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Computer Simulation of the Ionic Atmosphere around Z-DNA

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J. L. F. Abascal,*^† M. Domercq,^‡ and J. C. Gil Montoro^†

Departamento de Química-Física, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain, and I.E.S. Tierno Galván, 28914 Leganés, Spain

J. Phys. Chem. B, 2006, 110 (49), pp 25080–25090

DOI: 10.1021/jp064199z

Publication Date (Web): November 16, 2006

Section:

General Biochemistry

Abstract

We describe a coarse-grained model for Z-DNA that mimics the DNA shape with a relatively small number of repulsive interaction sites. In addition, negative charges are placed at the phosphate positions. The ionic atmosphere around this grooved Z-DNA model is then investigated with Monte Carlo simulation. Cylindrically averaged concentration profiles as well as the spatial distribution of ions have been calculated. The results are compared to those for other DNA models differing in the repulsive core. This allows the examination of the effect of the DNA shape in the ionic distribution. It is seen that the penetrability of the ions to the DNA groove plays an important role in the ionic distribution. The results are also compared with those reported for B-DNA. In both conformers the ions are structured in alternating layers of positive and negative charge. In Z-DNA the layers are more or less concentric to the molecular axis. Besides, no coions enter into the single groove of this conformer. On the contrary, the alternating layers of B-DNA are also structured along the axial coordinate with some coions penetrating into the major groove. In both cases we have found five preferred locations of the counterions and two for the coions. The concentration of counterions reaches its absolute maximum at the narrow Z-DNA groove and at the minor groove of B-DNA, the value of the maximum being higher in the Z conformer.

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