Monte Carlo simulation of the influence of solvent on nucleic acid base associations

Abstract

The results of Monte Carlo calculations of the associations between nucleic acid bases in a nonpolar solvent (CCl4) are described. The influence of the solvent on planar and stacked associations of bases was examined by analyzing the total energy of the system, including solute-solute, solute-solvent and solvent-solvent contributions. Good quantitative agreement with the available experimental data was obtained. Solute-solvent interactions are primarily determined by dispersion forces; consequently solute-solvent interactions vertical to the solute plane that maximize dispersion interactions are most favored, and a rough proportionality between solute-solvent energy and the surface of the solute was observed. Analysis of solvent-solvent energy shows that the presence of the solute induces significant changes in the structure of the solvent. As a result, solvent-solvent energy is not necessarily reduced when surface area decreases, contrary to the simple cavity concept. Single molecule probe calculations were performed to explain the differences in base associations in H2O and CCl4. In CCl4 dispersion forces dominate and planar complexes are stabilized by maximum exposure of molecular planes to the solvent. In H2O electrostatic forces dominate so that the most stable structures are stacked associations that allow the maximum number of hydrophilic centers to be exposed to the solvent.