Computer simulation results for the free-energy difference between B-DNA and Z-DNA
José L F Abascal; Juan Carlos Gil Montoro; José L F Abascal; Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040, Spain; Juan Carlos Gil Montoro; Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040, Spain
Журнал:
Journal of Physics: Condensed Matter
Дата:
2000-02-28
Аннотация:
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. Also, 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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