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Modeling the DNA-solvent interface.

W R Rudnicki·B M Pettitt
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Abstract

We extend the technique of using perpendicular distribution functions to salt solutions around nucleic acids. Both solute density averaged and nonaveraged reference frames are considered and compared. Using a previous simulation of DNA in salt water of over a nanosecond in duration, the aqueous distribution functions were found to be well coveraged, whereas the salt perpendicular distribution functions were less well determined. Three-dimensional density reconstructions reliably showed the prominent solvation features with transferable functions. The number of solute atom types needed for reconstructions of a given precision was determined in the context of the reference simulation data set with the goal of achieving a required level of reconstruction quality.

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Computer SimulationDNAModels, ChemicalSolutionsWaterJournal ArticleResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, Non-P.H.S.Research Support, U.S. Gov't, P.H.S.

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W R Rudnicki, B M Pettitt. 1997. Modeling the DNA-solvent interface.. https://doi.org/10.1002/(sici)1097-0282(199701)41%3A1%3C107%3A%3Aaid-bip10%3E3.0.co%3B2-l

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