The effect of water environment on the hopping conductivity of an aperiodic nucleotide base stack

Abstract

We have used the matrix block negative factor counting method to calculate the density of states of an aperiodic single stack of DNA (a part of a human oncogene), consisting of 100 nucleotide bases in the DNA B conformation. The nearest water molecules were taken into account in the calculation. The work refers to the valence bands region of the stacks. Consequently the inverse iteration method was used to determine the Anderson localization of the physically interesting wave functions. The hopping frequencies between the units were determined from these. They have been used as input in a random walk theory. According to the results obtained, the real part and the absolute value of the complex hopping conductivity gets saturated at the frequency of 10 12 s −1. Its value lies at ∼10 −4 Ω −1 cm −1, which is by two orders of magnitude larger than the one obtained previously in the absence of water (∼10 −6 Ω −1 cm −1). Different reasons for this rather large effect of water are discussed (e.g. basis set improvement by bases set superposition, the effect of the water dipoles).