COUNTERION DISTRIBUTION AROUND DNA STUDIED BY MOLECULAR-DYNAMICS AND QUANTUM-MECHANICAL SIMULATIONS

Quantum mechanical calculations and molecular dynamics (MD) simulation s have been used to obtain an accurate and time-averaged representatio n of the charge distribution of a DNA-water-Na+ system. Having derived a set of time-averaged charges for the phosphate and the sodium ions, two 150 ps MD simulations have been performed to obtain a more comple te picture of the dynamic characteristics of the DNA, including solven t and counterion environment. In agreement with other theoretical appr oaches to the analysis of DNA/ion interaction, about 80% of the counte rions are associated with the DNA. This occurs almost entirely through interaction with the phosphate groups, the counterions being distribu ted approximately equally between the first and second coordination sh ells of the phosphates. The revised partial charges for the phosphate group and sodium ion appear to result in structural parameters for the DNA which remain in somewhat better agreement with experimental data than when the standard charges are used.