Modeling the DNA-solvent interface

W. R. Rudnicki, Bernard Pettitt

Research output: Contribution to journalArticle

27 Citations (Scopus)

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 nonsecond 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 re-constructions 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.

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

Fingerprint

Distribution functions
DNA
Salts
Saline water
Nucleic acids
Solvation
Nucleic Acids
Atoms
Water
Datasets

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Biophysics

Cite this

Modeling the DNA-solvent interface. / Rudnicki, W. R.; Pettitt, Bernard.

In: Biopolymers, Vol. 41, No. 1, 01.1997, p. 107-119.

Research output: Contribution to journalArticle

Rudnicki, W. R. ; Pettitt, Bernard. / Modeling the DNA-solvent interface. In: Biopolymers. 1997 ; Vol. 41, No. 1. pp. 107-119.
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