature allows the single-stranded molecules to anneal or “hybridize” to each other. DNA replication and transcription of

pos: Nucleic acid hybridization natural positions within a chromosome). In 1969, the two scientists published a paper demonstrating that radioactive copies of a ribosomal DNA sequence could be used to detect complementary DNA sequences in the nucleus of a frog egg. Since those original observations, many refinements have increased the versatility and sensitivity of the procedure to the extent that in situ hybridization is now considered an essential tool in cytogenetics. Nucleic acid hybridization In molecular biology, hybridization (or hybridisation) is a phenomenon in which single-stranded deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) molecules anneal to complementary DNA or RNA. Though a double-stranded DNA

pos: RNA virus family of single negative stranded RNA viruses with a circular genome. The majority of fungal viruses are double-stranded RNA viruses. A small number of positive-strand RNA viruses have been described. One report has suggested the possibility of a negative stranded virus. RNA virus An RNA virus is a virus that has RNA (ribonucleic acid) as its genetic material. This nucleic acid is usually single-stranded RNA (ssRNA) but may be double-stranded RNA (dsRNA). Notable human diseases caused by RNA viruses include Ebola hemorrhoragic fever, SARS, Rabies, common cold, influenza, hepatitis C, West Nile fever, polio and measles. The International Committee on

neg: Bridged nucleic acid 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

neg: Nucleic acid molecules are probably the largest individual molecules known. Well-studied biological nucleic acid molecules range in size from 21 nucleotides (small interfering RNA) to large chromosomes (human chromosome 1 is a single molecule that contains 247 million base pairs). In most cases, naturally occurring DNA molecules are double-stranded and RNA molecules are single-stranded. There are numerous exceptions, however—some viruses have genomes made of double-stranded RNA and other viruses have single-stranded DNA genomes, and, in some circumstances, nucleic acid structures with three or four strands can form. Nucleic acids are linear polymers (chains) of nucleotides. Each nucleotide consists of three components: a

neg: Nucleic acid sequence 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

neg: Gene this is known as the 3' end of the molecule. The other end contains an exposed phosphate group; this is the 5' end. The two strands of a double-helix run in opposite directions. Nucleic acid synthesis, including DNA replication and transcription occurs in the 5'→3' direction, because new nucleotides are added via a dehydration reaction that uses the exposed 3' hydroxyl as a nucleophile. The expression of genes encoded in DNA begins by transcribing the gene into RNA, a second type of nucleic acid that is very similar to DNA, but whose monomers contain the sugar ribose rather than deoxyribose.

neg: Nucleic acid secondary structure Nucleic acid secondary structure Nucleic acid secondary structure is the basepairing interactions within a single nucleic acid polymer or between two polymers. It can be represented as a list of bases which are paired in a nucleic acid molecule. The secondary structures of biological DNA's and RNA's tend to be different: biological DNA mostly exists as fully base paired double helices, while biological RNA is single stranded and often forms complex and intricate base-pairing interactions due to its increased ability to form hydrogen bonds stemming from the extra hydroxyl group in the ribose sugar. In a non-biological context, secondary structure

neg: Xeno nucleic acid RNA or DNA. Strands of DNA and RNA are formed by stringing together long chains of molecules called nucleotides. A nucleotide is made up of three chemical components: a phosphate, a five-carbon sugar group (this can be either a deoxyribose sugar — which gives us the "D" in DNA — or a ribose sugar — the "R" in RNA), and one of five standard bases (adenine, guanine, cytosine, thymine or uracil). The molecules that piece together to form the six xeno nucleic acids are almost identical to those of DNA and RNA, with one exception: in XNA nucleotides, the deoxyribose

neg: Nucleic acid purine or pyrimidine nucleobase (sometimes termed "nitrogenous base" or simply "base"), a pentose sugar, and a phosphate group. The substructure consisting of a nucleobase plus sugar is termed a nucleoside. Nucleic acid types differ in the structure of the sugar in their nucleotides–DNA contains 2'-deoxyribose while RNA contains ribose (where the only difference is the presence of a hydroxyl group). Also, the nucleobases found in the two nucleic acid types are different: adenine, cytosine, and guanine are found in both RNA and DNA, while thymine occurs in DNA and uracil occurs in RNA. The sugars and phosphates in nucleic acids

neg: Nucleic acid analogue Nucleic acid analogue Nucleic acid analogues are compounds which are analogous (structurally similar) to naturally occurring RNA and DNA, used in medicine and in molecular biology research. Nucleic acids are chains of nucleotides, which are composed of three parts: a phosphate backbone, a pentose sugar, either ribose or deoxyribose, and one of four nucleobases. An analogue may have any of these altered. Typically the analogue nucleobases confer, among other things, different base pairing and base stacking properties. Examples include universal bases, which can pair with all four canonical bases, and phosphate-sugar backbone analogues such as PNA, which affect the properties

neg: Nucleotide or a pyrimidine base—i.e., the nitrogenous base molecule, also known as a nucleobase—and are termed "ribo"nucleotides if the sugar is ribose, or "deoxyribo"nucleotides if the sugar is deoxyribose. Individual phosphate molecules repetitively connect the sugar-ring molecules in two adjacent nucleotide monomers, thereby connecting the nucleotide monomers of a nucleic acid end-to-end into a long chain. These chain-joins of sugar and phosphate molecules create a 'backbone' strand for a single- or double helix. In any one strand, the chemical orientation (directionality) of the chain-joins runs from the 5'-end to the 3'-end ("read": 5 prime-end to 3 prime-end)—referring to the five carbon

neg: Nucleic acid analogue The possibility has been proposed and studied, both theoretically and experimentally, of implementing an orthogonal system inside cells independent of the cellular genetic material in order to make a completely safe system, with the possible increase in encoding potentials Several groups have focused on different aspects: Nucleic acid analogue Nucleic acid analogues are compounds which are analogous (structurally similar) to naturally occurring RNA and DNA, used in medicine and in molecular biology research. Nucleic acids are chains of nucleotides, which are composed of three parts: a phosphate backbone, a pentose sugar, either ribose or deoxyribose, and one of four nucleobases.

