Chapter 27 - Ballistic conductance for all-atom models of native and chemically modified DNA: A review of a Kubo-formula-based approach

Abstract

This chapter presents and discusses DNA conductance based upon the Kubo formula. Using this approach, the effects of base pair mismatches, different conformational changes, and base pair sequence on DNA electrical properties can be investigated. This makes possible the very fast estimation of conductance spectra for oligonucleotides with hundreds of base pairs and can be used to treat the arbitrary chemical modifications of DNA. This novel formulation estimates the ballistic transport through finite atomically resolved DNA fragments within the framework of the Kubo formalism, recast in its Green function representation. Such an approach permits the extremely fast evaluation of DNA conductance, with the computation time scaling linearly versus DNA duplex length. The chapter presents the method of calculation step by step. Results suggest that isolated DNA itself is at best a kind of poor semiconductor. Chemically, one could still select some special charge donor and/or acceptor moieties, which being properly attached to a DNA duplex, would use its specific channels to facilitate the charge transfer between them. The results clearly demonstrate the presence of such channels in different DNA duplexes. External effects, as well as internal structural alterations, should play a significant role in tuning the effectiveness of the DNA charge transfer channels. The application of the approach presented in the chapter would result in a noticeably faster estimation of the DNA conductance spectrum than the already available methods of the same class. This should enable to efficiently estimate conductance spectra for the DNA duplexes of arbitrary length as well as their complexes with diverse organic/inorganic molecular or polymeric agents.