Ionic distribution around simple B-DNA models II. Deviations from cylindrical symmetry

Juan Carlos Gil Montoro and JosÚ L.F. Abascal

Journal of Chemical Physics 109, 6200-6210 (1998)

ABSTRACT

The structure of the ions around two B-DNA models with added monovalent salt at the continuum solvent level is investigated by computer simulation. The salt concentrations cover a wide range, from 0.05 M to 4.5 M. The simplicity of the so-called grooved primitive model (unit electron charges at the phosphate positions of canonical DNA and the grooves shape approximated by means of simple geometric elements) enables a detailed study of the counterion and coion distributions with a very small statistical noise.

The inhomogeneity of the ionic distributions is noticeable along the axial direction up to distances of about 20 ┼ from the DNA axis. The counterions deeply penetrate into the DNA grooves even at very low added salt concentrations. In the minor groove, the counterions are preferentially located in its center whereas they lie at the sides of the major groove, close to the phosphate positions. The coions also enter within the major groove, especially in the systems at high added salt concentrations for which regions of absolute negative charge can be found within the groove. This can be explained in terms of an arrangement of ions with alternating charges. The grooved primitive model has also been solved in the context of the finite difference Poisson-Boltzmann theory. The theory accurately describes the ionic structure around DNA at low salt concentrations but the results deteriorate with increasing salt missing important qualitative features at or above molar concentrations.

The other model investigated differs from the more detailed one in that the shape of DNA is not taken into account; a soft cylinder is used instead. The counterions accumulate in this model in front of the phosphates and the axial inhomogeneity of the distribution quickly vanishes. These results together with those of previous investigations lead to the conclusion that the coupling of the discrete description of the DNA charge with the steric effects due to the presence of the grooves is the primary determinant of the final ionic distribution, especially at high salt concentrations. This effect may play a decisive role in those DNA properties which are strongly dependent on the salt concentration, like the B- to Z-DNA conformational transition.

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