Sodium and chloride ions as part of the DNA solvation shell

From: Biophysical Journal | Date: October 1, 1999| Author: | Copyright information

ABSTRACT The distribution of sodium and chlorine ions around DNA is presented from two molecular dynamics simulations of the DNA fragment d(C^sub 5^T^sub 5^) - (A^sub 5^G^sub 5^) in explicit solvent with 0.8 M additional NaCI salt. One simulation was carried out for 10 ns with the CHARMM force field that keeps the DNA structure close to A-DNA, the other for 12 ns with the AMBER force field that preferentially stabilizes B-DNA conformations (Feig and Pettitt, 1998, Biophys. J. 75:134-149). From radial distributions of sodium and chlorine ions a primary ion shell is defined. The ion counts and ...

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