5-(Hydroxymethyl)-2'-deoxycytidine

DNA methylation occurs mainly at the 5’-position of cytosine rings (5-methylcytosine) and occurs almost exclusively in CpG islands. Another epigenetic modification in DNA has been recently identified that involves hydroxymethylation of this same base (5-hydroxymethylcytosine), which potentially offers another level of transcriptional control.[1] 5-(Hydroxymethyl)-2’-deoxycytidine is a modified pyrimidine that is capable of producing interstrand cross-links in double-stranded DNA and has been used to quantify DNA hydroxymethylation levels in biological samples.[2],[3],[4]

Reference:
[1]. Song, C.X., Szulwach, K.E., Fu, Y., et al. Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat.Biotechnol. 29(1), 68-72 (2011).
[2]. Le, T., Kim, K.P., Fan, G., et al. A sensitive mass-spectrometry method for simultaneous quantification of DNA methylation and hydroxymethylation levels in biological samples. Analytical Biochemistry 412(2), 203-209 (2011).
[3]. Clark, T.A., Lu, X., Luong, K., et al. Enhanced 5-methylcytosine detection in single-molecule, real-time sequencing via Tet1 oxidation. BMC Biol. 11(4), 1-10 (2013).
[4]. Krais, A.M., Park, Y.J., Plass, C., et al. Determination of genomic 5-hydroxymethyl-2'-deoxycytidine in human DNA by capillary electrophoresis with laser induced fluorescence. Epigenetics 6(5), 560-565 (2011).