cytosine uracil and thymine are single-ringed nitrogen-containing organic bases called
Cyclic nucleotide


cytidine 3',5'-monophosphate, and cUMP is uridine 2',3'-cyclic phosphate. Each cyclic nucleotide has 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
525326
Nitrogenous base


C). Thymine and uracil are distinguished by merely the presence or absence of a methyl group on the fifth carbon (C5) of these heterocyclic six-membered rings. The nitrogenous bases form hydrogen bonds between opposing DNA strands to form the rungs of the "twisted ladder" or double helix of DNA or a biological catalyst that is found in the nucleotides. Adenine is always paired with thymine, and guanine is always paired with cytosine. These are known as base pairs. Adenine forms two hydrogen bonds with thymine in DNA
20919196
Pyrimidine


Pyrimidine is an aromatic heterocyclic organic compound similar to pyridine. One of the three diazines (six-membered heterocyclics with two nitrogen atoms in the ring), it has the nitrogen atoms at positions 1 and 3 in the ring. The other diazines are pyrazine (nitrogen atoms at the 1 and 4 positions) and pyridazine (nitrogen atoms at the 1 and 2 positions). In nucleic acids, three types of nucleobases are pyrimidine derivatives: cytosine (C), thymine (T), and uracil (U).
4150948
Biochemistry


(similar to a zipper). Adenine binds with thymine and uracil; thymine binds only with adenine; and cytosine and guanine can bind only with one another. Aside from the genetic material of the cell, nucleic acids often play a role as second messengers, as well as forming the base molecule for adenosine triphosphate (ATP), the primary energy-carrier molecule found in all living organisms. Also, the nitrogenous bases possible in the two nucleic acids are different: adenine, cytosine, and guanine occur in both RNA
3495070
Heterocyclic amine


. Pyridoxine or vitamin B6, it becomes a major compound in the metabolism of amino acids. Pyrimidine is a heterocyclic amine that contains two nitrogen atoms in an unsaturated six-membered ring. An example of a molecule that contains pyrimidine is thiamine, which is also known as vitamin B1. Thiamine decifiency produces beriberi. Pyrimidine is a component of the nucleobases cytosine, uracil, and thymine. The other two nucleobases, adenine and guanine, are also heterocyclic amines called purines; they are composed of a fused pyrimidine and imidazole.
8041838
Ribonucleotide


elements as members of its rings. Both RNA and DNA contain two major purine bases, adenine (A) and guanine (G), and two major pyrimidines. In both DNA and RNA, one of the pyrimdines is cytosine (C). However, DNA and RNA differ in the second major pyrimidine. DNA contains thymine (T) while RNA contains uracil (U). There are some rare cases where thymine does occur in RNA and uracil in DNA. Here are the 4 major ribonucleotides (ribonucleoside 5'-monophosphate)
20668721
Nucleoside triphosphate


four different nitrogenous bases: adenine, guanine, cytosine and thymine. RNA also contains adenine, guanine, and cytosine, but replaces thymine with uracil. Thus, DNA synthesis requires dATP, dGTP, dCTP, and dTTP as substrates, while RNA synthesis requires ATP, GTP, CTP, and UTP. Nucleic acid synthesis is catalyzed by either DNA polymerase or RNA polymerase for DNA and RNA synthesis respectively. These enzymes covalently link the free -OH group on the 3’ carbon of a growing chain of nucleotides to the α-
11913639
Nucleic acid structure


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 guanine. Purines consist of a double ring structure, a six membered and a five membered ring containing nitrogen. The pyrimidines are cytosine and thymine. It has a single ringed structure, a six membered ring containing nitrogen. A purine base always pairs with a pyrimidine base
912024
RNA world


-DNA structure to one more closely resembling A-DNA. RNA also uses a different set of bases than DNA—adenine, guanine, cytosine and uracil, instead of adenine, guanine, cytosine and thymine. Chemically, uracil is similar to thymine, differing only by a methyl group, and its production requires less energy. In terms of base pairing, this has no effect. Adenine readily binds uracil or thymine. Uracil is, however, one product of damage to cytosine that makes RNA particularly susceptible to mutations that
6211935
Base pair


" pairs to form stably. DNA with high GC-content is more stable than DNA with low GC-content. But, contrary to popular belief, the hydrogen bonds do not stabilize the DNA significantly; stabilization is mainly due to stacking interactions. The larger nucleobases, adenine and guanine, are members of a class of double-ringed chemical structures called purines; the smaller nucleobases, cytosine and thymine (and uracil), are members of a class of single-ringed chemical structures called pyrimidines. Purines are complementary only
3926441
Nitrogenous base


bases and relatively unreactive towards electrophilic aromatic substitution. In the biological sciences, nitrogenous bases are increasingly termed nucleobases because of their role in nucleic acids - their flat shape is particularly important when considering their roles as the building blocks of DNA and RNA. A set of five nitrogenous bases is used in the construction of nucleotides, which in turn build up nucleic acids like DNA and RNA. These nitrogenous bases are adenine (A), uracil (U), guanine (G), thymine (T), and cytosine (
20919195
Biochemistry


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 the nucleic acid, while the sequence of nitrogenous bases stores the information. The most common nitrogenous bases are adenine, cytosine, guanine, thymine, and uracil. The nitrogenous bases of each strand of a nucleic acid will form hydrogen bonds with certain other nitrogenous bases in a complementary strand of nucleic acid
3495069
Cytosine


