Effect of Structural Dynamics and Base Pair Sequence on the Nature of Excited States in DNA Hairpins

Abstract

In this article, a theoretical study of the electronic and spectroscopic properties of well-defined DNA hairpins is presented. The excited states in the hairpins are described in terms of an exciton Hamiltonan model, and the structural dynamics of the DNA model systems is explicitly taken into account by molecular dynamics simulations. The results show that the model reproduces the experimentally observed absorption and circular dichroism spectra accurately in most cases. It is shown that structural disorder leads to excited states that are largely localized on a single base pair, even for regular DNA sequences consisting only of AT base pairs. Variations in the base pair sequence have a significant effect on the appearance of the spectra but also on the degree of delocalization of the excited state.