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The methylation of deoxycytosine (dC) to 5-methylcytosine (5-mC) has long been studied for the important role it plays as an epigenetic marker in gene expression and regulation. Now researchers are turning their attention to 5-hydroxymethylcytosine (5-hmC), a recently discovered “sixth base” [1]. In mammalian cells, 5-hmC has been detected in all tissue types, with the highest levels observed in the brain and spinal cord [2,3]. Jin, Wu, et al. [4] were among the first to compare levels and locations of 5-hmC to 5-mC in human brain tissue and reported its enrichment at promoters and in intragenic regions. It has been reported that 5-mC is converted to 5-hmC by TET proteins, which perform various roles in gene expression. The exact biological function of 5-hmC is unknown, but it has been hypothesized that it may be an intermediate in a demethylation pathway or may act as an additional epigenetic factor [5].

To order an oligonucleotide modified with 5-hydroxymethylcytosine: select 5-Hydroxymethyl-dC from the modifications tab on the oligonucleotide order page. Alternatively, use the appropriate modification code.


  1. Kriaucionis S and Heintz N (2009) The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science, 324:929–930.
  2. Munzel M, Globisch et al. (2010) Quantification of the sixth DNA base hydroxymethylcytosine in the brain. Angew Chem Int Ed, 49:5375–5377.
  3. Globisch D, Munzel M, et al. (2010) Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PLoS ONE, 5:e15367.
  4. Jin SG, Wu X, et al. (2011) Genomic mapping of 5-hydroxymethylcytosine in the human brain. Nucleic Acids Res, 39:5015–5024.
  5. Tahiliani M, Koh KP, et al. (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science, 324:930–935.