Cytosine (; C) is one of the four main bases found in DNA and RNA, along with adenine, guanine, and thymine (uracil in RNA). It is a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached (an amine group at position 4 and a keto group at position 2). The nucleoside of cytosine is cytidine. In Watson-Crick base pairing, it forms three hydrogen bonds with guanine. Cytosine was discovered and named by Albrecht Kossel and Albert Neumann in 1894 when it was
6232880
Nucleic acid sequence


are also valid for RNA, except with U (uracil) replacing T (thymine). Apart from adenine (A), cytosine (C), guanine (G), thymine (T) and uracil (U), DNA and RNA also contain bases that have been modified after the nucleic acid chain has been formed. In DNA, the most common modified base is 5-methylcytidine (m5C). In RNA, there are many modified bases, including pseudouridine (Ψ), dihydrouridine (D), inosine (
18138376
Combined bisulfite restriction analysis


sodium bisulfite, which introduces methylation-dependent sequence differences. During sodium bisulfite treatment, unmethylated cytosine residues are converted to uracil, while methylated cytosine residues are unaffected. Bisulfite treated DNA is then PCR amplified, resulting in cytosine residues at originally methylated positions, and thymine residues at originally unmethylated position (that were converted to uracil). Primers used during this step do not contain CpG sites (the common target of cytosine methylation), so the amplificiation process does not discriminate between templates based on methylation status. PCR products are purified
6892192
GC-content


In molecular biology and genetics, GC-content (or guanine-cytosine content) is the percentage of nitrogenous bases on a DNA or RNA molecule that are either guanine or cytosine (from a possibility of four different ones, also including adenine and thymine in DNA and adenine and uracil in RNA). This may refer to a certain fragment of DNA or RNA, or that of the whole genome. When it refers to a fragment of the genetic material, it may denote the GC-content of section of a gene
204104
DNA


-inactivation of chromosomes. The average level of methylation varies between organisms—the worm "Caenorhabditis elegans" lacks cytosine methylation, while vertebrates have higher levels, with up to 1% of their DNA containing 5-methylcytosine. Despite the importance of 5-methylcytosine, it can deaminate to leave a thymine base, so methylated cytosines are particularly prone to mutations. Other base modifications include adenine methylation in bacteria, the presence of 5-hydroxymethylcytosine in the brain, and the glycosylation of uracil to produce the "J-base" in kinetoplastids. DNA can
8040213
Nucleobase


simple-ring structure of cytosine, uracil, and thymine is derived of pyrimidine, so those three bases are called the pyrimidine bases. Each of the base pairs in a typical double-helix DNA comprises a purine and a pyrimidine: either an A paired with a T or a C paired with a G. These purine-pyrimidine pairs, which are called "base complements", connect the two strands of the helix and are often compared to the rungs of a ladder. The pairing of purines and pyrimidines may result,
6797398
Nucleic acid structure


bond between their 9 nitrogen and the 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
912021
Whole genome bisulfite sequencing


Whole genome bisulfite sequencing (WGBS), is a next-generation sequencing technology used to determine the DNA methylation status of single cytosines by treating the DNA with sodium bisulfite before sequencing. Sodium bisulfite is a chemical compound that converts unmethylated cytosines into uracil. The cytosines that haven't converted in uracil are methylated. After sequencing, the unmethylated cytosines appear as thymines. This technique measures single-cytosine methylation levels genome-wide and directly estimates the ratio of molecules methylated rather than enrichment levels. However, this method requires essentially resequencing
4634574
Guanine


Guanine (; or G, Gua) is one of the four main nucleobases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, and thymine (uracil in RNA). In DNA, guanine is paired with cytosine. The guanine nucleoside is called guanosine. With the formula CHNO, guanine is a derivative of purine, consisting of a fused pyrimidine-imidazole ring system with conjugated double bonds. Being unsaturated, the bicyclic molecule is planar. Guanine, along with adenine and cytosine, is present in
12080248
Uracil


) during DNA synthesis. Uracil-DNA glycosylase excises uracil bases from double-stranded DNA. This enzyme would therefore recognize and cut out both types of uracil – the one incorporated naturally, and the one formed due to cytosine deamination, which would trigger unnecessary and inappropriate repair processes. This problem is believed to have been solved in terms of evolution, i.e. by "tagging" (methylating) uracil. Methylated uracil is identical to thymine. Hence the hypothesis that, over time, thymine became standard in DNA instead of uracil
18157288
DNA methylation


methylation has been observed in bacterial, plant, and recently in mammalian DNA, but has received considerably less attention. Methylation of cytosine to form 5-methylcytosine occurs at the same 5 position on the pyrimidine ring where the DNA base thymine's methyl group is located; the same position distinguishes thymine from the analogous RNA base uracil, which has no methyl group. Spontaneous deamination of 5-methylcytosine converts it to thymine. This results in a T:G mismatch. Repair mechanisms then correct it back to the original C:G pair; alternatively
11115649
Thymine


of DNA involves two adjacent thymines or cytosine, which, in presence of ultraviolet light, may form thymine dimers, causing "kinks" in the DNA molecule that inhibit normal function. Thymine could also be a target for actions of 5-fluorouracil (5-FU) in cancer treatment. 5-FU can be a metabolic analog of thymine (in DNA synthesis) or uracil (in RNA synthesis). Substitution of this analog inhibits DNA synthesis in actively dividing cells. Thymine bases are frequently oxidized to hydantoins over time after the death of an organism
13249187
DNA


biotechnology. Uracil is not usually found in DNA, occurring only as a breakdown product of cytosine. However, in several bacteriophages, such as "Bacillus subtilis" phages PBS1 and PBS2 and "Yersinia" phage piR1-37, thymine has been replaced by uracil. Another phage—Staphylococcal phage S6—has been identified with a genome where thymine has been replaced by uracil. Uracil is also found in the DNA of "Plasmodium falciparum" It is present is relatively small amounts (7–10 uracil residues per million bases). 5-hydroxymethyldeoxyuridine,(hm5dU)
8040183
Stem-loop


long helix) and the base composition of the paired region. Pairings between guanine and cytosine have three hydrogen bonds and are more stable compared to adenine-uracil pairings, which have only two. In RNA, adenine-uracil pairings featuring two hydrogen bonds are equal to the adenine-thymine bond of the DNA. Base stacking interactions, which align the pi bonds of the bases' aromatic rings in a favorable orientation, also promote helix formation. The stability of the loop also influences the formation of the stem-loop structure
3783040
Complementarity (molecular biology)


door to modern tools such as cDNA libraries. While most complementarity is seen between two separate strings of DNA or RNA, it is also possible for a sequence to have internal complementarity resulting in the sequence binding to itself in a folded configuration. Complementarity is achieved by distinct interactions between nucleobases: adenine, thymine (uracil in RNA), guanine and cytosine. Adenine and guanine are purines, while thymine, cytosine and uracil are pyrimidines. Purines are larger than pyrimidines. Both types of molecules complement each other and can only base
9710382
Uracil


