Synthesis of DNA oligos containing 2′-deoxy-2′-fluoro-d-arabinofuranosyl-5-carboxylcytosine as hTDG inhibitor

As an important step of the active demethylation of 5-methylcytosine (5mC), human thymine DNA glycosylase (hTDG) efficiently excises 5-carboxylcytosine (5caC) from double-stranded DNA (dsDNA). Here, we present synthesis of DNA oligos containing a 2′-deoxy-2′-fluoro-d-arabinofuranosyl-5-carboxylcytidine (F-5caC) modification that act as hTDG inhibitors. The glycosylase activity assay showed that F-5caC oligos were resistant to excision by the hTDG catalytic domain (hTDGcat, residues 111–308) and they could inhibit the excision of DNA oligos containing 5caC. The electrophoretic mobility shift assay confirmed that DNA oligos containing F-5caC could bind well with unmodified hTDGcat to form a stable complex, which makes it possible to obtain the crystal structure of the complex to reveal details on how hTDGcat recognizes the DNA substrate.