ELECTROSTATIC POTENTIALS NEAR-THE-SURFACE OF DNA - COMPARING THEORY AND EXPERIMENT

Electrostatic potentials near the surface of DNA were calculated using the nonlinear Poisson-Boltzmann (NLPB) equation. The results are foun d to be in good agreement with the potentials measured using ELDOR spe ctroscopy. In contrast, the linearized PB equation is found to signifi cantly underestimate the screening effects of salt and thus produces p otentials that are too negative. Several physical models including a c ylinder of radius 10 Angstrom and a detailed atomic structure built fr om crystallographic coordinates were used to examine the effect of loc al DNA structure on the calculated potentials. Two dielectric models f or the solvent were used; one in which the solvent has a uniform diele ctric of 80, and one in which a 5.6-Angstrom layer of solvent at the D NA surface was assigned a dielectric of 10 to simulate dielectric satu ration. We find no evidence for dielectric saturation; indeed, includi ng such effects reduces the agreement between theory and experiment. F inally, a simple model in which the charges on the phosphates have bee n reduced to a value of 0.24 and the potentials are given by Debye-Huc kel theory is shown to give a realistic representation of the electros tatic potentals near the surface of DNA.