The effects of 5R-5,6-dihydro-5-hydroxythymidine on duplex DNA stability and structure

Abstract

An improved method for the chemical synthesis of oligodeoxynucleotides containing 5R-5,6-dihydro-5-hydroxythymidine (1) at a defined site is reported. UV melting studies carried out on duplexes containing 1 synthesized in this manner correlate with previously reported enzyme inhibition experiments, as well as computational studies. The melting experiments suggest that 1 destabilizes duplex DNA, but that the lesion preferentially base pairs to deoxyadenosine. These experiments also suggest that the presence of 1 in a duplex disrupts base pairing at the 5'-adjacent nucleotide and results in the thermally preferred misincorporation of purines opposite the 5'-deoxyadenosine stacked above 1 at this position. Despite the disruptions in base stacking, the UV melting experiments and enzymatic ligation/electrophoretic migration assays are consistent with the predicted macroscopic duplex structure containing intrahelical nucleotides.