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[Biochemistry](https://durgical.com/en/biochemistry/) · Molecule

# 5-Methylcytosine

5-Methylcytosine is cytosine with an extra methyl group; it is the main epigenetic mark on DNA and usually switches genes off.

Updated 2026-11-01

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## Key facts

- It is found mostly in CpG dinucleotides; CpG islands in active promoters are unmethylated.
- Methylated promoter → silenced gene (binding of MBD proteins and histone deacetylases).
- Its spontaneous deamination gives thymine (not uracil), a C→T change that is hard to spot: CpGs are mutation 'hot spots'.
- TET enzymes oxidise it to 5-hydroxymethylcytosine and open the way to demethylation.

**Also called**
5mC, the 'fifth base' of DNA

**Formula**
C5H7N3O

**PubChem**
[CID 65040](https://pubchem.ncbi.nlm.nih.gov/compound/65040)

## Structure

- Cytosine with a methyl group (–CH₃) on carbon 5 of the pyrimidine ring.
- The methyl sits in the major groove: it does not change pairing with guanine, but it does change which proteins bind.
- In DNA it is made after replication: DNMT transfers the methyl from S-adenosylmethionine.

## Clinical notes

- Promoter hypermethylation (MLH1, BRCA1, MGMT) silences tumour-suppressor genes in cancer.
- The hypomethylating drugs azacitidine and decitabine lower 5-methylcytosine and reactivate genes in myelodysplastic syndromes.
- Methylation of the FMR1 promoter explains gene silencing in fragile X.

## Related conditions

- [Fragile X syndrome](https://durgical.com/en/conditions/fragile-x-syndrome/)

## Related

- [Epigenetics: DNA and histone methylation](https://durgical.com/en/biochemistry/topics/epigenetics-dna-and-histone-methylation/)
- [DNA structure and chromatin](https://durgical.com/en/biochemistry/topics/dna-structure-and-chromatin/)
- [S-adenosylmethionine (SAM)](https://durgical.com/en/biochemistry/molecules/s-adenosylmethionine/)
- [Nucleotide structure](https://durgical.com/en/biochemistry/topics/nucleotide-structure/)

## Test yourself

Think of the answer, then tap the question to see it.

## Which enzyme makes 5-methylcytosine, and what is the methyl donor?

DNA methyltransferases (DNMT), using S-adenosylmethionine.

## Why are CpG dinucleotides mutation hot spots?

5-Methylcytosine deaminates to thymine, a normal DNA base that repair struggles to recognise: a C→T transition remains.

## What does promoter methylation usually do?

It silences the gene, because it attracts proteins that compact chromatin and blocks activator binding.

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Molecules are shown in their neutral form, as the databases deposit them; in the cell the acids and phosphates are ionised.

Educational information, not medical advice. For any symptom, see a health professional.

Sources: [5-Methylcytosine (CID 65040)](https://pubchem.ncbi.nlm.nih.gov/compound/65040) (PubChem, NCBI, 2026) · Public domain; [What is epigenetics?: MedlinePlus Genetics](https://medlineplus.gov/genetics/understanding/howgeneswork/epigenome/) (MedlinePlus, US National Library of Medicine, 2026); [Epigenetic regulation of gene expression](https://reactome.org/PathwayBrowser/#/R-HSA-212165) (Reactome, 2026); Textbook of Biochemistry for Medical Students, 6th ed. (Jaypee Brothers Medical Publishers (Vasudevan DM, Sreekumari S, Vaidyanathan K), 2011).

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