Premium
Modeling the DNA‐solvent interface
Author(s) -
Rudnicki Witold R.,
Pettitt B. Montgomery
Publication year - 1997
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/(sici)1097-0282(199701)41:1<107::aid-bip10>3.0.co;2-l
Subject(s) - chemistry , aqueous solution , nucleic acid , context (archaeology) , perpendicular , salt (chemistry) , solvent , biological system , molecular dynamics , dna , algorithm , chemical physics , computational chemistry , computer science , geometry , organic chemistry , biochemistry , paleontology , mathematics , biology
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. © 1997 John Wiley & Sons, Inc.