title: Dynamics of water and ions near DNA: comparison of simulation to time-resolved stokes-shift experiments.
abstract: Time-resolved Stokes-shift experiments measure the dynamics of biomolecules and of the perturbed solvent near them on subnanosecond time scales, but molecular dynamics simulations are needed to provide a clear interpretation of the results. Here we show that simulations using standard methods quantitatively reproduce the main features of TRSS experiments in DNA and provide a molecular assignment for the dynamics. The simulations reproduce the magnitude and unusual power-law dynamics of the Stokes shift seen in recent experiments [ Andreatta, D., et al. J. Am. Chem. Soc. 2005, 127, 7270 ]. A polarization model is introduced to eliminate cross-correlations between the different components contributing to the signal. Using this model, well-defined contributions of the DNA, water, and counterion to the experimental signal are extracted. Water is found to have the largest contribution and to be responsible for the power-law dynamics. The counterions have a smaller, but non-negligible, contribution with a time constant of 220 ps. The contribution to the signal of the DNA itself is minor and fits a 30 ps stretched exponential. Both time-averaged and dynamic distributions are calculated. They show a small subset of ions with a different coupling but no other evidence of substates or rate heterogeneity.
authors.affiliation: School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067 India.
authors.forename: Sobhan
authors.initials: S
authors.lastname: Sen
authors.forename: Daniele
authors.initials: D
authors.lastname: Andreatta
authors.forename: Sergei Y
authors.initials: SY
authors.lastname: Ponomarev
authors.forename: David L
authors.initials: DL
authors.lastname: Beveridge
authors.forename: Mark A
authors.initials: MA
authors.lastname: Berg
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D004574:Electromagnetic Fields; D008956:Models, Chemical; D014867:Water / Q000737:chemistry*
chemical_list: D014867:Water; D004247:DNA