Nucleotide bases[1] (alsonucleobases,nitrogenous bases) arenitrogen-containing biological compounds that formnucleosides, which, in turn, are components ofnucleotides, with all of thesemonomers constituting the basic building blocks ofnucleic acids. The ability of nucleobases to formbase pairs and to stack one upon another leads directly to long-chain helical structures such asribonucleic acid (RNA) anddeoxyribonucleic acid (DNA). Five nucleobases—adenine (A),cytosine (C),guanine (G),thymine (T), anduracil (U)—are calledprimary orcanonical. They function as the fundamental units of thegenetic 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 distinguished by merely the presence or absence of a methyl group on the fifth carbon (C5) of these heterocyclic six-membered rings.[2][page needed]In addition, some viruses haveaminoadenine (Z) instead of adenine. It differs in having an extraamine group, creating a more stable bond to thymine.[3]
Adenine and guanine have afused-ring skeletal structure derived ofpurine, hence they are calledpurine bases.[4] The purine nitrogenous bases are characterized by their singleamino group (−NH2), at the C6 carbon in adenine and C2 in guanine.[5] Similarly, the simple-ring structure of cytosine, uracil, and thymine is derived ofpyrimidine, so those three bases are called thepyrimidine bases.[6]
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 calledbase complements, connect the two strands of the helix and are often compared to the rungs of a ladder. Only pairing purine with pyrimidine ensures a constant width for the DNA. The A–T pairing is based on twohydrogen bonds, while the C–G pairing is based on three. In both cases, the hydrogen bonds are between theamine andcarbonyl groups on the complementary bases.
Nucleobases such as adenine, guanine,xanthine,hypoxanthine, purine,2,6-diaminopurine, and 6,8-diaminopurine may have formed in outer space as well as on earth.[7][8][9]
The origin of the termbase reflects these compounds' chemical properties inacid–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 chainbiomolecule. These chain-joins of phosphates with sugars (ribose ordeoxyribose) 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 permits base pairing by providingcomplementarity between the two bases, and which is essential forreplication of ortranscription of the encoded information found in DNA.[citation needed]
DNA and RNA also contain other (non-primary) bases that have been modified after the nucleic acid chain has been formed. In DNA, the most common modified base is5-methylcytosine (m5C). In RNA, there are many modified bases, including those contained in the nucleosidespseudouridine (Ψ),dihydrouridine (D),inosine (I), and7-methylguanosine (m7G).[10][11]
Hypoxanthine andxanthine are two of the many bases created throughmutagen presence, both of them throughdeamination (replacement of the amine-group with a carbonyl-group). Hypoxanthine is produced from adenine, xanthine from guanine,[12] and uracil results from deamination of cytosine.
| Nucleobase |  |  |  |  |
|---|---|---|---|---|
| Hypoxanthine | Xanthine | 7-Methylguanine | 9H-purine | |
| Nucleoside |  |  |  |  |
| Inosine | Xanthosine | 7-Methylguanosine | Nebularine | |
| Short symbol | I | X | m7G | P[13] |
| Nucleobase |  |  |  |
|---|---|---|---|
| 5,6-Dihydrouracil | 5-Methylcytosine | 5-Hydroxymethylcytosine | |
| Nucleoside |  |  |  |
| Dihydrouridine | 5-Methylcytidine | Pseudouridine | |
| Short symbol | D, hU[14]: N3.2.1, N4.1 | m5C | Ψ |
A list of modified bases and their symbols can be found in the manynucleic acid modification databases and as part oftRNAdb.[15]
A vast number of nucleobase analogues exist.The most common applications are used as fluorescent probes, either directly or indirectly, such asaminoallyl nucleotide, which are used to label cRNA or cDNA inmicroarrays. Several groups are working on alternative "extra" base pairs to extend the genetic code, such asisoguanine andisocytosine or the fluorescent2-amino-6-(2-thienyl)purine andpyrrole-2-carbaldehyde.[16][17]
In medicine, severalnucleoside analogues are used as anticancer and antiviral agents. The viral polymerase incorporates these compounds with non-canonical bases. These compounds are activated in the cells by being converted into nucleotides; they are administered asnucleosides as charged nucleotides cannot easily cross cell membranes.[citation needed] At least one set of new base pairs has been announced as of May 2014.[18]
In order to understandhow life arose, knowledge is required of chemical pathways that permit formation of the key building blocks oflife under plausibleprebiotic conditions. According to theRNA world hypothesis, free-floatingribonucleotides were present in theprimordial soup. These were the fundamental molecules that combined in series to formRNA. Molecules as complex as RNA must have arisen from small molecules whose reactivity was governed by physico-chemical processes. RNA is composed ofpurine andpyrimidine nucleotides, both of which are necessary for reliable information transfer, and thusDarwinianevolution. Nam et al.[19] demonstrated the direct condensation of nucleobases with ribose to give ribonucleosides in aqueous microdroplets, a key step leading to RNA formation. Similar results were obtained by Becker et al.[20]
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