Molecular dynamics simulations of DNA in solution with different counter-ions

Molecular dynamics simulations of the [d(ATGCAGTCAG](2) fragment of DNA, in water and in the presence of three different counter-ions (Li+, Na+ and Cs +) are reported. Three-dimensional hydration structure and ion distribution have been calculated using spatial distribution functions for a detailed p icture of local concentrations of ions and water molecules around DNA. Acco rding to the simulations, Cs+ ions bind directly to the bases in the minor groove, Nac ions bind prevailing to the bases in the minor groove through o ne water molecule, whereas Li+ ions bind directly to the phosphate oxygens. The different behavior of the counter-ions is explained by specific hydrat ion structures around the DNA and the ions. It is proposed how the observed differences in the ion binding to DNA may explain different conformational behavior of DNA. Calculated self-diffusion coefficients for the ions agree well with the available NMR data.