DNA Methylation

One of the fastest growing fields in biology and cancer research is epigenetics. While the underlying genetic code defines which proteins and gene products are synthesized, it is epigenetic control that defines when and where they are expressed. This dynamic control of gene expression is essential for X chromosome inactivation, embryogenesis, cellular differentiation and appears integral to memory formation and synaptic plasticity.

In 2009, two reports^1,2 described the discovery of 5-hydroxymethyl-2’-deoxyCytidine (hmdC), a novel dC modification in Purkinje neurons and embryonic stem cells. Later, a third report found this modification to be strongly enriched in brain tissues associated with higher cognitive functions.³ This new dC modification is generated by the action of a-ketoglutarate dependent TET enzymes (ten eleven translocation), which oxidizes 5-Me-dC to hmdC. This finding stimulated discussion about active demethylation pathways that could occur, e.g., via base excision repair (BER), with the help of specialized DNA glycosylases. Alternatively, one could envision a process in which the hydroxymethyl group of hmdC is further oxidized to 5-formyl-dC (fdC) or 5-carboxy-dC (cdC) followed by elimination of either formic acid or carbon dioxide^4,5.

Glen Research has supported this research since its inception by providing the building blocks for the synthesis of oligonucleotides containing all the new dC derivatives - hmdC, fdC and cdC. The first generation hmdC phosphoramidite was fairly very well accepted but requires fairly harsh deprotection conditions. Therefore, a second generation building block (5-Hydroxymethyl-dC II) developed by Carell and co-workers that is compatible with UltraMild deprotection has been introduced.⁶ A second generation fdC-phosphoramidite (5-Formyl-dC II), also developed by Carell and co-workers, has been introduced since it does not require the post synthesis elimination step of the first generation version.⁷

5-Formyl-dC and 5-carboxy-dC may find uses in research into DNA damage and repair processes.