DMCA
Local dielectric environment of B-DNA in solution: Result from a 14 ns molecular dynamics trajectory
| Venue: | J. Phys. Chem., B 1998 |
| Citations: | 9 - 0 self |
BibTeX
@ARTICLE{Young_localdielectric,
author = {M. A. Young and B. Jayaram and D. L. Beveridge},
title = {Local dielectric environment of B-DNA in solution: Result from a 14 ns molecular dynamics trajectory},
journal = {J. Phys. Chem., B 1998},
year = {},
pages = {7666--7669}
}
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Abstract
The dielectric behavior of solvent water around DNA is elicited in terms of Kirkwood-Grunwald theory from a 14 ns molecular dynamics trajectory of B-DNA developed in a medium of explicit waters and sodium counterions with particle mesh Ewald for long-range electrostatics. The computed dielectric profile near DNA increases rather rapidly with distance and displays bulk behavior beyond 5 Å. A proximity analysis of the dielectric function reveals that the relative permittivities in the first shell of DNA obey the following trend in the simulations: phosphate backbone> major groove> minor groove. Estimates of the local dielectric constants in the major groove are consistent with interpretations based on fluorescence measurements, indicating that MD models of solvent around DNA are providing a reasonably accurate account of the local solution environment of a complicated polyelectrolyte. The calculated dielectric profile is fit to a sigmoidal function, which can be used in estimating the strength of charge-charge interactions around DNA. I.
Keyphrases
n molecular dynamic trajectory local dielectric environment calculated dielectric profile local dielectric constant explicit water sodium counterions particle mesh ewald kirkwood-grunwald theory dielectric function reveals following trend dielectric behavior reasonably accurate account computed dielectric profile first shell solvent water proximity analysis local solution environment complicated polyelectrolyte major groove md model relative permittivities sigmoidal function charge-charge interaction fluorescence measurement backbone major groove minor groove long-range electrostatics