neg: Amphibolic several intermediate that are phosphorylated five carbon sugars (pentoses). The pentose phosphate pathway provide monomers for many metabolic pathways by transform glucose into four carbon sugar ( erythrose) and five carbon sugar ( ribose), that are important monomers in many metabolic pathways .Many of the reactants in the pentose phosphate pathway are those similar in glycolysis, also both occurs in cytosol . The ribose -5-phosphate can be transport into nucleic acid metabolism, producing the basis of DNA and RNA monomers, the nucleotides . In meristematic cells, large amounts of DNA must be produce during the S-phase of a short cell

neg: Nucleic acid metabolism are both primarily produced in the liver. They both contain a sugar and a phosphate, but have nitrogenous bases that are different sizes. Because of this, the two different groups are synthesized in different ways. However, all nucleotide synthesis requires the use of phosphoribosyl pyrophosphate (PRPP) which donates the ribose and phosphate necessary to create a nucleotide. Adenine and guanine are the two nucleotides classified as purines. In purine synthesis, PRPP is turned into inosine monophosphate, or IMP. Production of IMP from PRPP requires glutamine, glycine, aspartate, and 6 ATP, among other things. IMP is then converted to AMP (adenosine

neg: Nucleic acid design 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

neg: Nucleic acid metabolism synthesis. This regulation helps to keep the purine/pyrimidine amounts similar, which is beneficial because equal amounts of purines and pyrimidines are required for DNA synthesis. Deficiencies of enzymes involved in pyrimidine synthesis can lead to the genetic disease Orotic aciduria which causes excessive excretion of orotic acid in the urine. Nucleotides are initially made with ribose as the sugar component, which is a feature of RNA. DNA, however, requires "deoxy"ribose, which is missing the 2'-hydroxyl (-OH group) on the ribose. The reaction to remove this -OH is catalyzed by ribonucleotide reductase. This enzyme converts NDPs (nucleoside-diphosphate) to dNDPs (deoxynucleoside-diphosphate). The

neg: Xeno nucleic acid and ribose sugar groups of DNA and RNA have been replaced. Some of these replacement molecules contain four carbons atoms instead of the standard five. Others cram in as many as seven carbons. FANA even contains a fluorine atom. These substitutions make XNAs functionally and structurally analogous to DNA and RNA, but they also make them unnatural and artificial. XNA exhibits a variety of structural chemical changes relative to its natural counterparts. Types of synthetic 'XNA' created so far include 1,5-anhydrohexitol nucleic acid (HNA) and cyclohexene nucleic acid (CeNA). Threose nucleic acid (TNA), glycol nucleic acid (GNA), locked nucleic acid

neg: Leslie Orgel the nucleobase attaches to the correct carbon on ribose, and in the correct orientation (the beta anomer). However, the synthesis was later criticised because it only worked most with hypoxanthine, a nucleobase that is not relevant to current life on Earth, and because it was not specific for the ribose sugar and could instead be applied to other sugars. Continuing his work exploring the prebiotic synthesis of RNA, Orgel suggested a solution to the problem of condensing nucleotides to form nucleic acid polymers, an energy-demanding process. To counteract this energy barrier, he proposed a nucleotide with an imidazole ring attached

neg: Albert Eschenmoser 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

neg: Locked nucleic acid Locked nucleic acid A locked nucleic acid (LNA), often referred to as inaccessible RNA, is a modified RNA nucleotide. The ribose moiety of an LNA nucleotide is modified with an extra bridge connecting the 2' oxygen and 4' carbon. The bridge "locks" the ribose in the 3'-"endo" (North) conformation, which is often found in the A-form duplexes. LNA nucleotides can be mixed with DNA or RNA residues in the oligonucleotide whenever desired and hybridize with DNA or RNA according to Watson-Crick base-pairing rules. Synthesis first reported in 1997. Such oligomers are synthesized chemically and are commercially available. The locked ribose

neg: Nucleoside analogue Nucleoside analogue Nucleoside analogues are nucleosides which contain a nucleic acid analogue and a sugar. Nucleotide analogs are nucleotides which contain a nucleic acid analogue, a sugar, and one to three phosphate groups. Nucleoside and nucleotide analogues can be used in therapeutic drugs, include a range of antiviral products used to prevent viral replication in infected cells. The most commonly used is acyclovir, although its inclusion in this category is uncertain, because it acts as a nucleoside but contains no actual sugar, as the sugar ring is replaced by an open-chain structure. These agents can be used against hepatitis B

neg: Nucleic acid 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

neg: Directionality (molecular biology) convention, single strands of DNA and RNA sequences are written in a 5′-to-3′ direction except as needed to illustrate the pattern of base pairing. The 5′-end (pronounced "five prime end") designates the end of the DNA or RNA strand that has the fifth carbon in the sugar-ring of the deoxyribose or ribose at its terminus. A phosphate group attached to the 5′-end permits ligation of two nucleotides, i.e., the covalent binding of a 5′-phosphate to the 3′-hydroxyl group of another nucleotide, to form a phosphodiester bond. Removal of the 5′-phosphate prevents ligation. To prevent unwanted nucleic acid ligation (e.g. self-ligation

neg: Bridged nucleic acid the S-type (C’-endo, B-form) as illustrated in the next figure. An increased conformational inflexibility of the sugar moiety in nucleosides (oligonucleotides) results in a gain of high binding affinity with complementary single-stranded RNA and/or double-stranded DNA. The first 2’,4’-BNA (LNA) monomers were first synthesized by Takeshi Imanishi’s group in 1997 followed independently by Jesper Wengel’s group in 1998. Chemical structures of other BNAs that were synthesized in the past years as indicated below the structures. BNA nucleotides can be incorporated into DNA or RNA oligonucleotides at any desired position. Such oligomers are synthesized chemically and are now commercially available. The

