Calculation of hopping conductivity in aperiodic nucleotide base stacks

Abstract

The electronic density of states (DOS) of aperiodic nucleotide base and base pair stacks were calculated previously by the negative factor counting (NFC) procedure. Applying the inverse iteration method, the localized electronic wave functions of the first 100 filled levels were determined. As a third step the primary hopping frequencies between the localized electronic wave functions (at different sites) were computed assuming interactions via acoustic phonons. Finally using the hopping frequencies as input of a random walk theory of Lax and coworkers the complex, frequency-dependent hopping conductivities σ( ω) were determined. This procedure was performed for two different 100 base or base pair long sequences in the stack and for a 200 units long segment for a single stack. The influence of the application of a better basis set and that of correlation effects were also investigated. The results show an increase of σ( ω) as compared to the ones of different protein chains and at ω=10 10 s −1 they are close to 1 Ω −1 cm −1 in the case of 100 base pairs in the stacks. Further, the application of the better (double ζ) basis and of correlation corrections of the level schemes increase σ( ω). One can conclude that in aperiodic DNA there is hopping hole conduction (if its interaction with nucleoproteins generates holes via charge transfer) and its value is about 1 Ω −1 cm −1 at high frequencies. This result agrees well with the available experimental data.