Hole Trapping, Detrapping, and Hopping in DNA

In this paper we present a self-consistent kinetic-quantum mechanical analysis of chemical yield data for hole trapping/detrapping in G + (T−A) m GGG duplexes (with free energy gaps Δ t ) and for hole hopping/trapping/detrapping in G + [(T) m G] n (T) m GGG duplexes of DNA. Bridge specificity of hole trapping/detrapping by GGG traps was specified by superexchange electronic contributions, inferred from electronic coupling matrix elements between nearest-neighbor nucleobases and semiempirical energy gaps, and energetic contributions, which determine the nuclear Franck−Condon factors. Unistep hole-trapping yields are accounted for by a weak bridge length dependence for short ( N = 1, 2) bridges, due to detrapping. Marked bridge specificity is manifested for short ( N = 1, 2) bridges, being distinct for (T) N and for [(A) m +1 (T) m ‘ ] n ( m, m ‘ ≥ 0 and N = n ( m + m ‘ + 1)) bridges. For long ( N > 2) bridges an exponential bridge size dependence of the trapping yields prevails. Multistep hole transport results in different reaction rates of G + (rate k d ) and of (GGG) + (rate k dt ) with water, i.e., k d / k dt = 1.6, which, in conjunction with the unistep trapping/detrapping data, results in the free energy gaps for hole trapping of Δ t = 0.096 eV in the G + (T) N GGG duplexes and of Δ t = 0.062 eV in the G + [(A) m +1 (T) m ‘ ] n GGG duplexes.