Uracil (; U) is one of the four nucleobases in the nucleic acid of RNA that are represented by the letters A, G, C and U. The others are adenine (A), cytosine (C), and guanine (G). In RNA, uracil binds to adenine via two hydrogen bonds. In DNA, the uracil nucleobase is replaced by thymine. Uracil is a demethylated form of thymine. Uracil is a common and naturally occurring pyrimidine derivative. The name "uracil" was coined in 1885 by the
18157282
Base excision repair


in base excision repair genes that occur in cancers are summarized below. MBD4 (methyl-CpG-binding domain protein 4) is a glycosylase employed in an initial step of base excision repair. MBD4 protein binds preferentially to fully methylated CpG sites and to the altered DNA bases at those sites. These altered bases arise from the frequent hydrolysis of cytosine to uracil (see image) and hydrolysis of 5-methylcytosine to thymine, producing G:U and G:T base pairs. If the improper uracils or thymines in these base pairs
19542975
5-Methylcytosine


function of this chemical varies significantly among species: While spontaneous deamination of cytosine forms uracil, which is recognized and removed by DNA repair enzymes, deamination of 5-methylcytosine forms thymine. This conversion of a DNA base from cytosine (C) to thymine (T) can result in a transition mutation. In addition, active enzymatic deamination of cytosine or 5-methylcytosine by the APOBEC family of cytosine deaminases could have beneficial implications on various cellular processes as well as on organismal evolution. The implications of deamination on 5-hydroxymethylcytosine, on the other hand,
6798726
Citric acid cycle


oxaloacetate" which forms aspartate and asparagine; and "alpha-ketoglutarate" which forms glutamine, proline, and arginine. Of these amino acids, aspartate and glutamine are used, together with carbon and nitrogen atoms from other sources, to form the purines that are used as the bases in DNA and RNA, as well as in ATP, AMP, GTP, NAD, FAD and CoA. The pyrimidines are partly assembled from aspartate (derived from "oxaloacetate"). The pyrimidines, thymine, cytosine and uracil, form the
6976409
De novo synthesis


translating to "from the new", but implying "anew", "from scratch", or "from the beginning." "De novo" pathways of nucleotides do not use free bases: adenine (abbreviated as A), guanine (G), cytosine (C), thymine (T), or uracil (U). The purine ring is built up one atom or a few atoms at a time and attached to ribose throughout the process. Pyrimidine ring is synthesized as orotate and attached to ribose
839068
DNA glycosylase


epimutations in DNA glycosylase genes that occur in cancers are summarized below. MBD4 (methyl-CpG-binding domain protein 4) is a glycosylase employed in an initial step of base excision repair. MBD4 protein binds preferentially to fully methylated CpG sites. These altered bases arise from the frequent hydrolysis of cytosine to uracil (see image) and hydrolysis of 5-methylcytosine to thymine, producing G:U and G:T base pairs. If the improper uracils or thymines in these base pairs are not removed before DNA replication, they will
12256725
Purine


adenine (2) and guanine (3). In DNA, these bases form hydrogen bonds with their complementary pyrimidines, thymine and cytosine, respectively. This is called complementary base pairing. In RNA, the complement of adenine is uracil instead of thymine. Other notable purines are hypoxanthine (4), xanthine (5), theobromine (6), caffeine (7), uric acid (8) and isoguanine (9). Aside from the crucial roles of purines (adenine and guanine) in DNA and RNA,
4150942
Nucleotide


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 of nucleic acids. The purine bases adenine and guanine and pyrimidine base cytosine occur in both DNA and RNA, while the pyrimidine bases thymine (in DNA) and uracil (in RNA) occur in just one. Adenine forms a base pair with thymine with two hydrogen bonds, while guanine pairs with cytosine
1764261
DNA


monomeric units called nucleotides. Each nucleotide is composed of one of four nitrogen-containing nucleobases (cytosine [C], guanine [G], adenine [A] or thymine [T]), a sugar called deoxyribose, and a phosphate group. The nucleotides are joined to one another in a chain by covalent bonds between the sugar of one nucleotide and the phosphate of the next, resulting in an alternating sugar-phosphate backbone. The nitrogenous bases of the two separate polynucleotide strands are bound together, according to base
8040169
Nucleic acid secondary structure


cytosine and thymine (and uracil), are members of a class of singly ringed chemical structures called pyrimidines. Purines are only complementary with pyrimidines: pyrimidine-pyrimidine pairings are energetically unfavorable because the molecules are too far apart for hydrogen bonding to be established; purine-purine pairings are energetically unfavorable because the molecules are too close, leading to overlap repulsion. The only other possible pairings are GT and AC; these pairings are mismatches because the pattern of hydrogen donors and acceptors do not correspond. The GU wobble base pair,
7174861
Sodium bisulfite


is used in the analysis of the methylation status of cytosines in DNA. In this technique, sodium bisulfite deaminates cytosine into uracil, but does not affect 5-methylcytosine, a methylated form of cytosine with a methyl group attached to carbon 5. When the bisulfite-treated DNA is amplified via polymerase chain reaction, the uracil is amplified as thymine and the methylated cytosines are amplified as cytosine. DNA sequencing techniques are then used to read the sequence of the bisulfite-treated DNA. Those cytosines that are read as cytosines after sequencing represent
8611656
Illumina Methylation Assay


to the methylated cytosine locus and the other will correspond to the unmethylated cytosine locus, which has been converted into uracil during bisulfite treatment and later amplified as thymine during whole-genome amplification. The bisulfite-converted amplified DNA products are denatured into single strands and hybridized to the chip via allele-specific annealing to either the methylation-specific probe or the non-methylation probe. Hybridization is followed by single-base extension with hapten-labeled dideoxynucleotides. The ddCTP and ddGTP are labeled with biotin while ddATP and ddUTP are labeled
17358624
Pyrimidine


