DNA sequences containing contiguous AA or TT mismatches, as well as sequences containing a 3-deazacytidine analogue were synthesized. Irradiation of anthraquinone abstracts an electron from the DNA. The loss of an electron from double-stranded DNA results in the formation of a radical cation that migrates through the DNA where it reacts irreversibly with H2O or O2 at GG steps. Subsequent treatment with piperidine or Fpg enzyme cleaves the backbone of the DNA at the site of reaction. DNA oligomers were designed to contain contiguous AA, TT, or G3-deazacytidine mismatches. It was revealed that the mismatches destabilize the duplex DNA; however, there is no measurable effect on the overall secondary structure of the DNA. The contiguous (AA)n mismatch, where n lt 7, was shown to have no effect on charge migration efficiency. In contrast, the contiguous (TT)n mismatch, where n gt 2, was shown to have near complete inhibition of charge migration through the mismatch region. Charge migration through the G3-deazacytidine mismatch was shown to have no effect on charge migration efficiency as well. Interestingly, reaction at the (G3-deazacytidine)2 base pairs revealed a change in the ratio of oxidative damage at the Gs. In (GC)2 base pairs, the ratio of damage at the two Gs is 10:1 with the majority of damage occurring at the 5-G. However, the (G3-deazacytidine)2 base pairs had an equal distribution of damage at the 5 and 3-Gs, with the amount of total reactivity equaling the (GC)2 base pairs. These findings indicate that the base composition in mismatched DNA determines the effect on charge migration efficiency and trapping reactivity.