title: Fluctuations at the base pair level effecting charge transfer in DNA.
abstract: We investigate the energetics of the basepair degrees of freedom and their effects on the overall charger transfer processes in DNA. We find that the rotational and translational basepair degrees of freedom can be broadly classified into soft and hard vibrational modes, with the stiffness of the modes depending on the nature of the basepair. We also find that the intrabasepair charge transfer, in the A:T and G:C basepairs, is strongly influenced by open (sigma) and stretch (Sy) vibrational modes. Our calculations for the AT-GC and GC-AT dinucleotide steps suggest that the fluctuations in the G:C basepair strongly influence the site energies when compared to fluctuations in the A:T basepair. However, for both the dinucleotide steps, we find that the charge transfer integrals are strongly influenced by the fluctuations at the basepair level. Overall, our studies suggest that for a better understanding of the overall charge transfer processes, it is important to account for the basepair fluctuations.
authors.affiliation: Theoretical Sciences Unit and DST Unit on Nanoscience, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur Campus, Bangalore 560 064, India.
authors.forename: Sairam S
authors.initials: SS
authors.lastname: Mallajosyula
authors.forename: Ashutosh
authors.initials: A
authors.lastname: Gupta
authors.forename: Swapan K
authors.initials: SK
authors.lastname: Pati
mesh_terms: D020029:Base Pairing; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004579:Electron Transport; D009068:Movement; D011506:Proteins / Q000378:metabolism; D012399:Rotation; D013816:Thermodynamics
chemical_list: D011506:Proteins; D004247:DNA