pyrimidine and photochemical reactions have been observed for substituted pyrimidines. Pyrimidine can be hydrogenated to give tetrahydropyrimidine. Three nucleobases found in nucleic acids, cytosine (C), thymine (T), and uracil (U), are pyrimidine derivatives: In DNA and RNA, these bases form hydrogen bonds with their complementary purines. Thus, in DNA, the purines adenine (A) and guanine (G) pair up with the pyrimidines thymine (T) and cytosine (C), respectively. In RNA, the complement of
4150957
Deamination


corrected by the enzyme thymine-DNA glycosylase, which removes the thymine base in a G/T mismatch. This leaves an abasic site that is repaired by AP endonucleases and polymerase, as with uracil-DNA glycosylase. Deamination of guanine results in the formation of xanthine. Xanthine, in a manner analogous to the enol tautomer of guanine, selectively base pairs with thymine instead of cytosine. This results in a post-replicative transition mutation, where the original G-C base pair transforms into an A-T base pair
6798722
Nucleic acid


ordering of nucleotides within the molecules of RNA and DNA. Strings of nucleotides are bonded to form helical backbones—typically, one for RNA, two for DNA—and assembled into chains of base-pairs selected from the five primary, or canonical, nucleobases, which are: adenine, cytosine, guanine, thymine, and uracil; note, thymine occurs only in DNA and uracil only in RNA. Using amino acids and the process known as protein synthesis, the specific sequencing in DNA of these nucleobase-pairs enables storing
1764070
Nucleobase


), thymine (T), and uracil (U)—are called "primary" or "canonical". They function as the fundamental units of the genetic code, with the bases A, G, C, and T being found in DNA while A, G, C, and U are found in RNA. Thymine and uracil are identical except that T includes a methyl group that U lacks. Adenine and guanine have a fused-ring skeletal structure derived of purine, hence they are called purine bases. Similarly, the
6797397
CpG site


would be expected to occur 0.21 * 0.21 = 4.41% of the time. The frequency of CpG dinucleotides in human genomes is 0.98%, less than one-quarter of the expected frequency. This underrepresentation is a consequence of the high mutation rate of methylated CpG sites: whereas the spontaneously occurring deamination of cytosine results in a uracil, which as a foreign base is quickly replaced by a cytosine by the base excision repair mechanism, deamination of a methylated cytosine results in a thymine, and the resulting G:T mismatched bases
20295871
Nucleic acid analogue


Additionally, HNO2, or nitrous acid is a potent mutagen that acts on replicating and non-replicating DNA. It can cause deamination of the amino groups of Adenine, Guanine and Cytosine. Adenine is deaminated to hypoxanthine, which base pairs to cytosine instead of thymine. Cytosine is deaminated to uracil, which base pairs with Adenine instead of Guanine. Deamination of Guanine is not mutagenic. Nitrous acid-induced mutations also are induced to mutate back to wild-type using nitrous acid. Commonly fluorophores (such as rhodamine or fluorescein
3866068
Uracil


by exposing it to ultraviolet light under space-like conditions. This suggests that one possible natural original source for uracil in the RNA world could have been panspermia. More recently, in March 2015, NASA scientists reported that, for the first time, additional complex DNA and RNA organic compounds of life, including uracil, cytosine and thymine, have been formed in the laboratory under outer space conditions, using starting chemicals, such as pyrimidine, found in meteorites. Pyrimidine, like polycyclic aromatic hydrocarbons (PAHs), the most
18157290
Thymine


. In March 2015, NASA scientists reported that, for the first time, complex DNA and RNA organic compounds of life, including uracil, cytosine and thymine, have been formed in the laboratory under outer space conditions, using starting chemicals, such as pyrimidine, found in meteorites. Pyrimidine, like polycyclic aromatic hydrocarbons (PAHs), the most carbon-rich chemical found in the Universe, may have been formed in red giants or in interstellar dust and gas clouds, according to the scientists. Thymine has not been found
13249188
Life


, based on studies with meteorites found on Earth, suggest DNA and RNA components (adenine, guanine and related organic molecules) may be formed in outer space. In March 2015, NASA scientists reported that, for the first time, complex DNA and RNA organic compounds of life, including uracil, cytosine and thymine, have been formed in the laboratory under outer space conditions, using starting chemicals, such as pyrimidine, found in meteorites. Pyrimidine, like polycyclic aromatic hydrocarbons (PAHs), the most carbon-rich chemical
18728895
Biosynthesis


and uracil (which is only found in RNA). Uridine monophosphate biosynthesis involves an enzyme that is located in the mitochondrial inner membrane and multifunctional enzymes that are located in the cytosol. After the uridine nucleotide base is synthesized, the other bases, cytosine and thymine are synthesized. Cytosine biosynthesis is a two-step reaction which involves the conversion of UMP to UTP. Phosphate addition to UMP is catalyzed by a kinase enzyme. The enzyme CTP synthase catalyzes the next reaction step: the conversion of UTP to CTP by transferring an
9183551
Meteorite


, including uracil, cytosine and thymine, have been formed in the laboratory under outer space conditions, using starting chemicals, such as pyrimidine, found in meteorites. Pyrimidine and polycyclic aromatic hydrocarbons (PAHs) may have been formed in red giants or in interstellar dust and gas clouds, according to the scientists. In January 2018, researchers found that 4.5 billion-year-old meteorites found on Earth contained liquid water along with prebiotic complex organic substances that may be ingredients for life. Most meteorite falls are recovered on the basis
20483361
Canine circovirus


strand of DNA 2,063 nucleotides in length. DNA in general is made up of four nitrogenous bases: adenine (A), thymine (T), cytosine (C), and guanine (G) in which A pairs with T and G pairs with C across complementary strands in double stranded DNA and occasionally in single stranded DNA with a specific sequence that promotes same-strand base pairing. CaCV exhibits this behavior in the form of stemloop structures. Guanine-Cytosine nucleotide base pairing makes up a little over half of the
7920766
Thymine


