The effect of a variable dielectric coefficient and finite ion size on Poisson-Boltzmann calculations of...

The results of variable dielectric coefficient Poisson-Boltzmann calculations of the counter-ion concentration in the vicinity of an all-atom model of the B-form of DNA are presented with an emphasis on the importance of spatial variations in the dielectric properties of the solvent, particularly at the macro-ion-solvent interface. Calculations of the distribution of hard-sphere electrolyte ions of various dimensions are reported. The presence of a dielectric boundary significantly increases the magnitude of the electrostatic potential with a concomitant increase in the accumulation of small counter-ions in the groove regions of DNA. Because ions with radii greater than 2 A have restricted access to the minor groove, the effect there is less significant than it is within the major groove. Changes in the dielectric coefficient for the electrolyte solution, allowing variation from 10 to 25, 40, 60, and 78.5 within the first 7.4 A of the surface of DNA, substantially increases the calculated surface concentration of counter-ions of all sizes. A lower dielectric coefficient near the macro-ion surface also tends to increase the counter-ion density in regions where the electrostatic potential is more negative than -kT. Regardless of the choice of dielectric coefficient, the number of ions in regions where the electrostatic potential is less than -kT remains the same for 0.153 M added 1-1 monovalent electrolyte as for the case without added salt. The strong dependence of the calculated distribution of counter-ion density on the choice of dielectric coefficients representing the solvent continuum suggests that care must be taken to properly characterize the physical system when studying electrostatic properties using these methods.