Oxidatively damaged nucleobases in duplex DNA oligomers: reaction at thymine-thymine mispairs

Thymine-thymine mispairs are barriers to long-distance radical cation migration and are high reactivity sites in duplex DNA oligomers. A DNA oligomer was prepared that contains only A/T base pairs, arranged into a regularly repeating series of TT steps, and a covalently linked anthraquinone photosensitizer. Its UV irradiation causes the one-electron oxidation of the DNA introducing a radical cation that reacts predominantly at the TT steps as revealed by subsequent strand cleavage. When a remote GG step is introduced into the DNA oligomer, there is little reaction at any of the TT steps and strand cleavage is detected almost exclusively at the GG step. However, when a TT step contains a thymine-thymine mispair, one electron oxidation of the oligomer results in strand cleavage at the mispair and at TT steps preceding it with little reaction at the remote GG step. Experiments in which a thymine in the mispair is replaced by uracil show that the mispair is both a highly reactive site and a barrier to radical cation hopping. These effects of the thymine-thymine mispairs may be associated with its wobble base pair structure.