Dynamics of water and ions near DNA: comparison of simulation to time-resolved stokes-shift experiments.
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.
Sen
Sobhan
S
School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067 India.
Andreatta
Daniele
D
Ponomarev
Sergei Y
SY
Beveridge
David L
DL
Berg
Mark A
MA
D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D004574:Electromagnetic Fields; D008956:Models, Chemical; D014867:Water / Q000737:chemistry*
D014867:Water; D004247:DNA