Differential electrostatic stabilization of A-, B-, and Z-forms of DNA

The static accessibility discrete charge algorithm for protein charge interactions is extended to the case of linear polyelectrolytes. In this model, the effective dielectric value between surface charge sites depends predominantly on the solvent ionic strength and the solvent accessibilities of the charge sites. This treatment accounts for the phenomena of specific ion binding in the context of a general electrostatic effect Matthew and Richards (1982) Biochemistry 21 , 4989]. Specific ion sites are determined by locating areas of high electrostatic potential at the solvent interface of the macromolecule. At a given ionic strength the calculated potential at a site is taken to describe a binding constant and therefore the ion site occupancy. For a 20-base-pair fragment of B-DNA, net charge of ?40, 16 ion sites are indicated in the minor groove. The partial occupancy of each site increases from 0.2 to 0.5 as the ionic strength is increased from 0.01 to 0.50. Over the same range of ionic strength, the electrostatic free energy of this charge array is calculated to change from +0.6 to ?0.05 kcal/bp. Parallel behavior is predicted for A- and Z-DNA charge geometries. The most stable configuration, based on electrostatic criteria, at high ionic strength (I = 0.1–0.5) is that of Z-DNA. In this range, the ratio of “bound” sodium to phosphate is predicted to be less than 0.4.