Modeling the DNA-solvent interface

✍ Scribed by Witold R. Rudnicki; B. Montgomery Pettitt

• Publisher: Wiley (John Wiley & Sons)
• Year: 1997
• Tongue: English
• Weight: 904 KB
• Volume: 41
• Category: Article
• ISSN: 0006-3525
• DOI: 10.1002/(sici)1097-0282(199701)41:1<107::aid-bip10>3.0.co;2-l

✦ Synopsis

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.