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Dynamics of Water and Ions Near DNA: Comparison of Simulation to Ti me-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 quanti...

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Published in:Journal of the American Chemical Society Vol. 131; no. 5; pp. 1724 - 1736
Main Authors: Sen, Sobhan, Andreatta, Daniele, Ponomarev, Sergei V., Beveridge, David L., Berg, Mark A.
Format: Article
Published: American Chemical Society 2/11/2009
Subjects:
Biomolecules
Molecular dynamics
DNA
Water
Hydrodynamics
Online Access:View this record in EBSCOhost
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      dt: 2/11/2009
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      pub: American Chemical Society
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        39147567
        10.1021/ja805405a
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      tig:
        atl: Dynamics of Water and Ions Near DNA: Comparison of Simulation to Ti me-Resolved Stokes-Shift Experiments.
      aug:
        au:
          Sen, Sobhan
          Andreatta, Daniele
          Ponomarev, Sergei V.
          Beveridge, David L.
          Berg, Mark A.
        affil:
          University of South Carolina
          Jawaharlal Nehru University
          Wesleyan University
      su:
        Biomolecules
        Molecular dynamics
        DNA
        Water
        Hydrodynamics
      sug:
        subj:
          Biomolecules
          Molecular dynamics
          DNA
          Water
          Hydrodynamics
      ab: 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.
      pubtype: Academic Journal
      doctype: Article
      src: R
    language: English
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