Ionic distribution around simple DNA models. I. Cylindrically averaged properties

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Abstract
Properties depending on the radial ionic concentration profiles are calculated by Monte Carlo simulation for several simple B‐DNA models in the presence of added (monovalent) salt up to 2.5 M concentration. The models include both homogeneously and discretely charged polyions. Besides, the effect of hard and soft repulsive forces is considered. A novel model which represents the DNA grooved structure in a simplified manner is introduced. From a methodological point of view, special attention is paid to the treatment of long‐range forces along the axial direction. Exact formulas for discretely charged polyelectrolytes are used. Regarding the density profile results, it is concluded that the main effect is not due to the discreteness of the positions of the charges, i.e., homogeneously charged models lead to properties not significantly different from discretely charged ones. A similar statement holds for the comparison between hard and soft models. Nevertheless, the inclusion of the grooved shape of DNA modifies this behavior. A double hump in the concentration profile function is brought about by the coupling between repulsive and coulombic forces in the grooved model. It is shown that not only this but also other properties of full atomic models of DNA are adequately predicted by our simplified grooved model. Finally, at high concentrations of added salt, it is seen that the condensed ionic cloud overneutralizes the polyelectrolyte charge. This charge reversal phenomenon, which is observed in all the models studied, has not been previously observed due to the high salt concentration required.