Thymine (T, Thy) is one of the four nucleobases in the nucleic acid of DNA that are represented by the letters G–C–A–T. The others are adenine, guanine, and cytosine. Thymine is also known as 5-methyluracil, a pyrimidine nucleobase. In RNA, thymine is replaced by the nucleobase uracil. Thymine was first isolated in 1893 by Albrecht Kossel and Albert Neumann from calves' thymus glands, hence its name. As its alternate name (5-methyluracil) suggests, thymine may be derived by methylation
13249185
Pyrimidine dimer


Pyrimidine dimers are molecular lesions formed from thymine or cytosine bases in DNA via photochemical reactions. Ultraviolet light (UV) induces the formation of covalent linkages between consecutive bases along the nucleotide chain in the vicinity of their carbon–carbon double bonds. The dimerization reaction can also occur among pyrimidine bases in dsRNA (double-stranded RNA)—uracil or cytosine. Two common UV products are cyclobutane pyrimidine dimers (CPDs) and 6–4 photoproducts. These premutagenic lesions alter the structure and possibly the base-pairing. Up to 50–100 such reactions per second
12220876
The mold, protozoan, and coelenterate mitochondrial code and the mycoplasma/spiroplasma code


The mold, protozoan, and coelenterate mitochondrial code and the mycoplasma/spiroplasma code (translation table 4) is the genetic code used by various organisms, in some cases with slight variations, notably the use of UGA as a tryptophan codon rather than a stop codon. Bases: adenine (A), cytosine (C), guanine (G) and thymine (T) or uracil (U). Amino acids: Alanine (Ala, A), Arginine (Arg, R), Asparagine (Asn, N
19140707
Pyrimidine


The pyrimidine ring system has wide occurrence in nature as substituted and ring fused compounds and derivatives, including the nucleotides cytosine, thymine and uracil, thiamine (vitamin B1) and alloxan. It is also found in many synthetic compounds such as barbiturates and the HIV drug, zidovudine. Although pyrimidine derivatives such as uric acid and alloxan were known in the early 19th century, a laboratory synthesis of a pyrimidine was not carried out until 1879, when Grimaux reported the preparation of barbituric acid from urea and malonic acid in the presence of
4150949
Uracil


= -3.4, while the acidic p"K" = 9.38. In the gas phase, uracil has 4 sites that are more acidic than water. Uracil is rarely found in DNA, and this may have been an evolutionary change to increase genetic stability. This is because cytosine can deaminate spontaneously to produce uracil through hydrolytic deamination. Therefore, if there were an organism that used uracil in its DNA, the deamination of cytosine (which undergoes base pairing with guanine) would lead to formation of uracil (which would base pair with adenine
18157287
Ribonucleotide


. The nitrogenous bases are classified into two parent compounds, purine and pyrimidine. The general structure of a ribonucleotide consists of a phosphate group, a ribose sugar group, and a nucleobase, in which the nucleobase can either be adenine, guanine, cytosine, or uracil. Without the phosphate group, the composition of the nucleobase and sugar is known as a nucleoside. The interchangeable nitrogenous nucleobases are derived from two parent compounds, purine and pyrimidine. Nucleotides are heterocyclic compounds, that is, they contain at least two different chemical
20668720
Uracil-DNA glycosylase


-containing DNA, but has no effect on natural (i.e., thymine-containing) DNA. The resulting apyrimidinic sites block replication by DNA polymerases, and are very labile to acid/base hydrolysis. Because UDG does not react with dTTP, and is also inactivated by heat denaturation prior to the actual PCR, carry-over contamination of PCRs can be controlled effectively if the contaminants contain uracils in place of thymines. Uracil "N"-glycosylase was also used in a study to detect evidence of ongoing low-level metabolic activity and
19818822
Cytosine


a point mutation if not repaired by the DNA repair enzymes such as uracil glycosylase, which cleaves a uracil in DNA. When found third in a codon of RNA, cytosine is synonymous with uracil, as they are interchangeable as the third base. When found as the second base in a codon, the third is always interchangeable. For example, UCU, UCC, UCA and UCG are all serine, regardless of the third base. Cytosine can also be methylated into 5-methylcytosine by an enzyme called DNA methyltransferase or be methylated and
6232883
Nucleobase


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, and uracil results from deamination of cytosine. These are examples of modified adenosine or guanosine. These are examples of modified cytosine, thymine or uridine. A vast number of nucleobase analogues exist. The most common applications are used as fluorescent probes, either directly or indirectly, such as aminoallyl nucleotide, which are used to label cRNA or
6797402
Uracil


an analysis of data from the Cassini mission orbiting in the Saturn system showed that Titan's surface composition may include uracil. In RNA, uracil base-pairs with adenine and replaces thymine during DNA transcription. Methylation of uracil produces thymine. In DNA, the evolutionary substitution of thymine for uracil may have increased DNA stability and improved the efficiency of DNA replication (discussed below). Uracil pairs with adenine through hydrogen bonding. When base pairing with adenine, uracil acts as both a hydrogen bond acceptor and a hydrogen bond donor.
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DNA replication


T. Adenine and guanine are purine bases, while cytosine and thymine are pyrimidines. These nucleotides form phosphodiester bonds, creating the phosphate-deoxyribose backbone of the DNA double helix with the nucleobases pointing inward (i.e., toward the opposing strand). Nucleobases are matched between strands through hydrogen bonds to form base pairs. Adenine pairs with thymine (two hydrogen bonds), and guanine pairs with cytosine (three hydrogen bonds). DNA strands have a directionality, and the different ends of a single strand are called the "3′ (
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Cytosine deaminase


In enzymology, a cytosine deaminase () is an enzyme that catalyzes the chemical reaction Thus, the two substrates of this enzyme are cytosine and HO, whereas its two products are uracil and NH. This enzyme belongs to the family of hydrolases, those acting on carbon-nitrogen bonds other than peptide bonds, specifically in cyclic amidines. The systematic name of this enzyme class is cytosine aminohydrolase. This enzyme is also called isocytosine deaminase. This enzyme participates in pyrimidine metabolism. As of late 2007, 13 structures have been solved
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Activation-induced cytidine deaminase


