Differential electronic states observed during A–B DNA duplex conformational transitions

Abstract

The conformational transitions and the sensitivity of the DNA structure to the surrounding environment are very relevant to its chemical and biological function and potential applications in nano-technology. Different conformations of DNA, even with the same sequence, exhibit different electronic structures, resulting in different conduction properties. We present theoretical work on the dynamical features of electronic states in the A- to B-type transition of a model DNA duplex of d(CGCGCGCGCG)₂ (10 base-pairs, 628 atoms) as the molecule undergoes conformational changes and thermal fluctuations at room temperature. We couple state-of-the art empirical force field molecular dynamics (MD) simulations with an ab initio electronic structure method based on a density-functional theory, called FIREBALL. For the A–B transition, we calculated the effects of conformational changes on the electronic structure for each snapshot obtained from nanosecond MD simulations.

PACS numbers: 71.15.Mb, 71.20.Rv, 73.40.Gk, 85.65.+ h