Computer simulation of the ionic atmosphere around Z-DNA
J.L.F. Abascal, M. Domercq and J.C. Gil Montoro
J. Phys. Chem B 110, 25080 (2006)
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[DOI]
ABSTRACT
We describe a coarse-grained model for Z-DNA which mimics the
DNA shape with a relative small number of repulsive interaction sites.
In addition, negative charges are placed at the phosphates positions.
The ionic atmosphere around this grooved Z-DNA model is then investigated
using 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 to examine 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 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.
