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

An improved method for the chemical synthesis of oligodeoxynucleotides containing 5 R -5,6-dihydro-5-hydroxythymidine (1) at a defined site is reported. UV melting studies carried out on duplexes containing1synthesized in this manner correlate with previously reported enzyme inhibition experiments, as well as computational studies. The melting experiments suggest that1destabilizes duplex DNA, but that the lesion preferentially base pairs to deoxyadenosine. These experiments also suggest that the presence of1in 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.