Activation-induced cytidine deaminase, also known as AICDA and AID, is a 24 kDa enzyme which in humans is encoded by the "AICDA" gene. It creates mutations in DNA by deamination of cytosine base, which turns it into uracil (which is recognized as a thymine). In other words, it changes a C:G base pair into a U:G mismatch. The cell's DNA replication machinery recognizes the U as a T, and hence C:G is converted to a T:A base
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Activation-induced cytidine deaminase


. AID is believed to initiate SHM in a multi-step mechanism. AID deaminates cytosine in the target DNA. Cytosines located within hotspot motifs are preferentially deaminated (WRCY motifs W=adenine or thymine, R=purine, C=cytosine, Y=pyrimidine, or the inverse RGYW G=guanine). The resultant U:G (U= uracil) mismatch is then subject to one of a number of fates. The level of AID activity in B cells is tightly controlled by modulating AID expression. AID is induced
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Palindromic sequence


antiparallel strands of nucleotides that run in opposite directions, and the nucleotides always pair in the same way (adenine (A) with thymine (T) in DNA or uracil (U) in RNA; cytosine (C) with guanine (G)), a (single-stranded) nucleotide sequence is said to be a palindrome if it is equal to its reverse complement. For example, the DNA sequence ACCTAGGT is palindromic because its nucleotide-by-nucleotide complement is TGGATCCA, and reversing the order of the nucleotides
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Cytosine


hydrolyzed from calf thymus tissues. A structure was proposed in 1903, and was synthesized (and thus confirmed) in the laboratory in the same year. In 1997 cytosine was used in an early demonstration quantum information processing when Oxford University researchers implemented the Deutsch-Jozsa algorithm on a two qubit nuclear magnetic resonance quantum computer (NMRQC). In March 2015, NASA scientists reported the formation of cytosine, along with uracil and thymine, from pyrimidine under the space-like laboratory conditions, which is of interest because pyrimidine has been
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APOBEC3A


Apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3A, also known as APOBEC3A, is a gene of the APOBEC3 family found in humans, non-human primates, and some other mammals. It is a DNA cytidine deaminase with antiviral effects. While other members of the family such as APOBEC3G are believed to act by editing ssDNA by removing an amino group from cytosine in DNA, introducing a cytosine to uracil change which can ultimately lead to a cytosine to thymine mutation, one study suggests that APOBEC3A can inhibit parvoviruses
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DNA glycosylase


, but also removes U from double-stranded DNA. In addition to unmodified uracil, SMUG1 can excise 5-hydroxyuracil, 5-hydroxymethyluracil and 5-formyluracil bearing an oxidized group at ring C5. TDG and MBD4 are strictly specific for double-stranded DNA. TDG can remove thymine glycol when present opposite guanine, as well as derivatives of U with modifications at carbon 5. Current evidence suggests that, in human cells, TDG and SMUG1 are the major enzymes responsible for the repair of the U:G mispairs caused by spontaneous cytosine deamination, whereas
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Nucleic acid structure


(guanine (G) pairs with cytosine (C) and adenine (A) pairs with thymine (T) or uracil (U)). DNA's secondary structure is predominantly determined by base-pairing of the two polynucleotide strands wrapped around each other to form a double helix. Although the two strands are aligned by hydrogen bonds in base pairs, the stronger forces holding the two strands together are stacking interactions between the bases. These stacking interactions are stabilized by Van der Waals forces and hydrophobic interactions, and show a
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GC-content


(domain), single gene, group of genes (or gene clusters), or even a non-coding region. Qualitativelty, G (guanine) and C (cytosine) undergo a specific hydrogen bonding, whereas A (adenine) bonds specifically with T (thymine, in DNA) or U (uracil, in RNA). Quantitatively, the GC pair is bound by three hydrogen bonds, while AT and AU pairs are bound by two hydrogen bonds. To emphasize this difference in the number of hydrogen bonds,
204105
Mesodinium nuclear code


The "Mesodinium" nuclear code (translation table 29) is a genetic code used by the nuclear genome of the ciliates "Mesodinium" and "Myrionecta". Bases: adenine (A), cytosine (C), guanine (G) and thymine (T) or uracil (U). Amino acids: Alanine (Ala, A), Arginine (Arg, R), Asparagine (Asn, N), Aspartic acid (Asp, D), Cysteine (Cys, C), Glutamic acid (
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Blastocrithidia nuclear code


The "Blastocrithidia" nuclear code (translation table 31) is a genetic code used by the nuclear genome of the trypanosomatid "Blastocrithidia". Bases: adenine (A), cytosine (C), guanine (G) and thymine (T) or uracil (U). Amino acids: Alanine (Ala, A), Arginine (Arg, R), Asparagine (Asn, N), Aspartic acid (Asp, D), Cysteine (Cys, C), Glutamic acid (Glu, E)
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Blepharisma nuclear code


The Blepharisma nuclear code (translation table 15) is a genetic code found in the nuclei of "Blepharisma". Bases: adenine (A), cytosine (C), guanine (G) and thymine (T) or uracil (U). Amino acids: Alanine (Ala, A), Arginine (Arg, R), Asparagine (Asn, N), Aspartic acid (Asp, D), Cysteine (Cys, C), Glutamic acid (Glu, E), Glutamine (Gln,
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Chlorophycean mitochondrial code


The chlorophycean mitochondrial code (translation table 16) is a genetic code found in the mitochondria of "Chlorophyceae". Bases: adenine (A), cytosine (C), guanine (G) and thymine (T) or uracil (U). Amino acids: Alanine (Ala, A), Arginine (Arg, R), Asparagine (Asn, N), Aspartic acid (Asp, D), Cysteine (Cys, C), Glutamic acid (Glu, E), Glutamine (Gln,
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Non-canonical base pairing


