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

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