MONTE-CARLO SIMULATION STUDIES ON THE STRUCTURE OF THE COUNTERION ATMOSPHERE OF B-DNA - VARIATIONS ON THE PRIMITIVE DIELECTRIC MODEL

Monte Carlo computer experiments on the structure and organization of counterions around a Β form of a DNA double helix in aqueous media have been carried out, treating water in the system as a modified homogeneous dielectric. The detailed shape of the DNA and, the finite size and spatial correlations of the counterions are taken into account. Convergence criteria, step size, single-particle versus mul-tiparticle moves, and other methodological issues in the Monte Carlo calculations are addressed. The potential influence of the dielectric discontinuity between the DNA and solvent and the implications of dielectric saturation around DNA are examined. Results of studies on the structure and equilibrium properties of NaDNA solutions in the absence and presence of excess Na+Cl- salt are presented and discussed. We find in all cases a concentration of counterions near DNA (~10 Å) that is in excess of 1 Μ even in the absence of excess salt, consistent with previous theoretical studies. A comparison of the simulation results on the basis of different dielectric models for the solvent showed that the effects of dielectric saturation on the total energetics, the internal energies of counterion binding, and the local counterion distributions are significant. Saturation favors increased counterion condensation relative to the coulombic model, with DNA-counterion interactions dominating the small ion repulsions. A consideration of the lowering of the solvent dielectric constant near DNA and near small ions due to dielectric saturation in water results in an essentially salt-independent estimate of the net counterionic charge per phosphate around DNA over the added salt concentration range of 25-150 mM studied here. This observation is also consistent with the counterion condensation theory and the current inferences from23Na NMR experiments. © 1990, American Chemical Society. All rights reserved.