WARNING: This product is for research use only, not for human or veterinary use.

MedKoo CAT#: 530639

CAS#: 4425-59-6

Description: 5-Formylcytosine, also known as 5fC, is a rare base found in mammalian DNA and thought to be involved in active DNA demethylation. 5-Formylcytosine can be a stable DNA modification in mammals. 5-Formylcytosine alters the structure of the DNA double helix. 5-formylcytosine and 5-carboxylcytosine reduce the rate and substrate specificity of RNA polymerase II transcription.

Price and Availability




5-Formylcytosine is not in stock, may be available through custom synthesis. For cost-effective reason, minimum 1 gram order is requested. The product will be characterized by NMR, HPLC and MS analysis. Purity (HPLC) is usually >98%. CoA, QC data, MSDS will be provided when product is successfully made. The estimated lead time is 2-3 months. Please send email to sales@medkoo.com to inquire quote.

Chemical Structure


Theoretical Analysis

MedKoo Cat#: 530639
Name: 5-Formylcytosine
CAS#: 4425-59-6
Chemical Formula: C5H5N3O2
Exact Mass: 139.0382
Molecular Weight: 139.114
Elemental Analysis: C, 43.17; H, 3.62; N, 30.21; O, 23.00

Synonym: 5-Formylcytosine

IUPAC/Chemical Name: 6-Amino-2-oxo-1H-pyrimidine-5-carbaldehyde


InChi Code: InChI=1S/C5H5N3O2/c6-4-3(2-9)1-7-5(10)8-4/h1-2H,(H3,6,7,8,10)


Technical Data

Solid powder

>98% (or refer to the Certificate of Analysis)

Shipping Condition:
Shipped under ambient temperature as non-hazardous chemical. This product is stable enough for a few weeks during ordinary shipping and time spent in Customs.

Storage Condition:
Dry, dark and at 0 - 4 C for short term (days to weeks) or -20 C for long term (months to years).

Soluble in DMSO

Shelf Life:
>2 years if stored properly

Drug Formulation:
This drug may be formulated in DMSO

Stock Solution Storage:
0 - 4 C for short term (days to weeks), or -20 C for long term (months).

Harmonized System Code:


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3: Zhu C, Gao Y, Guo H, Xia B, Song J, Wu X, Zeng H, Kee K, Tang F, Yi C. Single-Cell 5-Formylcytosine Landscapes of Mammalian Early Embryos and ESCs at Single-Base Resolution. Cell Stem Cell. 2017 May 4;20(5):720-731.e5. doi: 10.1016/j.stem.2017.02.013. Epub 2017 Mar 23. PubMed PMID: 28343982.

4: Van Haute L, Powell CA, Minczuk M. Dealing with an Unconventional Genetic Code in Mitochondria: The Biogenesis and Pathogenic Defects of the 5-Formylcytosine Modification in Mitochondrial tRNA(Met). Biomolecules. 2017 Mar 2;7(1). pii: E24. doi: 10.3390/biom7010024. Review. PubMed PMID: 28257121; PubMed Central PMCID: PMC5372736.

5: Xia B, Han D, Lu X, Sun Z, Zhou A, Yin Q, Zeng H, Liu M, Jiang X, Xie W, He C, Yi C. Bisulfite-free, base-resolution analysis of 5-formylcytosine at the genome scale. Nat Methods. 2015 Nov;12(11):1047-50. doi: 10.1038/nmeth.3569. Epub 2015 Sep 7. PubMed PMID: 26344045; PubMed Central PMCID: PMC4626315.

6: Dai Q, Sanstead PJ, Peng CS, Han D, He C, Tokmakoff A. Weakened N3 Hydrogen Bonding by 5-Formylcytosine and 5-Carboxylcytosine Reduces Their Base-Pairing Stability. ACS Chem Biol. 2016 Feb 19;11(2):470-7. doi: 10.1021/acschembio.5b00762. Epub 2015 Dec 17. PubMed PMID: 26641274; PubMed Central PMCID: PMC4782585.

7: Bachman M, Uribe-Lewis S, Yang X, Burgess HE, Iurlaro M, Reik W, Murrell A, Balasubramanian S. 5-Formylcytosine can be a stable DNA modification in mammals. Nat Chem Biol. 2015 Aug;11(8):555-7. doi: 10.1038/nchembio.1848. Epub 2015 Jun 22. PubMed PMID: 26098680.

