Modeling the DNA-solvent interface

Witold R. Rudnicki, B. Montgomery Pettitt

Research output: Contribution to journalArticle

27 Scopus citations

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 converged, whereas the salt perpendicular distribution functions were less well determined. Three-dimensional density reconstructions reliably showed the prominent salvation 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.

Original languageEnglish (US)
Pages (from-to)107-119
Number of pages13
JournalBiopolymers
Volume41
Issue number1
StatePublished - Dec 1 1997
Externally publishedYes

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Biomaterials
  • Organic Chemistry

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    Rudnicki, W. R., & Pettitt, B. M. (1997). Modeling the DNA-solvent interface. Biopolymers, 41(1), 107-119.