Calculation of the HOMO localization of Tetrahymena and Oxytricha telomeric quadruplex DNA.

Abstract Several guanine-rich sequences exist in many important regions, such as telomeres, and these sequences can form quadruplex DNA structures. It was previously reported that 3′-guanines are mainly oxidized in the Tetrahymena and Oxytricha telomeric quadruplex DNA, d(TGGGGT) 4 , and 5′-guanines are mainly oxidized in the human telomeric quadruplex DNA, d(TAGGGT) 4 T. We speculated that the differences in site reactivity between d(TGGGGT) 4 and d(TAGGGT) 4 T are induced by the localization of the HOMO. The HOMOs of the possible quadruplex structures were thus determined and the results showed that the HOMOs of d(TGGGGT) 4 +3K + and d(TAGGGT) 4 T +2K + localized at the 5′-guanine, and that the HOMO shifted from the 5′-guanine to the 3′-guanine by the addition of a 5′-capping cation. Furthermore, we determined the influence of the cation and demonstrated that localization of the HOMO at the G-quartet plane located immediately adjacent to the cation is disfavored. The calculated HOMO localization of d(TGGGGT) 4 +4K + and d(TAGGGT) 4 T +2K + matched the experimental results and suggest that d(TGGGGT) 4 contains a 5′-capping cation in solution.