Conformations of poly{G}-poly{C} pi stacks with high hole mobility.

Charge transfer properties of DNA depend strongly on the pi stack conformation. In the present paper, we identify conformations of homogeneous poly-{G}-poly-{C} stacks that should exhibit high charge mobility. Two different computational approaches were applied. First, we calculated the electronic coupling squared, V(2), between adjacent base pairs for all 1 ps snapshots extracted from 15 ns molecular dynamics trajectory of the duplex G(15). The average value of the coupling squared <V(2)> is found to be 0.0065 eV(2). Then we analyze the base-pair and step parameters of the configurations in which V(2) is at least an order of magnitude larger than <V(2)>. To obtain more consistent data, approximately 65,000 configurations of the (G:C)(2) stack were built using systematic screening of the step parameters shift, slide, and twist. We show that undertwisted structures (twist<20 degrees) are of special interest, because the pi stack conformations with strong electronic couplings are found for a wide range of slide and shift. Although effective hole transfer can also occur in configurations with twist=30 degrees and 35 degrees, large mutual displacements of neighboring base pairs are required for that. Overtwisted conformation (twist> or =38 degrees) seems to be of limited interest in the context of effective hole transfer. The results may be helpful in the search for DNA based elements for nanoelectronics.