5-Hydroxymethylcytosine and 5-formylcytosine containing deoxyoligonucleotides: facile syntheses and melting temperature studies.

An oxidation-based synthetic approach was developed for facile preparation of 5-formyl-2'-deoxycytidine and 5-hydroxymethyl-2'-deoxycytidine phosphoramidites. Upon introducing organic solvent components and copper catalysts, C5-methyl groups of 5-methyl-2'-deoxycytidine and thymidine were readily oxidized to formyl and hydroxyl functionality, respectively. Standard solid phase DNA synthesis and conventional deprotection methods were applicable to synthesize 5-formyl- or 5-hydroxymethyl-cytosine containing DNA oligonucleotides, which were used to study the effect of epigenetic modifications on DNA thermal dynamic stability.