Modeling the DNA-solvent interface

Biopolymers. 1997 Jan;41(1):107-19. doi: 10.1002/(SICI)1097-0282(199701)41:1<107::AID-BIP10>3.0.CO;2-L.

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Computer Simulation
  • DNA / chemistry*
  • Models, Chemical*
  • Solutions / chemistry*
  • Water / chemistry*

Substances

  • Solutions
  • Water
  • DNA