Editing Uracil (section)

==Properties==
In RNA, uracil [[base pair|base-pairs]] with adenine and replaces thymine during DNA transcription. [[Methylation]] of uracil produces thymine.<ref name="madsci1">{{cite web|url=http://www.madsci.org|title=MadSciNet: The 24-hour exploding laboratory|website=www.madsci.org|url-status=live|archive-url=https://web.archive.org/web/20050718075407/http://www.madsci.org/|archive-date=18 July 2005}}</ref> 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. In RNA, uracil binds with a [[ribose]] sugar to form the [[ribonucleoside]] [[uridine]]. When a [[phosphate]] attaches to uridine, uridine 5′-monophosphate is produced.<ref name="Horton1">{{cite book|title=Principles of Biochemistry|vauthors=Horton HR, Moran LA, Ochs RS, Rawn DJ, Scrimgeour KG|publisher=Prentice Hall|year=2002|isbn=9780130266729|edition=3rd|location=Upper Saddle River, NJ}}</ref>

Uracil undergoes amide-imidic acid tautomeric shifts because any nuclear instability the molecule may have from the lack of formal [[aromaticity]] is compensated by the cyclic-amidic stability.<ref name="brown1"/> The amide [[tautomer]] is referred to as the [[lactam]] structure, while the imidic acid tautomer is referred to as the [[lactim]] structure. These tautomeric forms are predominant at [[pH]]&nbsp;7. The lactam structure is the most common form of uracil.

:[[Image:Uracil tautomers.png|left|thumb|Uracil [[tautomers]]: [[Amide]] or [[lactam]] structure (left) and [[imide]] or [[lactim]] structure (right)]]{{clear left}}

Uracil also recycles itself to form nucleotides by undergoing a series of phosphoribosyltransferase reactions.<ref name="Garrett1"/> Degradation of uracil produces the substrates [[β-alanine]], [[carbon dioxide]], and [[ammonia]].<ref name = "Garrett1"/>

:{{chem2|C4H4N2O2}}→ {{chem2|H3NCH2CH2COO-}} + {{chem2|NH4+}} + {{chem2|CO2}}

Oxidative degradation of uracil produces urea and maleic acid in the presence of [[hydrogen peroxide|H<sub>2</sub>O<sub>2</sub>]] and [[Iron|Fe]]<sup>2+</sup> or in the presence of diatomic [[oxygen]] and Fe<sup>2+</sup>.

Uracil is a [[weak acid]]. The first site of [[ionization]] of uracil is not known.<ref name="Zorbach1">{{cite book|title=Synthetic Procedures in Nucleic Acid Chemistry: Physical and physicochemical aids in determination of structure|vauthors=Zorbach WW, Tipson RS|publisher=Wiley-Interscience|year=1973|isbn=9780471984184|volume=2|location=New York, NY}}</ref> The negative charge is placed on the oxygen anion and produces a [[Acid dissociation constant|p''K''<sub>a</sub>]] of less than or equal to 12. The basic p''K''<sub>a</sub>&nbsp;=&nbsp;−3.4, while the acidic p''K''<sub>a</sub>&nbsp;=&nbsp;9.38<sub>9</sub>. In the gas phase, uracil has four sites that are more acidic than water.<ref name="Lee1">{{cite journal | vauthors = Kurinovich MA, Lee JK | title = The acidity of uracil and uracil analogs in the gas phase: four surprisingly acidic sites and biological implications | journal = Journal of the American Society for Mass Spectrometry | volume = 13 | issue = 8 | pages = 985–995 | date = August 2002 | pmid = 12216739 | doi = 10.1016/S1044-0305(02)00410-5 | doi-access = free | bibcode = 2002JASMS..13..985K }}</ref>

===In DNA===
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) 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.<ref>{{Cite journal|vauthors=Békési A, Vértessy BG|date=2011|title=Uracil in DNA: error or signal?|url=https://www.scienceinschool.org/2011/issue18/uracil|journal=Science in School|pages=18|archive-url=https://web.archive.org/web/20160323021752/http://www.scienceinschool.org/2011/issue18/uracil|archive-date=23 March 2016}}</ref>

This problem is believed to have been solved in terms of evolution, that is by "tagging" (methylating) uracil. Methylated uracil is identical to thymine. Hence the hypothesis that, over time, thymine became standard in DNA instead of 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: 
* DNA of several [[phage]]s<ref>{{cite journal | vauthors = Wang Z, Mosbaugh DW | title = Uracil-DNA glycosylase inhibitor of bacteriophage PBS2: cloning and effects of expression of the inhibitor gene in Escherichia coli | journal = Journal of Bacteriology | volume = 170 | issue = 3 | pages = 1082–1091 | date = March 1988 | pmid = 2963806 | pmc = 210877 | doi = 10.1128/JB.170.3.1082-1091.1988 }}</ref>
* [[Endopterygote]] development
* Hypermutations during the synthesis of vertebrate antibodies.{{citation needed|date=December 2018}}