Charge transfer equilibria of aqueous single stranded DNA

Abstract

The charge transfer thermodynamics of a simple model of DNA, a single stranded 10-mer poly-adenine oligonucleotide, in water is investigated by means of a computational/theoretical procedure, in which all the relevant environmental effects are considered. Our data indicate that water and counterions ultimately dominate the DNA reduction and oxidation free energies, which are also strongly influenced by the base position along the strand. In fact, we estimated that reduction free energies are large and negative, particularly for the bases close to the 5′ and 3′ positions, whereas the electron detachment is thermodynamically unfavoured all along the strand, but with a higher free energy cost in the central region of the molecule. Further investigation on double charging, i.e. one nucleobase is oxidized and one is reduced within the strand, predicts that charge-separated states are possible and thermodynamically largely stable when the ionic forms are separated by several nucleobases.