5-Carboxylcytosine

5-Carboxylcytosine
Names
	IUPAC name 4-Amino-2-oxo-1,2-dihydropyrimidine-5-carboxylic acid
	Other names Cytosine-5-carboxylic acid; 5caC;
Identifiers
CAS Number	3650-93-9;
3D model (JSmol)	Interactive image;
ChEBI	CHEBI:76793;
ChemSpider	69639;
ECHA InfoCard	100.020.810
EC Number	222-890-1;
KEGG	C20769;
PubChem CID	77213;
UNII	760CU98B9K;
CompTox Dashboard (EPA)	DTXSID70190003 ;
	InChI InChI=1S/C5H5N3O3/c6-3-2(4(9)10)1-7-5(11)8-3/h1H,(H,9,10)(H3,6,7,8,11) Key: BLQMCTXZEMGOJM-UHFFFAOYSA-N;
	SMILES C1=NC(=O)NC(=C1C(=O)O)N;
Properties
Chemical formula	C5H5N3O3
Molar mass	155.113 g·mol−1
Hazards
	Occupational safety and health (OHS/OSH):
Main hazards	Irritant
	Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa). Infobox references

5-Carboxylcytosine (5caC) is a modified nucleobase, derived from cytosine, that plays a significant role as an intermediate in the process of active DNA demethylation. It is generated through the oxidation of 5-methylcytosine (5mC) via 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC), catalyzed by the TET family of dioxygenases.^[1] 5caC represents the final oxidative state in this pathway before the base is typically removed and replaced with an unmodified cytosine by Terminal deoxynucleotidyl transferase (TdT) or Thymine DNA glycosylase (TDG) by base excision repair.^[2]

Discovery

5-Carboxylcytosine, along with 5-formylcytosine (5fC), was identified as an oxidation product generated by the TET enzymes acting on 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Studies published around 2011 demonstrated that TET enzymes could iteratively oxidize 5mC, leading first to 5hmC, then 5fC, and finally 5caC.^[1]^[3] Researchers subsequently confirmed the presence of both 5fC and 5caC, albeit at very low levels, in the genomic DNA of mouse embryonic stem cells and various mouse organs, establishing them as endogenous DNA modifications.^[4]

Structure and properties

5-Carboxylcytosine is structurally identical to cytosine except for the presence of a carboxyl group (–COOH) attached to the C5 position of the pyrimidine ring. The carboxyl group is electron-withdrawing and distinguishes it significantly from cytosine, 5mC, and 5hmC in terms of chemical properties (weakened hydrogen bonding) and biological recognition (reduced base pair stability).^[5] At physiological pH, the carboxyl group (with a pK_a around 2.1) is typically ionized (–COO⁻), while the N3 position has a pK_a around 4.2.^[5]

Significance

The primary significance of 5caC lies in its role as a key intermediate in active DNA demethylation. By facilitating the removal of methylation marks through the TET-TDG-BER pathway, 5caC contributes to the dynamic regulation of DNA methylation patterns, which is crucial for epigenetic regulation. However, recent studies suggest that 5caC may have its own functional significance such as increased pausing, backtracking, and reduced fidelity of RNAPII.^[6]^[7]

