5-Hydroxymethyl-dC for epigenetic research

Naturally occurring 5-hydroxymethylcytosine (5-hmC) has been hypothesized to be an intermediate in a demethylation pathway or an additional epigenetic factor. Learn more about this exciting new modification.

Apr 11, 2012

Revised/updated Nov 1, 2017

Quick facts:

Availability: DNA
Location: 5′, 3′, or internal
Scale: 100 nmol, 250 nmol, 1 µmol, 5 µmol, and 10 µmol
HPLC required
Ordering symbols:
     For 5′ placement, use /55HydMe-dC/
     For 3′ placement, use /35HydMe-dC/
     For internal placement, use /i5HydMe-dC/

FOF - 5-Hydroxymethyl-dC_structure

Figure 1. 5-Hydroxymethyl-dC modification.

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. While the exact biological function of 5-hmC is unknown, it has been hypothesized that it may be an intermediate in a demethylation pathway or may act as an additional epigenetic factor [5].

Ordering oligos with 5-Hydroxymethyl-dC

You can order oligos with this modification introduced at any position using standard. 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.

Other modifications to facilitate your research

See what other modifications are available from IDT. You can find a list of standard modifications we make to oligonucleotides on the Modifications page of our online catalog. And if you don’t find what you are looking for, just send us a request. We often synthesize special, non-catalog requests. Contact us at


  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.