Dynamic properties and electrostatic potential surface of neutral DNA heteropolymers

Molecular dynamics simulations of fully substituted methylphosphonate (MP) dsDNA of d[AT]5-d[AT]5 and d[GC]5-d[GC]5 were carried out by using explicit water with periodic boundaries at 300 K for 50 ps. MP substitution increased the hydrophobic behavior and neutralized the negative charge of the phosphate backbone of the dsDNA heteropolymers, resulting in a series of specific conformational and physicochemical changes in the dsDNA heteropolymers. The electrostatic potential surface of these neutral dsDNA heteropolymers was calculated by use of a 6-31G* basis set, and a difference was observed in the electrostatic potential for the two neutral DNA helices. These findings support that the role of the negative phosphate backbone is important for interactions with the solvent and counterions, and that charge neutralization of the backbone has relatively small effects upon the conformational properties of DNA.