Reaction Path Averaging: Characterizing the Structural Response of the DNA Double Helix to Electron Transfer

TL;DR

This study investigates the structural response of DNA to electron transfer using reaction path averaging of extensive molecular dynamics simulations, revealing relaxation along a key collective coordinate over nanoseconds.

Contribution

It introduces the reaction path averaging (RPA) method to analyze conformational relaxation in DNA after electron transfer, a novel approach in this context.

Findings

DNA relaxes along a single collective coordinate.

Structural relaxation occurs on nanosecond timescales.

Solvent motions dominate energy relaxation.

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.