Effective potentials for ion-DNA interactions

Effective, solvent-mediated interaction potentials between alkali metal ion s (Li+, Na+, K+, and Cs+) and selected sites on the DNA surface are derived from molecular dynamics simulations data. The effective potentials reprodu ce the corresponding ion-ion and ion-DNA radial distribution functions, obt ained in the detailed full-atomistic molecular dynamics simulations. In thi s work, we have first calculated the ion-DNA and ion-ion radial distributio n functions from molecular dynamics simulations of a periodic fragment of d ouble-helix DNA in ionic aqueous solution. Thereafter we applied the invers e Monte Carlo method, previously suggested by us [Phys. Rev. E 52, 3730 (19 95)], to derive the effective interaction potentials. Finally, a considerab ly larger DNA fragment was constructed together with its surrounding solven t environment and Monte Carlo simulations were performed to calculate the i on distributions and the relative binding affinities of different alkali io ns to DNA. The results agree well with available experimental data. (C) 199 9 American Institute of Physics. [S0021-9606(99)50548-5].