8: Zhang HY, Xiong J, Qi BL, Feng YQ, Yuan BF. The existence of 5-hydroxymethylcytosine and 5-formylcytosine in both DNA and RNA in mammals. Chem Commun (Camb). 2016 Jan 14;52(4):737-40. doi: 10.1039/c5cc07354e. PubMed PMID: 26562407.

9: Gackowski D, Zarakowska E, Starczak M, Modrzejewska M, Olinski R. Tissue-Specific Differences in DNA Modifications (5-Hydroxymethylcytosine, 5-Formylcytosine, 5-Carboxylcytosine and 5-Hydroxymethyluracil) and Their Interrelationships. PLoS One. 2015 Dec 14;10(12):e0144859. doi: 10.1371/journal.pone.0144859. eCollection 2015. PubMed PMID: 26660343; PubMed Central PMCID: PMC4682766.

10: Xu L, Chen YC, Chong J, Fin A, McCoy LS, Xu J, Zhang C, Wang D. Pyrene-based quantitative detection of the 5-formylcytosine loci symmetry in the CpG duplex content during TET-dependent demethylation. Angew Chem Int Ed Engl. 2014 Oct 13;53(42):11223-7. doi: 10.1002/anie.201406220. Epub 2014 Aug 27. PubMed PMID: 25159856; PubMed Central PMCID: PMC4227401.

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12: Raiber EA, Murat P, Chirgadze DY, Beraldi D, Luisi BF, Balasubramanian S. 5-Formylcytosine alters the structure of the DNA double helix. Nat Struct Mol Biol. 2015 Jan;22(1):44-9. doi: 10.1038/nsmb.2936. Epub 2014 Dec 15. PubMed PMID: 25504322; PubMed Central PMCID: PMC4287393.

13: Zhang L, Chen W, Iyer LM, Hu J, Wang G, Fu Y, Yu M, Dai Q, Aravind L, He C. A TET homologue protein from Coprinopsis cinerea (CcTET) that biochemically converts 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine. J Am Chem Soc. 2014 Apr 2;136(13):4801-4. doi: 10.1021/ja500979k. Epub 2014 Mar 25. PubMed PMID: 24655109; PubMed Central PMCID: PMC3985729.

14: Jin L, Wang W, Hu D, Lü J. A new insight into the 5-carboxycytosine and 5-formylcytosine under typical bisulfite conditions: a deamination mechanism study. Phys Chem Chem Phys. 2014 Feb 28;16(8):3573-85. doi: 10.1039/c3cp54266a. PubMed PMID: 24413472.

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17: Maiti A, Michelson AZ, Armwood CJ, Lee JK, Drohat AC. Divergent mechanisms for enzymatic excision of 5-formylcytosine and 5-carboxylcytosine from DNA. J Am Chem Soc. 2013 Oct 23;135(42):15813-22. doi: 10.1021/ja406444x. Epub 2013 Oct 7. PubMed PMID: 24063363; PubMed Central PMCID: PMC3930231.

18: Mao W, Hu J, Hong T, Xing X, Wang S, Chen X, Zhou X. A convenient method for selective detection of 5-hydroxymethylcytosine and 5-formylcytosine sites in DNA sequences. Org Biomol Chem. 2013 Jun 7;11(21):3568-72. doi: 10.1039/c3ob40447a. Epub 2013 Apr 30. PubMed PMID: 23629475.

19: Song CX, Szulwach KE, Dai Q, Fu Y, Mao SQ, Lin L, Street C, Li Y, Poidevin M, Wu H, Gao J, Liu P, Li L, Xu GL, Jin P, He C. Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming. Cell. 2013 Apr 25;153(3):678-91. doi: 10.1016/j.cell.2013.04.001. Epub 2013 Apr 18. PubMed PMID: 23602153; PubMed Central PMCID: PMC3657391.

20: Hu J, Xing X, Xu X, Wu F, Guo P, Yan S, Xu Z, Xu J, Weng X, Zhou X. Selective chemical labelling of 5-formylcytosine in DNA by fluorescent dyes. Chemistry. 2013 May 3;19(19):5836-40. doi: 10.1002/chem.201300082. Epub 2013 Mar 19. PubMed PMID: 23512548.