neg: Deoxyribose component of DNA, 2-deoxyribose derivatives have an important role in biology. The DNA (deoxyribonucleic acid) molecule, which is the main repository of genetic information in life, consists of a long chain of deoxyribose-containing units called nucleotides, linked via phosphate groups. In the standard nucleic acid nomenclature, a DNA nucleotide consists of a deoxyribose molecule with an organic base (usually adenine, thymine, guanine or cytosine) attached to the 1′ ribose carbon. The 5′ hydroxyl of each deoxyribose unit is replaced by a phosphate (forming a nucleotide) that is attached to the 3′ carbon of the deoxyribose in the preceding unit. The

neg: Biomolecular engineering which are biopolymers consisting of chains of biomolecules. These two molecules are the genetic code and template that make life possible. Manipulation of these molecules and structures causes major changes in function and expression of other macromolecules. Nucleosides are glycosylamines containing a nucleobase bound to either ribose or deoxyribose sugar via a beta-glycosidic linkage. The sequence of the bases determine the genetic code. Nucleotides are nucleosides that are phosphorylated by specific kinases via a phosphodiester bond. Nucleotides are the repeating structural units of nucleic acids. The nucleotides are made of a nitrogenous base, a pentose (ribose for RNA or deoxyribose

neg: Nucleic acid structure units in the ribosome or spliceosome. Nucleic acid structure Nucleic acid structure refers to the structure of nucleic acids such as DNA and RNA. Chemically speaking, DNA and RNA are very similar. Nucleic acid structure is often divided into four different levels: primary, secondary, tertiary and quaternary. Primary structure consists of a linear sequence of nucleotides that are linked together by phosphodiester bonds. It is this linear sequence of nucleotides that make up the Primary structure of DNA or RNA. Nucleotides consist of 3 components: The nitrogen bases adenine and guanine are purine in structure and form a glycosidic bond

neg: Nucleic acid structure Nucleic acid structure Nucleic acid structure refers to the structure of nucleic acids such as DNA and RNA. Chemically speaking, DNA and RNA are very similar. Nucleic acid structure is often divided into four different levels: primary, secondary, tertiary and quaternary. Primary structure consists of a linear sequence of nucleotides that are linked together by phosphodiester bonds. It is this linear sequence of nucleotides that make up the Primary structure of DNA or RNA. Nucleotides consist of 3 components: The nitrogen bases adenine and guanine are purine in structure and form a glycosidic bond between their 9 nitrogen and the

neg: Nucleic acid metabolism 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

neg: Nucleotide 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

neg: Locked nucleic acid conformation enhances base stacking and backbone pre-organization. This significantly increases the hybridization properties (melting temperature) of oligonucleotides. |issue=14|pages=3607–3630 Locked nucleic acid A locked nucleic acid (LNA), often referred to as inaccessible RNA, is a modified RNA nucleotide. The ribose moiety of an LNA nucleotide is modified with an extra bridge connecting the 2' oxygen and 4' carbon. The bridge "locks" the ribose in the 3'-"endo" (North) conformation, which is often found in the A-form duplexes. LNA nucleotides can be mixed with DNA or RNA residues in the oligonucleotide whenever desired and hybridize with DNA or RNA according to Watson-Crick base-pairing

neg: DNA nanotechnology acid structures easy to control through nucleic acid design. This property is absent in other materials used in nanotechnology, including proteins, for which protein design is very difficult, and nanoparticles, which lack the capability for specific assembly on their own. The structure of a nucleic acid molecule consists of a sequence of nucleotides distinguished by which nucleobase they contain. In DNA, the four bases present are adenine (A), cytosine (C), guanine (G), and thymine (T). Nucleic acids have the property that two molecules will only bind to each other to form a double helix if the two sequences are complementary,

neg: Ribose 5-phosphate of the gene for pyruvate kinase isozyme, PKM. PKM creates a bottleneck in the glycolytic pathway, allowing intermediates to be utilized by the PPP to synthesize NADPH and R5P. This process is further enabled by triosephosphate isomerase inhibition by phosphoenolpyruvate, the PKM substrate. R5P and its derivatives serve as precursors to many biomolecules, including DNA, RNA, ATP, coenzyme A, FAD (Flavin adenine dinucleotide), and histidine. Nucleotides serve as the building blocks for nucleic acids, DNA and RNA. They are composed of a nitrogenous base, a pentose sugar, and at least one phosphate group. Nucleotides contain either a purine or a

neg: Nucleic acid analogue RNA ribozymes; As a tool with resistance to RNA hydrolysis; Investigation of the mechanisms used by enzyme; Investigation of the structural features of nucleic acids. To overcome the fact that ribose's 2' hydroxy group that reacts with the phosphate linked 3' hydroxy group (RNA is too unstable to be used or synthesized reliably), a ribose analogue is used. The most common RNA analogues are 2'-O-methyl-substituted RNA, locked nucleic acid (LNA) or bridged nucleic acid (BNA), morpholino, and peptide nucleic acid (PNA). Although these oligonucleotides have a different backbone sugar or, in the case of PNA, an amino acid residue in

neg: Nucleic acid Nucleic acid molecules are usually unbranched, and may occur as linear and circular molecules. For example, bacterial chromosomes, plasmids, mitochondrial DNA, and chloroplast DNA are usually circular double-stranded DNA molecules, while chromosomes of the eukaryotic nucleus are usually linear double-stranded DNA molecules. Most RNA molecules are linear, single-stranded molecules, but both circular and branched molecules can result from RNA splicing reactions. The total amount of pyrimidine is equal to the total amount of purines. The diameter of the helix is about 20A. One DNA or RNA molecule differs from another primarily in the sequence of nucleotides. Nucleotide sequences are of

