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 Delta (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 MN and for [(A).+1(T),J,, (m, m' i 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 kd) 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 Delta (t) 0.096 eV in the G(+)(T)(N)GGG duplexes and of Delta (t) = 0.062 eV in the G(+)[(A)(m+1)(T)(m ')](n)GGG duplexes.