Isocytosine

Isocytosine
Names
	Preferred IUPAC name 2-Amino-3H-pyrimidin-4-one
	Other names 2-Aminouracil
Identifiers
CAS Number	108-53-2 ;
3D model (JSmol)	Interactive image;
ChEBI	CHEBI:55502 ;
ChEMBL	ChEMBL56260 ;
ChemSpider	60309 ;
ECHA InfoCard	100.003.266
PubChem CID	66950;
CompTox Dashboard (EPA)	DTXSID00148350 ;
	InChI InChI=1S/C4H5N3O/c5-4-6-2-1-3(8)7-4/h1-2H,(H3,5,6,7,8) Key: XQCZBXHVTFVIFE-UHFFFAOYSA-N ; InChI=1/C4H5N3O/c5-4-6-2-1-3(8)7-4/h1-2H,(H3,5,6,7,8) Key: XQCZBXHVTFVIFE-UHFFFAOYAD;
	SMILES O=C1/C=C\N=C(\N)N1;
Properties
Chemical formula	C4H5N3O
Molar mass	111.104 g·mol−1
	Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa). verify (what is ?) Infobox references

Isocytosine or 2-aminouracil is a pyrimidine base that is an isomer of cytosine. The nucleoside form is called isocytidine (iC).^[1]

It is used in combination with isoguanine in studies of unnatural nucleic acid analogues of the normal base pairs in DNA.^[2] In particular, it is used as a nucleobase of hachimoji RNA with the abbreviation rS.^[3]

Synthesis

It can be synthesized from guanidine and malic acid.^[4]

Isocytosine can also be obtained by condensing guanidine hydrochloride with 3-oxopropanoic acid. However, the C₃ component is not storable in this case and was, therefore, replaced with malic acid. This is decarbonylated in concentrated sulfuric acid with elimination of water, thus losing carbon monoxide. The 3-oxopropanoic acid formed in situ condenses with the guanidine in the sulfuric acid solution with double elimination of water.^[5]

Uses

It is also used in physical chemical studies involving metal complex binding, hydrogen bonding, and tautomerism and proton transfer effects in nucleobases.^[6]

References

^ Hopfinger, MC; Kirkpatrick, CC; Znosko, BM (18 September 2020). "Predictions and analyses of RNA nearest neighbor parameters for modified nucleotides". Nucleic Acids Research. 48 (16): 8901–8913. doi:10.1093/nar/gkaa654. PMC 7498315. PMID 32810273.
^ "Isocytosine". Molecule of the Week. American Chemical Society. Retrieved November 1, 2012.
^ Hoshika, Shuichi; et al. (22 February 2019). "Hachimoji DNA and RNA: A genetic system with eight building blocks". Science. 363 (6429): 884–887. doi:10.1126/science.aat0971. PMC 6413494. PMID 30792304.
^ William T. Caldwell , Harry B. Kime (1940). "A New Synthesis of Isocytosine". J. Am. Chem. Soc. 62 (9): 2365–2365. doi:10.1021/ja01866a028.
^ Caldwell, William T.; Kime, Harry B. (1 September 1940). "A New Synthesis of Isocytosine". Journal of the American Chemical Society. 62 (9): 2365–2365. doi:10.1021/ja01866a028. ISSN 0002-7863. Retrieved 17 June 2025.
^ "Isocytosine". Sigma-Aldrich. Retrieved November 1, 2012.

[1] Hopfinger, MC; Kirkpatrick, CC; Znosko, BM (18 September 2020). "Predictions and analyses of RNA nearest neighbor parameters for modified nucleotides". Nucleic Acids Research. 48 (16): 8901–8913. doi:10.1093/nar/gkaa654. PMC 7498315. PMID 32810273.

[2] "Isocytosine". Molecule of the Week. American Chemical Society. Retrieved November 1, 2012.

[SCI-20190222-3] Hoshika, Shuichi; et al. (22 February 2019). "Hachimoji DNA and RNA: A genetic system with eight building blocks". Science. 363 (6429): 884–887. doi:10.1126/science.aat0971. PMC 6413494. PMID 30792304.

[4] William T. Caldwell , Harry B. Kime (1940). "A New Synthesis of Isocytosine". J. Am. Chem. Soc. 62 (9): 2365–2365. doi:10.1021/ja01866a028.

[5] Caldwell, William T.; Kime, Harry B. (1 September 1940). "A New Synthesis of Isocytosine". Journal of the American Chemical Society. 62 (9): 2365–2365. doi:10.1021/ja01866a028. ISSN 0002-7863. Retrieved 17 June 2025.

[6] "Isocytosine". Sigma-Aldrich. Retrieved November 1, 2012.

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