A non-canonical base pairing is an interaction between two bases of a nucleic acid other than the standard base pairings, which are adenine–thymine in DNA, adenine–uracil in RNA, and cytosine–guanine in both. There are three main types of non-canonical base pairs: those stabilized by polar hydrogen bonds, those having interactions among C−H and O/N groups, and those that have hydrogen bonds between the bases themselves. Non-canonical base pairings commonly occur in the secondary structure of RNA (e.g.
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Melanoma


called cyclobutane pyrimidine dimers (CPDs). Thymine-thymine, cytosine-cytosine or cytosine-thymine dimers are formed by the joining of two adjacent pyrimidine bases within a DNA strand. Somewhat similarly to UVB, UVA light (longer wavelengths between 400–315 nm) from the sun or from tanning beds can also be directly absorbed by skin DNA (at about 100 to 1000 fold lower efficiency than UVB is absorbed). Exposure to ultraviolet radiation (UVA and UVB) is one of the major contributors to the development of melanoma.
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Life


macromolecule that are essential for all known forms of life. Most DNA molecules consist of two biopolymer strands coiled around each other to form a double helix. The two DNA strands are known as polynucleotides since they are composed of simpler units called nucleotides. Each nucleotide is composed of a nitrogen-containing nucleobase—either cytosine (C), guanine (G), adenine (A), or thymine (T)—as well as a sugar called deoxyribose and a phosphate group. The nucleotides are joined to one another in a chain by
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Aromaticity


, phenylalanine, tryptophan, and tyrosine each serve as one of the 20 basic building-blocks of proteins. Further, all 5 nucleotides (adenine, thymine, cytosine, guanine, and uracil) that make up the sequence of the genetic code in DNA and RNA are aromatic purines or pyrimidines. The molecule heme contains an aromatic system with 22 π-electrons. Chlorophyll also has a similar aromatic system. Aromatic compounds are important in industry. Key aromatic hydrocarbons of commercial interest are benzene, toluene, "ortho"-xylene and "
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Uracil


. So cells continue to use uracil in RNA, and not in DNA, because RNA is shorter-lived than DNA, and any potential uracil-related errors do not lead to lasting damage. Apparently, either there was no evolutionary pressure to replace uracil in RNA with the more complex thymine, or uracil has some chemical property that is useful in RNA, which thymine lacks. Uracil-containing DNA still exists, for example in In a scholarly article published in October 2009, NASA scientists reported having reproduced uracil from pyrimidine
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Karyorelict nuclear code


The karyorelictid nuclear code (translation table 27) is a genetic code used by the nuclear genome of the Karyorelictea ciliate "Parduczia" sp. Bases: adenine (A), cytosine (C), guanine (G) and thymine (T) or uracil (U). Amino acids: Alanine (Ala, A), Arginine (Arg, R), Asparagine (Asn, N), Aspartic acid (Asp, D), Cysteine (Cys, C), Glutamic acid (Glu, E)
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Condylostoma nuclear code


The "Condylostoma" nuclear code (translation table 28) is a genetic code used by the nuclear genome of the heterotrich ciliate "Condylostoma magnum". Bases: adenine (A), cytosine (C), guanine (G) and thymine (T) or uracil (U). Amino acids: Alanine (Ala, A), Arginine (Arg, R), Asparagine (Asn, N), Aspartic acid (Asp, D), Cysteine (Cys, C), Glutamic acid (Glu,
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Peritrich nuclear code


The peritrich nuclear code (translation table 30) is a genetic code used by the nuclear genome of the peritrich ciliates "Vorticella" and "Opisthonecta". Bases: adenine (A), cytosine (C), guanine (G) and thymine (T) or uracil (U). Amino acids: Alanine (Ala, A), Arginine (Arg, R), Asparagine (Asn, N), Aspartic acid (Asp, D), Cysteine (Cys, C), Glutamic acid (Glu
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Yeast mitochondrial code


The yeast mitochondrial code (translation table 3) is a genetic code used by the mitochondrial genome of yeasts, notably "Saccharomyces cerevisiae", "Candida glabrata", "Hansenula saturnus", and "Kluyveromyces thermotolerans". Bases: adenine (A), cytosine (C), guanine (G) and thymine (T) or uracil (U). Amino acids: Alanine (Ala, A), Arginine (Arg, R), Asparagine (Asn, N), Aspartic acid (Asp, D
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Invertebrate mitochondrial code


The invertebrate mitochondrial code (translation table 5) is a genetic code used by the mitochondrial genome of invertebrates. Bases: adenine (A), cytosine (C), guanine (G) and thymine (T) or uracil (U). Amino acids: Alanine (Ala, A), Arginine (Arg, R), Asparagine (Asn, N), Aspartic acid (Asp, D), Cysteine (Cys, C), Glutamic acid (Glu, E), Glutamine (Gln, Q
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Ascidian mitochondrial code


The ascidian mitochondrial code (translation table 13) is a genetic code found in the mitochondria of Ascidia. Bases: adenine (A), cytosine (C), guanine (G) and thymine (T) or uracil (U). Amino acids: Alanine (Ala, A), Arginine (Arg, R), Asparagine (Asn, N), Aspartic acid (Asp, D), Cysteine (Cys, C), Glutamic acid (Glu, E), Glutamine (Gln, Q)
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Cephalodiscidae mitochondrial code


, and AGG and AGA to an amino acid other than arginine. However, the assignment of AGG to lysine in pterobranchian mitogenomes is not found elsewhere in deuterostome mitochondria but it occurs in some taxa of Arthropoda. Bases: adenine (A), cytosine (C), guanine (G) and thymine (T) or uracil (U). Amino acids: Alanine (Ala, A), Arginine (Arg, R), Asparagine (Asn, N), Aspartic acid (Asp, D), Cysteine
6538400
The euplotid nuclear code