neg: Biopolymer non-peptide components, such as saccharide chains and lipids. The convention for a nucleic acid sequence is to list the nucleotides as they occur from the 5' end to the 3' end of the polymer chain, where 5' and 3' refer to the numbering of carbons around the ribose ring which participate in forming the phosphate diester linkages of the chain. Such a sequence is called the primary structure of the biopolymer. Sugar-based biopolymers are often difficult with regards to convention. Sugar polymers can be linear or branched and are typically joined with glycosidic bonds. The exact placement of the linkage

neg: Reading frame 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

neg: Nucleic acid nomenclature Nucleic acid nomenclature Molecular biologists use several shorthand terms when referring to nucleic acid molecules, such as DNA and RNA, collectively referred to as nucleic acid nomenclature. The most common is the representation of the base pairs as letters—an adenine nucleotide is abbreviated as A, guanine as G, cytosine as C, thymine as T, and in RNA, uracil as U. Additionally, the positions of the carbons in the ribose sugar that forms the backbone of the nucleic acid chain are numbered, and are used to indicate the direction of nucleic acids (5'->3' versus 3'->5'). This is referred to as directionality.

neg: Ribonucleotide are some rare cases where thymine does occur in RNA and uracil in DNA. Here are the 4 major ribonucleotides (ribonucleoside 5'-monophosphate) which are the structural units of RNAs. In ribonucleotides, the sugar component is ribose while in deoxyribonucleotides, the sugar component is deoxyribose. Instead of a hydroxyl group at the second carbon in the ribose ring, it is replaced by a hydrogen atom. Both types of pentoses in DNA and RNA are in their β-furanose (closed five-membered ring) form and they define the identity of a nucleic acid. DNA is defined by containing 2'-deoxy-ribose nucleic acid while RNA is

neg: Gel electrophoresis of nucleic acids a fluorescent dye specific for DNA, such as ethidium bromide. The gel shows bands corresponding to different nucleic acid molecules populations with different molecular weight. Fragment size is usually reported in "nucleotides", "base pairs" or "kb" (for thousands of base pairs) depending upon whether single- or double-stranded nucleic acid has been separated. Fragment size determination is typically done by comparison to commercially available DNA markers containing linear DNA fragments of known length. The types of gel most commonly used for nucleic acid electrophoresis are agarose (for relatively long DNA molecules) and polyacrylamide (for high resolution of short DNA molecules, for

neg: Adenine 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.

neg: Ribonucleotide Kossel, who, in 1878, isolated the non-protein components of “nuclein”, and discovered the five nucleobases present in nucleic acids: adenine, cytosine, guanine, thymine and uracil. Although some fundamental facts were known about nucleic acids due to these early discoveries, its structure and function remained a mystery. It wasn’t until the discovery of nucleotides in 1919 by Phoebus Levene, a Russian-Lithuanian biochemist that re-opened the gates of the DNA discovery. Levene first identified the carbohydrate component present in yeast RNA was in fact ribose. However, it was not until his discovery that the carbohydrate component in thymus nucleic acid was also

neg: Directionality (molecular biology) Directionality (molecular biology) Directionality, in molecular biology and biochemistry, is the end-to-end chemical orientation of a single strand of nucleic acid. In a single strand of DNA or RNA, the chemical convention of naming carbon atoms in the nucleotide sugar-ring means that there will be a 5′-end, which frequently contains a phosphate group attached to the 5′ carbon of the ribose ring, and a 3′-end (usually pronounced "five prime end" and "three prime end"), which typically is unmodified from the ribose -OH substituent. In a DNA double helix, the strands run in opposite directions to permit base pairing between them,

neg: Backbone chain phosphate group via a phosphodiester bond. This bond is formed through with the help of a class of cellular enzymes called polymerases. In this enzymatically driven condensation reaction, all incoming nucleotides have a triphosphorylated ribose which loses a pyrophosphate group to form the inherent phosphodiester bond. This reaction is driven by the large negative free energy change associated with the release of pyrophosphate. The sequence of bases in the nucleic acid backbone is also known as the primary structure. Nucleic acids can be millions of nucleotides long thus leading to the genetic diversity of life. The bases stick out from

neg: Totivirus open reading frames. "Totivirus" have a genome of 4700–6700 nucleotides in length and only a single copy of the genome is present in the particle. The nucleic acid content of "Totivirus" is usually of one molecule but can also contain three or four segments of linear double stranded RNA. The genome contains two large overlapping open reading frames (ORFs). These open reading frames (ORFs) code for a capsid protein (CP) and an RNA-dependent RNA polymerase (RDRP). The 5' end of the positive strand of the dsRNA genome has no cap and is very structured."Totivirus" contains a long 5' untranslated region

neg: Nucleic acid double helix Nucleic acid double helix In molecular biology, the term double helix refers to the structure formed by double-stranded molecules of nucleic acids such as DNA. The double helical structure of a nucleic acid complex arises as a consequence of its secondary structure, and is a fundamental component in determining its tertiary structure. The term entered popular culture with the publication in 1968 of "The Double Helix: A Personal Account of the Discovery of the Structure of DNA, by James Watson" The DNA double helix polymer of nucleic acid, held together by nucleotides which base pair together. In B-DNA, the most

neg: Cyclic nucleotide Cyclic nucleotide A cyclic nucleotide (cNMP) is a single-phosphate nucleotide with a cyclic bond arrangement between the sugar and phosphate groups. Like other nucleotides, cyclic nucleotides are composed of three functional groups: a sugar, a nitrogenous base, and a single phosphate group. As can be seen in the cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP) images, the 'cyclic' portion consists of two bonds between the phosphate group and the 3' and 5' hydroxyl groups of the sugar, very often a ribose. Their biological significance includes a broad range of protein-ligand interactions. They have been identified as secondary messengers

neg: Nucleic acid thermodynamics 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

