Probing the solvent accessibility and electron density of adenine: oxidation of 7-deazaadenine in bent DNA and purine doublets

The effect of DNA bending on nucleobase electron transfer was investigated by studying the oxidation of double-stranded sequences containing seven repeats of the known bent sequence d(GGCA(1)A(2)A(3)A(4)A(5)A(6)C) where 7-deazaadenine (zA) was substituted at the A(3) position. Native gel electrophoresis was used to show that the sequence remained bent upon substitution of zA, which provides for oxidation of the sequence by Ru(bpy)(3)(3+) (bpy = 2,2'-bipyridine). The Ru(III) oxidant was generated by photolysis of Ru(bpy)(3)(2+) in the presence of ferricyanide, and the oxidation was visualized by high-resolution gel electrophoresis of the radiolabeled DNA sequence following base treatment. Cleavage of the DNA strand at the guanine residues and at the zA residues was observed. Comparison of the oxidation of zA in bent DNA versus the normal B form showed that hybridization of the B form sequence to its Watson-Crick complement produced a reduction in cleavage by a factor of 5.19 +/- 0.46 while hybridization of the bent sequence only reduced cleavage by a factor of 1.58 +/- 0.23. This result implies that the zA in the double-stranded, bent sequence is much more solvent-exposed than in normal B-form DNA. When the zA occurred in a B-form 5'-zA-G doublet, the reactivity was 6.63 +/- 0.10 times higher for the zA compared to the G. This implies an even greater effect of a 3'-guanine on the oxidation potential of zA than in the well-known 5'-GG doublet.