Base Sequence Effects on Transport in DNA

Abstract

Given the success of the polaron model based on solvation in accounting for the width of a hole polaron on an all-adenine (A) sequence on DNA, we extend the calculations to other sequences. We find excellent agreement with the free energy differences measured by Lewis et al. (J. Am. Chem. Soc. 2000, 122, 12037-12038) between a guanine (G) cation and a pair of bases, GG, or a triple of bases, GGG, in all cases surrounded by As, by treating AGGA and AGGGA as solvated polarons. There is additional support for hole polaron formation in DNA from experiments in which oxidative damage due to injected holes is investigated in sequences involving Gs and As. Theory and comparison with transport measurements on repeated sequences involving multiple thymines (Ts) or combinations such as ATs or GCs, where C is cytosine, led to the suggestion that the basic sequences in these cases must be polarons whose wave functions have substantial amplitudes on both chains in a duplex. The size of an electron polaron in DNA is predicted to be similar to that of a hole polaron, approximately 4 or 5 bases. Although experiments have shown that polaron hopping is the dominant mode of charge transport in DNA with repeated sequences such as AGGA, further investigations, particularly of temperature dependence of site energies and transfer integrals, are needed to determine to what extent hole transport takes place by polaron hopping for arbitrary DNA sequences.