neg: Biosynthesis a five-membered ring formed from ribose sugar in RNA, and deoxyribose sugar in DNA; these sugars are linked to a purine or pyrimidine base with a glycosidic bond and a phosphate group at the 5' location of the sugar. The DNA nucleotides adenosine and guanosine consist of a purine base attached to a ribose sugar with a glycosidic bond. In the case of RNA nucleotides deoxyadenosine and deoxyguanosine, the purine bases are attached to a deoxyribose sugar with a glycosidic bond. The purine bases on DNA and RNA nucleotides are synthesized in a twelve-step reaction mechanism present in most single-celled

neg: Ribonucleotide defined by containing ribose nucleic acid. In some occasions, DNA and RNA may contain some minor bases. Methylated forms of the major bases are most common in DNA. In viral DNA, some bases may be hydroxymethylated or glucosylated. In RNA, minor or modified bases occur more frequently. Some examples include hypoxanthine, dihydrouracil, methylated forms of uracil, cytosine, and guanine, as well as modified nucleoside pseudouridine. Nucleotides with phosphate groups in positions other than on the 5' carbon have also been observed. Examples include ribonucleoside 2',3'-cyclic monophosphates which are isolatable intermediates, and ribonucleoside 3'-monophosphates which are end products of the hydrolysis

neg: RNA world not contain these nucleobases seen in life's nucleic acids. The nucleoside cytosine has a half-life in isolation of 19 days at and 17,000 years in freezing water, which some argue is too short on the geologic time scale for accumulation. Others have questioned whether ribose and other backbone sugars could be stable enough to find in the original genetic material, and have raised the issue that all ribose molecules would have had to be the same enantiomer, as any nucleotide of the wrong chirality acts as a chain terminator. Pyrimidine ribonucleosides and their respective nucleotides have been prebiotically synthesised by

neg: Denaturation (biochemistry) hydrogen bonding between nucleotides is disrupted, and results in the separation of previously annealed strands. For example, denaturation of DNA due to high temperatures results in the disruption of base pairs and the separation of the double stranded helix into two single strands. Nucleic acid strands are capable of re-annealling when "normal" conditions are restored, but if restoration occurs too quickly, the nucleic acid strands may re-anneal imperfectly resulting in the improper pairing of bases. The non-covalent interactions between antiparallel strands in DNA can be broken in order to "open" the double helix when biologically important mechanisms such as DNA

neg: Nucleic acid structure determination in double stranded regions by protection from CMCT, which is the absence of a band. CMCT, like DMS can detect secondary and tertiary structure changes, but still has the same weaknesses as the method of modification is the same as DMS. 1,1-Dihydroxy-3-ethoxy-2-butanone, known as kethoxal, is used like DMS and CMCT, where treatment with kethoxal causes the modification of guanine, specifically altering the N1 and the exocyclic amino group simultaneously by covalent interaction. The modification by kethoxal prevents single stranded guanine nucleotides to become modified, so that when reverse transcriptase reaches the modified guanine it falls off resulting in a

neg: Glycol nucleic acid Meggers is however novel, and the specificity of interaction well-demonstrated. DNA and RNA have a deoxyribose and ribose sugar backbone, respectively, whereas GNA's backbone is composed of repeating glycol units linked by phosphodiester bonds. The glycol unit has just three carbon atoms and still shows Watson-Crick base pairing. The Watson-Crick base pairing is much more stable in GNA than its natural counterparts DNA and RNA as it requires a high temperature to melt a duplex of GNA. It is possibly the simplest of the nucleic acids, so making it a hypothetical precursor to RNA. Glycol nucleic acid Glycol nucleic acid

neg: Nucleic acid structure a four-base pairs hairpin RNA structure. There are three common families of tetraloop in ribosomal RNA: UNCG, GNRA, and CUUG (N is one of the four nucleotides and R is a purine).UNCG is the most stable tetraloop. Pseudoknot is a RNA secondary structure first identified in turnip yellow mosaic virus. Pseudoknots are formed when nucleotides from the hairpin loop pairs with a single stranded region outside of the hairpin to form a helical segment. H-type fold pseudoknots are best characterized. In H-type fold, nucleotides in the hairpin loop pairs with the bases outside the hairpin stem forming second stem and

neg: Nucleic acid structure Nucleic acid sequence is the order of nucleotides within a DNA (GACT) or RNA (GACU) molecule that is determined by a series of letters. Sequences are presented from the 5' to 3' end and determine the covalent structure of the entire molecule. Sequences can be complementary to another sequence in that the base on each position is complementary as well as in the reverse order. An example of a complementary sequence to AGCT is TCGA. DNA is double-stranded containing both a sense strand and an antisense strand. Therefore, the complementary sequence will be to the sense strand. There are three

neg: DNA virus about 1.5 µm in length. Another virus - Cedratvirus - may be related this group. DNA virus A DNA virus is a virus that has DNA as its genetic material and replicates using a DNA-dependent DNA polymerase. The nucleic acid is usually double-stranded DNA (dsDNA) but may also be single-stranded DNA (ssDNA). DNA viruses belong to either "Group I" or "Group II" of the Baltimore classification system for viruses. Single-stranded DNA is usually expanded to double-stranded in infected cells. Although "Group VII" viruses such as hepatitis B contain a DNA genome, they are not considered DNA viruses according to the

neg: DNA virus DNA virus A DNA virus is a virus that has DNA as its genetic material and replicates using a DNA-dependent DNA polymerase. The nucleic acid is usually double-stranded DNA (dsDNA) but may also be single-stranded DNA (ssDNA). DNA viruses belong to either "Group I" or "Group II" of the Baltimore classification system for viruses. Single-stranded DNA is usually expanded to double-stranded in infected cells. Although "Group VII" viruses such as hepatitis B contain a DNA genome, they are not considered DNA viruses according to the Baltimore classification, but rather reverse transcribing viruses because they replicate through an RNA intermediate. Notable

neg: Nucleic acid modification of the standard nucleosides within the DNA molecule or the primary (initial) RNA transcript. Transfer RNA (tRNA) molecules contain a particularly large number of modified nucleosides. Double-stranded nucleic acids are made up of complementary sequences, in which extensive Watson-Crick base pairing results in a highly repeated and quite uniform double-helical three-dimensional structure. In contrast, single-stranded RNA and DNA molecules are not constrained to a regular double helix, and can adopt highly complex three-dimensional structures that are based on short stretches of intramolecular base-paired sequences including both Watson-Crick and noncanonical base pairs, and a wide range of complex tertiary interactions.

