The oxidization potential of AA steps in single strand DNA oligomers

Abstract

Adiabatic ionization energies of short (3-mers) single strand oligonucleotides containing cytosine and adenine have been computed and compared with the oxidation potentials determined by differential pulse voltammetry. Different functionals and different ways of compensating backbone electric charges have been employed. In line with the experimental results, a lowering of the oxidation potential is predicted for oligomers containing two consecutive adenines. The computed oxidation potential shifts are slightly lower than the experimental one and in most of the cases the spin density distribution of the oligonucleotide radical cations is localized over a single adenine. Both results depend on electrostatic interactions between adenine and cytosine, which stabilize the radical cation containing a single adenine and make the two adenines inequivalent in sequences possessing two consecutive adenines.