Journal
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
Volume 131, Issue 5, Pages 1724-1735Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ja805405a
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Funding
- National Institutes of Health [GM-61292]
- National Science Foundation [CHE-0809306]
- Division Of Chemistry
- Direct For Mathematical & Physical Scien [0809306] Funding Source: National Science Foundation
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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.
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