Editing Nucleotide base

{{Short description|Nitrogen-containing biological compounds that form nucleosides}}
{{Redirect|ACGT|the Japanese animation production company|A.C.G.T}}
{{Use dmy dates|date=June 2021}}
[[File:AGCT RNA mini.png|thumb|350px|Base pairing: two [[base pair]]s are produced by four nucleotide monomers, nucleobases are in blue. Guanine (G) is paired with cytosine (C) via three [[hydrogen bond]]s, in red. Adenine (A) is paired with uracil (U) via two hydrogen bonds, in red.]]
[[File:Blausen 0323 DNA Purines.png|thumb|230px|Purine nucleobases are fused-ring molecules.]]
[[File:Blausen 0324 DNA Pyrimidines.png|thumb|230px|Pyrimidine nucleobases are simple ring molecules.]]

'''Nucleotide bases'''<ref>{{Cite journal|url=https://doi.org/10.1351/goldbook.N04254|title=IUPAC - nucleotide bases (N04254)|last=The International Union of Pure and Applied Chemistry (IUPAC)|website=goldbook.iupac.org|doi=10.1351/goldbook.N04254 |doi-access=free}}</ref> (also '''nucleobases''', '''nitrogenous bases''') are [[nitrogen]]-containing biological compounds that form [[nucleosides]], which, in turn, are components of [[nucleotide]]s, with all of these [[monomer]]s constituting the basic building blocks of [[nucleic acids]]. The ability of nucleobases to form [[base pair]]s and to stack one upon another leads directly to long-chain helical structures such as [[ribonucleic acid]] (RNA) and [[deoxyribonucleic acid]] (DNA). Five nucleobases—[[adenine]] (A), [[cytosine]] (C), [[guanine]] (G), [[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 distinguished by merely the presence or absence of a methyl group on the fifth carbon (C5) of these heterocyclic six-membered rings.<ref>{{cite book|last=Soukup|first=Garrett A.|title=eLS|date=2003|chapter=Nucleic Acids: General Properties|publisher=American Cancer Society|language=en|doi=10.1038/npg.els.0001335|isbn=9780470015902}}</ref>{{page needed|date=January 2021}}
In addition, some viruses have [[2,6-diaminopurine|aminoadenine]] (Z) instead of adenine. It differs in having an extra [[amine]] group, creating a more stable bond to thymine.<ref>{{Cite web|url=https://www.sciencenews.org/article/virus-dna-z-bacteriophage-genetic-alphabet-bond-life|title=Some viruses thwart bacterial defenses with a unique genetic alphabet|date=5 May 2021}}</ref>

Adenine and guanine have a [[ring (chemistry)|fused-ring]] skeletal structure derived of [[purine]], hence they are called '''purine bases'''.<ref>{{Cite journal|url=https://goldbook.iupac.org/terms/view/P04953|title=IUPAC - purine bases (P04953)|last=The International Union of Pure and Applied Chemistry (IUPAC)|website=goldbook.iupac.org|doi=10.1351/goldbook.p04953|doi-access=free}}</ref> The purine nitrogenous bases are characterized by their single [[amino group]] ({{chem2|\sNH2}}), at the C6 carbon in adenine and C2 in guanine.<ref name="NIH.gov">{{cite journal | vauthors = Berg JM, Tymoczko JL, Stryer L | title = Section 25.2, Purine Bases Can Be Synthesized de Novo or Recycled by Salvage Pathways. | journal = Biochemistry. 5th Edition | url = https://www.ncbi.nlm.nih.gov/books/NBK22385/| access-date = 2019-12-11 }}</ref> Similarly, the simple-ring structure of cytosine, uracil, and thymine is derived of [[pyrimidine]], so those three bases are called the '''pyrimidine bases'''.<ref>{{Cite journal|url=https://goldbook.iupac.org/terms/view/P04958|title=IUPAC - pyrimidine bases (P04958)|last=The International Union of Pure and Applied Chemistry (IUPAC)|website=goldbook.iupac.org|doi=10.1351/goldbook.p04958|doi-access=free}}</ref>

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 [[complementarity (molecular biology)|''base 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 two [[hydrogen bond]]s, while the C–G pairing is based on three. In both cases, the hydrogen bonds are between the [[amine]] and [[carbonyl]] 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.<ref name="Callahan">{{cite journal | vauthors = Callahan MP, Smith KE, Cleaves HJ, Ruzicka J, Stern JC, Glavin DP, House CH, Dworkin JP | title = Carbonaceous meteorites contain a wide range of extraterrestrial nucleobases | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 108 | issue = 34 | pages = 13995–8 | date = August 2011 | pmid = 21836052 | pmc = 3161613 | doi = 10.1073/pnas.1106493108 | publisher = [[PNAS]] | bibcode = 2011PNAS..10813995C | doi-access = free }}</ref><ref name="Steigerwald">{{cite web |last=Steigerwald |first=John |title=NASA Researchers: DNA Building Blocks Can Be Made in Space |url=http://www.nasa.gov/topics/solarsystem/features/dna-meteorites.html |publisher=[[NASA]] |date=8 August 2011 |access-date=2011-08-10 }}</ref><ref name="DNA">{{cite web |author=ScienceDaily Staff |title=DNA Building Blocks Can Be Made in Space, NASA Evidence Suggests |url=https://www.sciencedaily.com/releases/2011/08/110808220659.htm |date=9 August 2011 |website=[[ScienceDaily]] |access-date=2011-08-09}}</ref>

