title: Reaction Path Averaging: Characterizing the Structural Response of the DNA Double Helix to Electron Transfer.
abstract: A polarizable environment, prominently the solvent, responds to electronic changes in biomolecules rapidly. The knowledge of conformational relaxation of the biomolecule itself, however, may be scarce or missing. In this work, we describe in detail the structural changes in DNA undergoing electron transfer between two adjacent nucleobases. We employ an approach based on averaging of tens to hundreds of thousands of nonequilibrium trajectories generated with molecular dynamics simulation, and a reduction of dimensionality suitable for DNA. We show that the conformational response of the DNA proceeds along a single collective coordinate that represents the relative orientation of two consecutive base pairs, namely, a combination of helical parameters shift and tilt. The structure of DNA relaxes on time scales reaching nanoseconds, contributing marginally to the relaxation of energies, which is dominated by the modes of motion of the aqueous solvent. The concept of reaction path averaging (RPA), conveniently exploited in this context, makes it possible to filter out any undesirable noise from the nonequilibrium data, and is applicable to any chemical process in general.
authors.affiliation: Institute for Advanced Simulations (IAS-5) and Institute of Neuroscience and Medicine (INM-9), Forschungszentrum Jülich , 52428 Jülich, Germany.|Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences , 16610 Praha, Czech Republic.
authors.forename: Michal H
authors.initials: MH
authors.lastname: Kolář
authors.affiliation: Institute of Physical Chemistry & Center for Functional Nanostructures, Karlsruhe Institute of Technology , 76131 Karlsruhe, Germany.
authors.forename: Tomáš
authors.initials: T
authors.lastname: Kubař
mesh_terms: D020029:Base Pairing; D004583:Electrons; D004735:Energy Transfer; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D010084:Oxidation-Reduction; D013995:Time
chemical_list: D009838:Oligodeoxyribonucleotides