THE EFFECT OF A VARIABLE DIELECTRIC COEFFICIENT AND FINITE ION SIZE ON POISSON-BOLTZMANN CALCULATIONS OF DNA-ELECTROLYTE SYSTEMS

The results of variable dielectric coefficient Poisson-Boltzmann calcu lations of the counter-ion concentration in the vicinity of an all-ato m model of the B-form of DNA are presented with an emphasis on the imp ortance of spatial variations in the dielectric properties of the solv ent, 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 inc reases the magnitude of the electrostatic potential with a concomitant increase in the accumulation of small counter-ions in the groove regi ons of DNA. Because ions with radii greater than 2 angstrom have restr icted access to the minor groove, the effect there is less significant than it is within the major groove. Changes in the dielectric coeffic ient for the electrolyte solution, allowing variation from 10 to 25, 4 0, 60, and 78.5 within the first 7.4 angstrom of the surface of DNA, s ubstantially 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 wher e the electrostatic potential is more negative than -kT. Regardless of the choice of dielectric coefficient, the number of ions in regions w here the electrostatic potential is less than -kT remains the same for 0.153 M added 1-1 monovalent electrolyte as for the case without adde d salt. The strong dependence of the calculated distribution of counte r-ion density on the choice of dielectric coefficients representing th e solvent continuum suggests that care must be taken to properly chara cterize the physical system when studying electrostatic properties usi ng these methods.