The origin of the term ''[[Base (chemistry)|base]]'' reflects these compounds' chemical properties in [[acid–base reaction]]s, but those properties are not especially important for understanding most of the biological functions of nucleobases.

==Structure==
[[File:DNA chemical structure.svg|thumb|350px|Chemical structure of DNA, showing four nucleobase pairs produced by eight nucleotides: adenine (A) is joined to thymine (T), and guanine (G) is joined to cytosine (C). +&nbsp;This structure also shows the [[directionality (molecular biology)|directionality]] of each of the two phosphate-deoxyribose backbones, or strands. The 5' to 3' (''read'' "5 prime to 3 prime") directions are: ''down'' the strand on the left, and ''up'' the strand on the right. The strands twist around each other to form a double helix structure.]]

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 permits base pairing by providing [[complementarity (molecular biology)|complementarity]] between the two bases, and which is essential for [[DNA replication|replication]] of or [[transcription (genetics)|transcription]] of the encoded information found in DNA.{{cn|date=May 2024}}

==Modified nucleobases==
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 is [[5-methylcytosine]] (m<sup>5</sup>C). In RNA, there are many modified bases, including those contained in the nucleosides [[pseudouridine]] (Ψ), [[dihydrouridine]] (D), [[inosine]] (I), and [[7-methylguanosine]] (m<sup>7</sup>G).<ref>{{cite web |last1=Stavely |first1=Brian E. |title=BIOL2060: Translation |url=https://www.mun.ca/biology/desmid/brian/BIOL2060/BIOL2060-22/CB22.html |website=www.mun.ca |access-date=17 August 2020}}</ref><ref>[http://www.biogeo.uw.edu.pl/research/grupaC_en.html "Role of 5' mRNA and 5' U snRNA cap structures in regulation of gene expression"] – Research – Retrieved 13 December 2010.</ref>

[[Hypoxanthine]] and [[xanthine]] are two of 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,<ref name="pmid1557408">{{cite journal | vauthors = Nguyen T, Brunson D, Crespi CL, Penman BW, Wishnok JS, Tannenbaum SR | title = DNA damage and mutation in human cells exposed to nitric oxide in vitro | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 89 | issue = 7 | pages = 3030–4 | date = April 1992 | pmid = 1557408 | pmc = 48797 | doi = 10.1073/pnas.89.7.3030 | bibcode = 1992PNAS...89.3030N | doi-access = free }}</ref> and uracil results from deamination of cytosine.

===Modified purine nucleobases===
These are examples of modified adenosine or guanosine.
{| class="wikitable skin-invert-image"
|- align="center" valign="bottom"
| '''Nucleobase'''|| [[File:Hypoxanthin.svg|70px|Chemical structure of hypoxanthine]]<br />[[Hypoxanthine]]|| [[File:Xanthin.svg|75px|Chemical structure of xanthine]]<br />[[Xanthine]]|| [[File:7methylguanine.svg|93px|Chemical structure of 7-methylguanine]]<br />[[7-Methylguanine]]
|- align="center" valign="bottom"
| '''Nucleoside'''|| [[File:Inosin.svg|95px|Chemical structure of inosine]]<br />[[Inosine]]<br />I || [[File:Xanthosin.svg|105px|Chemical structure of xanthosine]]<br />[[Xanthosine]]<br />X || [[File:7-Methylguanosine.svg|140px|Chemical structure of 7-methylguanosine]]<br />[[7-Methylguanosine]]<br />m<sup>7</sup>G
|}

===Modified pyrimidine nucleobases===
These are examples of modified cytidine, thymidine or uridine.
{| class="wikitable skin-invert-image"
|- align="center" valign="bottom"
| '''Nucleobase'''|| [[File:Dihydrouracil.svg|55px|Chemical structure of dihydrouracil]]<br />[[5,6-Dihydrouracil]]|| [[File:5-Methylcytosine.svg|75px|Chemical structure of 5-methylcytosine]]<br />[[5-Methylcytosine]]|| [[File:Hydroxymethylcytosine.png|60px|Chemical structure of 5-hydroxymethylcytosine]]<br />[[5-Hydroxymethylcytosine]]
|- align="center" valign="bottom"
| '''Nucleoside'''|| [[File:Dihydrouridine.svg|87px|Chemical structure of dihydrouridine]]<br />[[Dihydrouridine]]<br />D || [[File:5-Methylcytidine.svg|87px|Chemical structure of 5-methylcytidine]]<br />[[5-Methylcytidine]]<br />m<sup>5</sup>C ||[[File:Pseudouridine.svg|87px]]<br />[[Pseudouridine]]
|}

