ArticleJournal of the American Chemical Society2009
Dynamics of water and ions near DNA: comparison of simulation to time-resolved stokes-shift experiments.
Article in Journal of the American Chemical Society, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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Who cites it
11 citing papers in PubMed.
- Long-range DNA-water interactions.Biophysical journal · 2021Article
- Dynamics of water and ions around DNA: What is so special about them?Journal of biosciences · 2018Review
- Water Dynamics in the Hydration Shells of Biomolecules.Chemical reviews · 2017Review
- On the absence of intrahelical DNA dynamics on the μs to ms timescale.Nature communications · 2014Article
- Ion counting from explicit-solvent simulations and 3D-RISM.Biophysical journal · 2014Article
- The ABCs of molecular dynamics simulations on B-DNA, circa 2012.Journal of biosciences · 2012Review
- Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations.Journal of biosciences · 2012Article
- A Surrogate for Debye-Waller Factors from Dynamic Stokes Shifts.The journal of physical chemistry letters · 2011Article
- Computational exploration of mobile ion distributions around RNA duplex.The journal of physical chemistry. B · 2010Article
- Mechanisms for DNA charge transport.Chemical reviews · 2010Review
- Ultrafast dynamics in DNA: "fraying" at the end of the helix.Journal of the American Chemical Society · 2006Article
Corrections and comments
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Authors and funding
5 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.