A method for the computer simulation of the free energy difference in conformational changes of polyelectrolytes. Application to the B to Z-DNA transition

J.C. Gil Montoro and J.L.F. Abascal

ABSTRACT

A method for calculating the free energy difference between two dissimilar conformational states of a nucleic acid is proposed. The procedure is especially suited for computer simulation. The calculation of the free energy of each conformer is split into two steps; the first one consists in the buildup of the uncharged conformers while the other one ---which leads to the more important contribution--- corresponds to the charging process of such structures. We report preliminary results on the application of the method to evaluate the free energy difference for the the salt induced conformational change between the B and Z forms of DNA. This is the first rigorous evaluation of the dependence of the free energy difference on the added salt concentration.