neg: Nucleic acid tertiary structure of the active site of the functional ribozyme. The ribosome contains numerous examples of coaxial stacking, including stacked segments as long as 70 bp. Two common motifs involving coaxial stacking are kissing loops and pseudoknots. In kissing loop interactions, the single-stranded loop regions of two hairpins interact through base pairing, forming a composite, coaxially stacked helix. Notably, this structure allows all of the nucleotides in each loop to participate in base-pairing and stacking interactions. This motif was visualized and studied using NMR analysis by Lee and Crothers. The pseudoknot motif occurs when a single stranded region of a hairpin loop

neg: Spherical nucleic acid final structure, whereas SNAs and other forms of three-dimensional nucleic acids (structures templated with a triangular prism, rod, octahedra, or rhombic dodecadhedra-shaped nanoparticles) utilize the nanoparticle core to arrange the linear nucleic acid components into functional forms. Indeed, it is the particle core that dictates the shape of the SNA, and to date, single-stranded and double-stranded versions of these materials have been created that consist of DNA, LNA, and RNA. SNAs should also not be confused with their monovalent analogues – individual particles coupled to a single DNA strand. Such single strand-nanoparticle conjugate structures have led to interesting advances in

neg: Sugar phosphates Sugar phosphates Sugar phosphates (sugars that have added or substituted phosphate groups) are often used in biological systems to store or transfer energy. They also form the backbone for DNA and RNA (DNA having two sugar molecules, and RNA having just one). Sugar phosphate backbone geometry is altered in the vicinity of the modified nucleotides. Sugar phosphates may be divided into two groups - those that are acid-labile (aldose 1-phosphates) and those that are not. Consequently, too low a pH was to be avoided during the elution of glucose 1-phosphate and ribose 1-phosphate. On the other hand, in order to

neg: Bridged nucleic acid observed whereas the histopathological analysis revealed no severe hepatic toxicities. The same group, also in 2012, reported that the 2’,4’-BNA[NMe] analog when used in antisense oligonucleotides showed significantly stronger inhibitory activities which is more pronounced in shorter (13- to 16mer) oligonucleotides. Their data led the researchers to conclude that the 2’,4’-BNA[NMe] analog may be a better alternative to conventional LNAs. Some of the benefits of BNAs include: Application of BNAs include: 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,

neg: Nucleic acid quantitation more light absorbed by the sample, the higher the nucleic acid concentration in the sample. The resulting effect is that less light will strike the photodetector and this will produce a higher optical density (OD) Using the Beer-Lambert Law it is possible to relate the amount of light absorbed to the concentration of the absorbing molecule. At a wavelength of 260 nm, the average extinction coefficient for double-stranded DNA is 0.020 (μg/ml) cm, for single-stranded DNA it is 0.027 (μg/ml) cm, for single-stranded RNA it is 0.025 (μg/ml) cm and for short single-stranded oligonucleotides it is dependent on the length

neg: Nucleic acid structure potential metal binding groups on nucleic acids: phosphate, sugar and base moieties. Solid-state structure of complexes with alkali metal ions have been reviewed. Secondary structure is the set of interactions between bases, i.e., which parts of strands are bound to each other. In DNA double helix, the two strands of DNA are held together by hydrogen bonds. The nucleotides on one strand base pairs with the nucleotide on the other strand. The secondary structure is responsible for the shape that the nucleic acid assumes. The bases in the DNA are classified as purines and pyrimidines. The purines are adenine and

neg: Nucleic acid structure determination no band corresponding to that position on the gel. This process can be used to evaluate an entire area, where analogs are placed in site specific locations, differing by a single nucleotide, then when functional RNAs are isolated and run on a gel, all areas where bands are produced indicate non-essential nucleotides, but areas where bands are absent from the functional RNA indicate that inserting a nucleotide analog in that position caused the RNA molecule to become non-functional Nucleic acid structure determination Structure probing of nucleic acids is the process by which biochemical techniques are used to determine nucleic acid

neg: Oxocarbenium oxocarbenium ring reduction for a diastereoselective hydride addition. In biological systems, oxocarbenium ions are mostly seen during reactions of carbohydrates. Since sugars are present in the structure of nucleic acids, with a ribose sugar present in RNA and a deoxyribose present in the structure of DNA, their chemistry plays an important role in wide range of cellular functions of nucleic acids. In addition to their functions in nucleotides, sugars are also used for structural components of organisms, as energy storage molecules, cell signaling molecules, protein modification and play key roles in the immune system, fertilization, preventing pathogenesis, blood clotting, and

neg: Nucleic acid structure determination exposed bases of specific nucleotides, which are uridine, and to a smaller extent guanine. CMCT reacts primarily with N3 of uridine and N1 of guanine modifying two sites responsible for hydrogen bonding on the bases. Modification using CMCT is analogous in detection to DMS as modification prevents basepairing at specific nucleotides which are then detected using rt-PCR and running of the PCR products on an agarose gel as shown in Figure 1. Structure probing of RNA by CMCT indicates the presence of uridine and guanine in single stranded regions by accessibility to modification or the presence of uridine and guanine

