Distributions of electrostatic potentials and forces in a DNA molecule by a concentric cylindrical model. II. Effects of the Debye-Huckel parameter

摘要

We have developed a mathematical method to compute the three-dimensional distributions of potentials, circumferential forces, and electrostatic free energy in a DNA molecule. A DNA molecule was described by a three-layered concentric cylinder. For geometric reasons, discrete point phosphate charges are arranged helically around the central axis of the DNA in equivocal circumferential steps. The Debye-Huckel theory was applied to linearize the Poisson-Boltzmann equation and obtain analytical solutions. As the value of the Debye-Huckel parameter K increased, the potentials in the inner region increased, and the reaction potentials and the middle-region potentials decreased. Forces in the inner, middle, and outer regions decreased, while the reaction force increased. The influence of the Debye-Huckel parameter strongly depended on the radial position of the DNA. Changes in the dielectrical constant of the middle region had a significant influence on the electrostatic energy of the DNA. This method will be useful for evaluating the interaction between the physiological ionic circumstances around DNA, the ion adsorption, and the melting process of the DNA double strand.