The euplotid nuclear code (translation table 10) is the genetic code used by Euplotidae. Bases: adenine (A), cytosine (C), guanine (G) and thymine (T) or uracil (U). Amino acids: Alanine (Ala, A), Arginine (Arg, R), Asparagine (Asn, N), Aspartic acid (Asp, D), Cysteine (Cys, C), Glutamic acid (Glu, E), Glutamine (Gln, Q), Glycine (
6543757
Trematode mitochondrial code


The trematode mitochondrial code (translation table 21) is a genetic code found in the mitochondria of Trematoda. Bases: adenine (A), cytosine (C), guanine (G) and thymine (T) or uracil (U). Amino acids: Alanine (Ala, A), Arginine (Arg, R), Asparagine (Asn, N), Aspartic acid (Asp, D), Cysteine (Cys, C), Glutamic acid (Glu, E), Glutamine (Gln, Q)
8422324
Alternative flatworm mitochondrial code


The alternative flatworm mitochondrial code (translation table 14) is a genetic code found in the mitochondria of Platyhelminthes and Nematodes. Bases: adenine (A), cytosine (C), guanine (G) and thymine (T) or uracil (U). Amino acids: Alanine (Ala, A), Arginine (Arg, R), Asparagine (Asn, N), Aspartic acid (Asp, D), Cysteine (Cys, C), Glutamic acid (Glu, E), Glutamine (Gln
1611288
Pterobranchia mitochondrial code


code shares with many other mitochondrial codes the reassignment of the UGA STOP to tryptophan, and AGG and AGA to an amino acid other than arginine. The initiation codons in "Rhabdopleura compacta" are ATG and GTG. Bases: adenine (A), cytosine (C), guanine (G) and thymine (T) or uracil (U). Amino acids: Alanine (Ala, A), Arginine (Arg, R), Asparagine (Asn, N), Aspartic acid (Asp, D),
1746255
Echinoderm and flatworm mitochondrial code


The echinoderm and flatworm mitochondrial code (translation table 9) is a genetic code used by the mitochondria of certain echinoderm and flatworm species. Bases: adenine (A), cytosine (C), guanine (G) and thymine (T) or uracil (U). Amino acids: Alanine (Ala, A), Arginine (Arg, R), Asparagine (Asn, N), Aspartic acid (Asp, D), Cysteine (Cys, C), Glutamic acid (Glu, E),
6354175
Alternative yeast nuclear code


The alternative yeast nuclear code (translation table 12) is a genetic code found in certain yeasts. However, other yeast, including "Saccharomyces cerevisiae", "Candida azyma", "Candida diversa", "Candida magnoliae", "Candida rugopelliculosa", "Yarrowia lipolytica", and "Zygoascus hellenicus", definitely use the standard (nuclear) code. Bases: adenine (A), cytosine (C), guanine (G) and thymine (T) or uracil (U). Amino acids:
6543966
Thymidine


deoxythymidine under standard temperature and pressure (STP) is very high. Deoxythymidine is non-toxic and as part of one of the four nucleosides in DNA it is a naturally occurring compound that exists in all living organisms and DNA viruses. Instead of thymidine, RNA contains uridine (uracil joined to ribose). Uracil is chemically very similar to thymine, which is also known as 5-methyluracil. Since thymine nucleotides are precursors of DNA (but not RNA), the prefix "deoxy" is often left out, i.e., deoxythymidine
6798681
Chimeric RNA


data. DNA is replicated and serves as its own template for replication. DNA forms a double helix structure and is a composed of a sugar-phosphate backbone and nitrogenous bases; this can be thought of as a ladder structure where the sides of the ladder are constructed of deoxyribose sugar and phosphate while the rungs of the ladder are composed of paired nitrogenous bases. There are four bases in a DNA molecule: adenine (A), cytosine (C), thymine (T), and guanine (G). Nucleotides
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Molecular evolution


in point mutations. Other types of mutations modify larger segments of DNA and can cause duplications, insertions, deletions, inversions, and translocations. Most organisms display a strong bias in the types of mutations that occur with strong influence in GC-content. Transitions (A ↔ G or C ↔ T) are more common than transversions (purine (adenine or guanine)) ↔ pyrimidine (cytosine or thymine, or in RNA, uracil)) and are less likely to alter amino acid sequences of proteins. Mutations are stochastic
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Albrecht Kossel


Ludwig Karl Martin Leonhard Albrecht Kossel (16 September 1853 – 5 July 1927) was a German biochemist and pioneer in the study of genetics. He was awarded the Nobel Prize for Physiology or Medicine in 1910 for his work in determining the chemical composition of nucleic acids, the genetic substance of biological cells. Kossel isolated and described the five organic compounds that are present in nucleic acid: adenine, cytosine, guanine, thymine, and uracil. These compounds were later shown to be nucleobases, and are key in the formation of
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Albrecht Kossel


Institute at the University of Berlin. In this post, he succeeded Eugen Baumann and worked under the supervision of Emil du Bois-Reymond. Kossel continued his previous work on the nucleic acids. During the period 1885 to 1901, he was able to isolate and name its five constituent organic compounds: adenine, cytosine, guanine, thymine, and uracil. These compounds are now known collectively as nucleobases, and they provide the molecular structure necessary in the formation of stable DNA and RNA molecules. In 1895, Kossel was professor
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Cosmic dust


in the Universe, and are associated with new stars and exoplanets. In March 2015, NASA scientists reported that, for the first time, complex DNA and RNA organic compounds of life, including uracil, cytosine and thymine, have been formed in the laboratory under outer space conditions, using starting chemicals, such as pyrimidine, found in meteorites. Pyrimidine, like polycyclic aromatic hydrocarbons (PAHs), the most carbon-rich chemical found in the Universe, may have been formed in red giants or in interstellar dust and gas
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Panspermia


, more than 20% of the carbon in the universe may be associated with PAHs, possible starting materials for the formation of life. PAHs seem to have been formed shortly after the Big Bang, are widespread throughout the universe, and are associated with new stars and exoplanets. In March 2015, NASA scientists reported that, for the first time, complex DNA and RNA organic compounds of life, including uracil, cytosine and thymine, have been formed in the laboratory under outer space conditions, using starting chemicals, such as
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