References

^ ^a ^b Ito, Shinsuke; Shen, Li; Dai, Qing; Wu, Susan C.; Collins, Leonard B.; Swenberg, James A.; He, Chuan; Zhang, Yi (2011-09-02). "Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine". Science. 333 (6047): 1300–1303. Bibcode:2011Sci...333.1300I. doi:10.1126/science.1210597. ISSN 1095-9203. PMC 3495246. PMID 21778364.
^ Zhang, Liang; Lu, Xingyu; Lu, Junyan; Liang, Haihua; Dai, Qing; Xu, Guo-Liang; Luo, Cheng; Jiang, Hualiang; He, Chuan (2012-02-12). "Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA". Nature Chemical Biology. 8 (4): 328–330. doi:10.1038/nchembio.914. ISSN 1552-4469. PMC 3307914. PMID 22327402.
^ He, Yu-Fei; Li, Bin-Zhong; Li, Zheng; Liu, Peng; Wang, Yang; Tang, Qingyu; Ding, Jianping; Jia, Yingying; Chen, Zhangcheng; Li, Lin; Sun, Yan; Li, Xiuxue; Dai, Qing; Song, Chun-Xiao; Zhang, Kangling (2011-09-02). "Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA". Science. 333 (6047): 1303–1307. Bibcode:2011Sci...333.1303H. doi:10.1126/science.1210944. PMC 3462231. PMID 21817016.
^ Inoue, Azusa; Shen, Li; Dai, Qing; He, Chuan; Zhang, Yi (December 2011). "Generation and replication-dependent dilution of 5fC and 5caC during mouse preimplantation development". Cell Research. 21 (12): 1670–1676. doi:10.1038/cr.2011.189. ISSN 1748-7838. PMC 3357997. PMID 22124233.
^ ^a ^b Dai, Qing; Sanstead, Paul J.; Peng, Chunte Sam; Han, Dali; He, Chuan; Tokmakoff, Andrei (2016-02-19). "Weakened N3 Hydrogen Bonding by 5-Formylcytosine and 5-Carboxylcytosine Reduces Their Base-Pairing Stability". ACS Chemical Biology. 11 (2): 470–477. doi:10.1021/acschembio.5b00762. ISSN 1554-8937. PMC 4782585. PMID 26641274.
^ Kellinger, Matthew W.; Song, Chun-Xiao; Chong, Jenny; Lu, Xing-Yu; He, Chuan; Wang, Dong (August 2012). "5-formylcytosine and 5-carboxylcytosine reduce the rate and substrate specificity of RNA polymerase II transcription". Nature Structural & Molecular Biology. 19 (8): 831–833. doi:10.1038/nsmb.2346. ISSN 1545-9985. PMC 3414690. PMID 22820989.
^ "5-carboxylcytosine (5caC)". EpiGenie | Epigenetics, Stem Cell, and Synthetic Biology News. Retrieved 2025-04-24.

[:0-1] Ito, Shinsuke; Shen, Li; Dai, Qing; Wu, Susan C.; Collins, Leonard B.; Swenberg, James A.; He, Chuan; Zhang, Yi (2011-09-02). "Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine". Science. 333 (6047): 1300–1303. Bibcode:2011Sci...333.1300I. doi:10.1126/science.1210597. ISSN 1095-9203. PMC 3495246. PMID 21778364.

[2] Zhang, Liang; Lu, Xingyu; Lu, Junyan; Liang, Haihua; Dai, Qing; Xu, Guo-Liang; Luo, Cheng; Jiang, Hualiang; He, Chuan (2012-02-12). "Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA". Nature Chemical Biology. 8 (4): 328–330. doi:10.1038/nchembio.914. ISSN 1552-4469. PMC 3307914. PMID 22327402.

[3] He, Yu-Fei; Li, Bin-Zhong; Li, Zheng; Liu, Peng; Wang, Yang; Tang, Qingyu; Ding, Jianping; Jia, Yingying; Chen, Zhangcheng; Li, Lin; Sun, Yan; Li, Xiuxue; Dai, Qing; Song, Chun-Xiao; Zhang, Kangling (2011-09-02). "Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA". Science. 333 (6047): 1303–1307. Bibcode:2011Sci...333.1303H. doi:10.1126/science.1210944. PMC 3462231. PMID 21817016.

[4] Inoue, Azusa; Shen, Li; Dai, Qing; He, Chuan; Zhang, Yi (December 2011). "Generation and replication-dependent dilution of 5fC and 5caC during mouse preimplantation development". Cell Research. 21 (12): 1670–1676. doi:10.1038/cr.2011.189. ISSN 1748-7838. PMC 3357997. PMID 22124233.

[:1-5] Dai, Qing; Sanstead, Paul J.; Peng, Chunte Sam; Han, Dali; He, Chuan; Tokmakoff, Andrei (2016-02-19). "Weakened N3 Hydrogen Bonding by 5-Formylcytosine and 5-Carboxylcytosine Reduces Their Base-Pairing Stability". ACS Chemical Biology. 11 (2): 470–477. doi:10.1021/acschembio.5b00762. ISSN 1554-8937. PMC 4782585. PMID 26641274.

[6] Kellinger, Matthew W.; Song, Chun-Xiao; Chong, Jenny; Lu, Xing-Yu; He, Chuan; Wang, Dong (August 2012). "5-formylcytosine and 5-carboxylcytosine reduce the rate and substrate specificity of RNA polymerase II transcription". Nature Structural & Molecular Biology. 19 (8): 831–833. doi:10.1038/nsmb.2346. ISSN 1545-9985. PMC 3414690. PMID 22820989.

[7] "5-carboxylcytosine (5caC)". EpiGenie | Epigenetics, Stem Cell, and Synthetic Biology News. Retrieved 2025-04-24.

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[2]

[3]

[4]

[5]

[6]

[7]

Discovery

Structure and properties

Significance

See also

References