neg: Nucleic acid structure of RNA are helices, loops, bulges, and junctions. Stem-loop or hairpin loop is the most common element of RNA secondary structure. Stem-loop is formed when the RNA chains fold back on themselves to form a double helical tract called the stem, the unpaired nucleotides forms single stranded region called the loop. Secondary structure of RNA can be predicted by experimental data on the secondary structure elements, helices, loops and bulges. Bulges and internal loops are formed by separation of the double helical tract on either one strand (bulge) or on both strands (internal loops) by unpaired nucleotides. A tetraloop is

neg: Nucleoside dideoxynucleotides are used. These nucleotides possess the non-canonical sugar dideoxyribose, which lacks 3' hydroxyl group (which accepts the phosphate). It therefore cannot bond with the next base and terminates the chain, as DNA polymerases cannot distinguish between it and a regular deoxyribonucleotide. Nucleoside Nucleosides are glycosylamines that can be thought of as nucleotides without a phosphate group. A nucleoside consists simply of a nucleobase (also termed a nitrogenous base) and a five-carbon sugar (either ribose or deoxyribose), whereas a nucleotide is composed of a nucleobase, a five-carbon sugar, and one or more phosphate groups. In a nucleoside, the anomeric carbon

neg: Nucleic acid structure determination bases modified by DMS. This enables modification sites to be detected by RT-PCR, as modified sites cannot be basepaired, which results in the reverse transcriptase to fall off and produce different band sizes. DMS may modify adenines and cytosines that are single stranded, base paired at the end of a helix, or in a base pair next to a GU pair. Detection of these modifications is done by examination of a gel and looking at bands present. One thing of note is that since modification prevents the addition of nucleotides at the modification site each of the bands generated is

neg: Nucleic acid thermodynamics neighbor method agree reasonably well with experimental results, but some unexpected outlying sequences, calling for further insights, do exist. Finally, we should also mention the increased accuracy provided by single molecule unzipping assays which provide a wealth of new insight into the thermodynamics of DNA hybridization and the validity of the nearest-neighbour model as well. Nucleic acid thermodynamics Nucleic acid thermodynamics is the study of how temperature affects the nucleic acid structure of double-stranded DNA (dsDNA). The melting temperature ("T") is defined as the temperature at which half of the DNA strands are in the random coil or single-stranded (ssDNA)

neg: Vesicular exanthema of swine virus not enveloped, round with icosahedral symmetry. The isometric capsid has a diameter of 35–39 nm. Capsids appear round to hexagonal in outline. The capsid surface structure reveals a regular pattern with distinctive features. The capsomer arrangement is clearly visible. Capsid with 32 cup-shaped depressions. Under in vitro conditions, virions are inactivated in acid environment of pH 3–5. The genome is not segmented and contains a single molecule of linear positive-sense, single-stranded RNA. Minor species of non-genomic nucleic acid are also found in virions. The complete genome is 7900 nucleotides long. The 5'-end of the genome has a viral protein genome-linked

neg: Depurination Depurination Depurination is a chemical reaction of purine deoxyribonucleosides, deoxyadenosine and deoxyguanosine, and ribonucleosides, adenosine or guanosine, in which the β-N-glycosidic bond is hydrolytically cleaved releasing a nucleic base, adenine or guanine, respectively. The second product of depurination of deoxyribonucleosides and ribonucleosides is sugar, 2'-deoxyribose and ribose, respectively. More complex compounds containing nucleoside residues, nucleotides and nucleic acids, also suffer from depurination. Deoxyribonucleosides and their derivatives are substantially more prone to depurination than their corresponding ribonucleoside counterparts. Loss of pyrimidine bases (cytosine and thymine) occurs by a similar mechanism, but at a substantially lower rate. When depurination occurs with DNA,

neg: Deoxyribonucleotide synthesis. New nucleotides are always added to the 3' carbon of the last nucleotide, so synthesis always proceeds from 5' to 3'. Deoxyribonucleotide A deoxyribonucleotide is the monomer, or single unit, of DNA, or deoxyribonucleic acid. Each deoxyribonucleotide comprises three parts: a nitrogenous base, a deoxyribose sugar, and one phosphate group. The nitrogenous base is always bonded to the 1' carbon of the deoxyribose, which is distinguished from ribose by the presence of a proton on the 2' carbon rather than an -OH group. The phosphate groups bind to the 5' carbon of the sugar. When deoxyribonucleotides polymerize to form

neg: Nucleobase formed in outer space as well as on earth. The origin of the term "base" reflects these compounds' chemical properties in acid-base reactions, but those properties are not especially important for understanding most of the biological functions of nucleobases. At the sides of nucleic acid structure, phosphate molecules successively connect the two sugar-rings of two adjacent nucleotide monomers, thereby creating a long chain biomolecule. These chain-joins of phosphates with sugars (ribose or deoxyribose) create the "backbone" strands for a single- or double helix biomolecule. In the double helix of DNA, the two strands are oriented chemically in opposite directions, which

neg: Nucleic acid other biological data made available through the NCBI web site. Deoxyribonucleic acid (DNA) is a nucleic acid containing the genetic instructions used in the development and functioning of all known living organisms. The DNA segments carrying this genetic information are called genes. Likewise, other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information. Along with RNA and proteins, DNA is one of the three major macromolecules that are essential for all known forms of life. DNA consists of two long polymers of simple units called nucleotides, with backbones made of sugars and phosphate

neg: Nuclear magnetic resonance spectroscopy of nucleic acids 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

neg: Nucleic acid analogue 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

neg: Nucleotide common unit of length for single-stranded nucleic acids, similar to how base pair is a unit of length for double-stranded nucleic acids. A study done by the Department of Sports Science at the University of Hull in Hull, UK has shown that nucleotides have significant impact on cortisol levels in saliva. Post exercise, the experimental nucleotide group had lower cortisol levels in their blood than the control or the placebo. Additionally, post supplement values of Immunoglobulin A were significantly higher than either the placebo or the control. The study concluded, "nucleotide supplementation blunts the response of the hormones associated with