==Artificial nucleobases==
{{Main|Nucleic acid analogue}}
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 cDNA in [[microarrays]]. Several groups are working on alternative "extra" base pairs to extend the genetic code, such as [[isoguanine]] and [[isocytosine]] or the fluorescent [[2-amino-6-(2-thienyl)purine]] and [[pyrrole-2-carbaldehyde]].<ref name="pmid15051811">{{cite journal|vauthors=Johnson SC, Sherrill CB, Marshall DJ, Moser MJ, Prudent JR|date=2004|title=A third base pair for the polymerase chain reaction: inserting isoC and isoG|journal=Nucleic Acids Research|volume=32|issue=6|pages=1937–41|doi=10.1093/nar/gkh522|pmc=390373|pmid=15051811}}</ref><ref>{{cite journal|vauthors=Kimoto M, Mitsui T, Harada Y, Sato A, Yokoyama S, Hirao I|year=2007|title=Fluorescent probing for RNA molecules by an unnatural base-pair system|journal=Nucleic Acids Research|volume=35|issue=16|pages=5360–69|doi=10.1093/nar/gkm508|pmc=2018647|pmid=17693436}}</ref>

In medicine, several [[nucleoside analogue]]s 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 as [[nucleoside]]s as charged nucleotides cannot easily cross cell membranes.{{Citation needed|date=April 2012}} At least one set of new base pairs has been announced as of May 2014.<ref>{{cite journal | vauthors = Malyshev DA, Dhami K, Lavergne T, Chen T, Dai N, Foster JM, Corrêa IR, Romesberg FE | title = A semi-synthetic organism with an expanded genetic alphabet | journal = Nature | volume = 509 | issue = 7500 | pages = 385–8 | date = May 2014 | pmid = 24805238 | pmc = 4058825 | doi = 10.1038/nature13314 | bibcode = 2014Natur.509..385M }}</ref>

==Prebiotic condensation of nucleobases with ribose==

In order to understand [[Abiogenesis|how life arose]], knowledge is required of chemical pathways that permit formation of the key building blocks of [[life]] under plausible [[abiogenesis|prebiotic conditions]]. According to the [[RNA world]] hypothesis, free-floating [[ribonucleotide]]s were present in the [[primordial soup]]. These were the fundamental molecules that combined in series to form [[RNA]]. Molecules as complex as RNA must have arisen from small molecules whose reactivity was governed by physico-chemical processes. RNA is composed of [[purine]] and [[pyrimidine]] nucleotides, both of which are necessary for reliable information transfer, and thus [[Darwinism|Darwinian]] [[evolution]]. Nam et al.<ref>{{Cite journal |doi=10.1073/pnas.1718559115 |pmc=5776833 |pmid=29255025 |doi-access=free|title=Abiotic synthesis of purine and pyrimidine ribonucleosides in aqueous microdroplets |year=2018 |last1=Nam |first1=Inho |last2=Nam |first2=Hong Gil |last3=Zare |first3=Richard N. |journal=Proceedings of the National Academy of Sciences |volume=115 |issue=1 |pages=36–40 |bibcode=2018PNAS..115...36N }}</ref> 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.<ref>{{Cite journal |doi=10.1126/science.aax2747 |pmid=31604305|title=Unified prebiotically plausible synthesis of pyrimidine and purine RNA ribonucleotides |year=2019 |last1=Becker |first1=Sidney |last2=Feldmann |first2=Jonas |last3=Wiedemann |first3=Stefan |last4=Okamura |first4=Hidenori |last5=Schneider |first5=Christina |last6=Iwan |first6=Katharina |last7=Crisp |first7=Antony |last8=Rossa |first8=Martin |last9=Amatov |first9=Tynchtyk |last10=Carell |first10=Thomas |journal=Science |volume=366 |issue=6461 |pages=76–82 |bibcode=2019Sci...366...76B |s2cid=203719976 |url=https://epub.ub.uni-muenchen.de/71503/1/Science_Becker_2019.pdf }}</ref>

== See also ==
* {{annotated link|Nucleoside}}
* {{annotated link|Nucleotide}}
* {{annotated link|Nucleic acid notation}}
* {{annotated link|Nucleic acid sequence}}

== References ==
{{Reflist}}

== External links ==
* [https://web.archive.org/web/20060621234655/http://www.elmhurst.edu/~chm/vchembook/582dnadoublehelix.html Base pairing in DNA Double Helix (shows specific hydrogen bonds)]

{{Nucleobases, nucleosides, and nucleotides}}
{{Authority control}}

[[Category:Nucleobases| ]]
[[Category:DNA]]
[[Category:RNA]]