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Biophys J, October 1999, p. 1769-1781, Vol. 77, No. 4
Department of Chemistry and Institute for Molecular Design, University of Houston, 4800 Calhoun, Houston, Texas 77204-5641 USA
The distribution of sodium and chlorine ions around DNA
is presented from two molecular dynamics simulations of the DNA
fragment d(C5T5) · (A5G5) in explicit solvent with 0.8 M
additional NaCl 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 residence times
of ions within this shell are compared between conformations and with experiment. Ordered sodium ion sites were found in minor and major grooves around both A and B-DNA conformations. Changes in the surrounding hydration structure are analyzed and implications for the
stabilization of A-DNA and B-DNA conformations are discussed.
Biophys J, October 1999, p. 1769-1781, Vol. 77, No. 4
© 1999 by the Biophysical Society 0006-3495/99/10/1769/13 $2.00
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