Computer simulation results for the B- to Z-DNA free energy difference

Josť L.F. Abascal and Juan Carlos Gil Montoro

J. Phys.: Condens. Matter 12, A327-A332 (2000)

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ABSTRACT

The aim of the present work is to characterize by computer simulation the free energy difference between B- and Z-DNA in saline solutions. We use a new scheme to rigorously calculate the electrostatic contribution and we use it to test the theoretical predictions for a so-called `empty' DNA model (a set of charged hard spheres placed at the phosphate positions). The ions are considered as charged spheres in a continuum medium of dielectric constant equal to that of water. Besides we investigate the total free energy difference for three different models differing exclusively in the degree of definition of the molecular shape. The comparison against experimental data shows that a precise shape is not required to give acceptable results. Finally, we use a simple grooved primitive model to study the effect of the ionic size and the ionic charges.

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