neg: Nucleic acid thermodynamics Nucleic acid thermodynamics Nucleic acid thermodynamics is the study of how temperature affects the nucleic acid structure of double-stranded DNA (dsDNA). The melting temperature ("T") is defined as the temperature at which half of the DNA strands are in the random coil or single-stranded (ssDNA) state. "T" depends on the length of the DNA molecule and its specific nucleotide sequence. DNA, when in a state where its two strands are dissociated (i.e., the dsDNA molecule exists as two independent strands), is referred to as having been denatured by the high temperature. Hybridization is the process of establishing a non-covalent, sequence-specific

neg: Fatty acid synthesis a general principle that NADPH is consumed during biosynthetic reactions, whereas NADH is generated in energy-yielding reactions. (Thus NADPH is also required for the synthesis of cholesterol from acetyl-CoA; while NADH is generated during glycolysis.) The source of the NADPH is two-fold. When malate is oxidatively decarboxylated by "NADP-linked malic enzyme" to form pyruvate, CO and NADPH are formed. NADPH is also formed by the pentose phosphate pathway which converts glucose into ribose, which can be used in synthesis of nucleotides and nucleic acids, or it can be catabolized to pyruvate. In humans, fatty acids are formed from carbohydrates predominantly

neg: Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid features of the many different life forms on Earth are made possible by proteins. Structurally, proteins are long chains of amino acid subunits. In some way, the genetic molecule, DNA, had to contain instructions for how to make the thousands of proteins found in cells. From the DNA double helix model, it was clear that there must be some correspondence between the linear sequences of nucleotides in DNA molecules to the linear sequences of amino acids in proteins. The details of how sequences of DNA instruct cells to make specific proteins was worked out by molecular biologists during the period

neg: History of RNA biology differences between RNA and DNA were not apparent, and they were named after the materials from which they were isolated; RNA was initially known as "yeast nucleic acid" and DNA was "thymus nucleic acid". Using diagnostic chemical tests, carbohydrate chemists showed that the two nucleic acids contained different sugars, whereupon the common name for RNA became "ribose nucleic acid". Other early biochemical studies showed that RNA was readily broken down at high pH, while DNA was stable (although denatured) in alkali. Nucleoside composition analysis showed first that RNA contained similar nucleobases to DNA, with uracil instead of thymine, and that

neg: Heteroduplex 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

neg: Vesivirus is not segmented and contains a single molecule of linear positive-sense, single-stranded RNA. Minor species of non-genomic nucleic acid are some times also found in virions. The complete genome is 7700 nucleotides long. The genome has a guanine + cytosine content of 45–49%. The 5' end of the genome has a genome-linked protein (VPg). The 3' terminus has a poly (A) tract. Each virion contains a full length copy, or defective interfering copies. The viral genome encodes viral structural protein. Virions consist of 1 viral structural protein (major species), or 2 Viral structural proteins (detected in Norwalk virus, amyelosis chronic

neg: Influenza A virus double-stranded DNA, many viral genomes are made up of a different, single-stranded nucleic acid called RNA. Unusually for a virus, though, the influenza type A virus genome is not a single piece of RNA; instead, it consists of segmented pieces of negative-sense RNA, each piece containing either one or two genes which code for a gene product (protein). The term negative-sense RNA just implies that the RNA genome cannot be translated into protein directly; it must first be transcribed to positive-sense RNA before it can be translated into protein products. The segmented nature of the genome allows for the exchange

neg: Cyclic nucleotide three components. It contains a nitrogenous base (meaning it contains nitrogen): for example, adenine in cAMP and guanine in cGMP. It also contains a sugar, specifically the five-carbon ribose. And finally, a cyclic nucleotide contains a phosphate. A double-ring purine is the nitrogenous base for cAMP and cGMP, while cytosine, thymine, and uracil each have a single-ring nitrogenous base (pyrimidine). These three components are connected so that the nitrogenous base is attached to the first carbon of ribose (1’ carbon), and the phosphate group is attached to the 5’ carbon of ribose. While all nucleotides have this structure, the phosphate

neg: Spherical nucleic acid 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

neg: Nucleic acid sequence Nucleic acid sequence A nucleic acid sequence is a succession of letters that indicate the order of nucleotides forming alleles within a DNA (using GACT) or RNA (GACU) molecule. By convention, sequences are usually presented from the 5' end to the 3' end. For DNA, the sense strand is used. Because nucleic acids are normally linear (unbranched) polymers, specifying the sequence is equivalent to defining the covalent structure of the entire molecule. For this reason, the nucleic acid sequence is also termed the primary structure. The sequence has capacity to represent information. Biological deoxyribonucleic acid represents the information which directs

neg: Nucleoside Nucleoside Nucleosides are glycosylamines that can be thought of as nucleotides without a phosphate group. A nucleoside consists simply of a nucleobase (also termed a nitrogenous base) and a five-carbon sugar (either ribose or deoxyribose), whereas a nucleotide is composed of a nucleobase, a five-carbon sugar, and one or more phosphate groups. In a nucleoside, the anomeric carbon is linked through a glycosidic bond to the N9 of a purine or the N1 of a pyrimidine. Examples of nucleosides include cytidine, uridine, adenosine, guanosine, thymidine and inosine. While a nucleoside is a nucleobase linked to a sugar, a nucleotide is

neg: Nucleic acid structure 1' -OH group of the deoxyribose. Cytosine, thymine and uracil are pyrimidines, hence the glycosidic bonds forms between their 1 nitrogen and the 1' -OH of the deoxyribose. For both the purine and pyrimidine bases, the phosphate group forms a bond with the deoxyribose sugar through an ester bond between one of its negatively charged oxygen groups and the 5' -OH of the sugar. The polarity in DNA and RNA is derived from the oxygen and nitrogen atoms in the backbone. Nucleic acids are formed when nucleotides come together through phosphodiester linkages between the 5' and 3' carbon atoms. A