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)_mGGG duplexes (with free energy gaps Δ_t) and for hole hopping/trapping/detrapping in G⁺[(T)_mG]_n(T)_mGGG 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)_NGGG duplexes and of Δ_t = 0.062 eV in the G⁺[(A)_m+1(T)_m']_nGGG duplexes.