Dependence of Electronic Properties of DNA Single Strands on Size and Environment

Abstract

Modeling DNA at the electronic structure level remains a computational challenge. However, for a detailed understanding of possible reaction pathways, consideration of the electron distribution is essential. Here, we report a density functional theory study on the length dependence of electronic properties of DNA single strands consisting of up to eight cytosine units. We also study systems in which the cytosine either at the 5′-end or 3′-end is replaced by the anticancer agent gemcitabine. These systems are investigated without and with Na counterions, both in the gas phase and in a polarizable continuum to model an aqueous solvent. We calculate the vertical electron affinities, vertical ionization energies, and solvation energies. We find a pronounced odd−even oscillation for the vertical electron affinity and vertical ionization energy for all systems without counterions in the gas phase as well as in the polarizable continuum. These oscillations completely vanish by adding the Na counterions. We discuss the implications of our results with respect to comparisons between experimental and numerical investigations. For studies involving, for example, oligonucleotides, comparison of size-dependent properties derived from theory and experiment might lead to a better understanding of experimental conditions, which are sometimes difficult to determine.