Simulations of the solvent structure for macromolecules. III. Determination of the Na+ counter ion structure

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Abstract
We report on a computer experiment in which, using Monte Carlo techniques, we considered a three‐turn (30‐base‐pairs) B‐DNA fragment as a solute and a set of 1200 water molecules and 60 sodium counterions (at a temperature of 300 K) as a solvent. From a statistical analysis of the Monte Carlo simulation (applied to the water molecules and counterions in the B‐DNA field), we determined that the counterions themselves conform to two helical structures intertwined with the two strands. The strutures of the water molecules solvating both counterion helices and the two B‐DNA strands are fully analyzed and described in detail. A model for base‐pair recognition based on the above findings is proposed. Aspects of the unwinding mechanism are discussed.