Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University,
S 106 91, Stockholm, Sweden
Abstract
Effective, solvent-mediated interaction potentials between alkali metal
ions (Li+, Na+, K+ and Cs+) and selected sites on the DNA surface are derived
from molecular dynamics simulation data. The effective potentials reproduce
the corresponding ion-ion and ion-DNA radial distribution functions, obtained
in the detailed full-atomistic molecular dynamics simulations. In this
work, we have first calculated the ion-DNA and ion-ion radial distribution
functions from molecular dynamics simulations of a periodic fragment of
double-helix DNA in ionic aqueous solution. Thereafter we applied the Inverse
Monte Carlo method, previously suggested by us [Phys.
Rev.E, 52, 3730 (1995)], to derive the effective interaction potentials.
Finally, a considerably larger DNA fragment was constructed together with
its surrounding solvent environment and Monte Carlo simulations were performed
to calculate the ion distributions and the relative binding affinities
of different alkali ions to DNA. The results agree well with available
experimental data.