Solvent effect on DNA base stacked dimers: An isodensity polarizable continuum model approach

摘要

The role of solvent on the base stacking properties of various stacked dimers has been analyzed. Ab initio calculations have been performed on the various stacked dimers using the isodensity polarizable continuum model (IPCM), in the framework of the HF/6-31G** level. It is observed that the stacked dimers undergo different levels of stabilization for different rotated conformations, and the total energy of stacked dimers depends on the twist angle. The results reveal that DNA stacked dimers prefer the twisted (rotated conformation) conformation in water environment, so as to escape from water, due to their hydrophobic nature. In addition, the presence of solvent stabilizes the stacking interaction between bases. (C) 2001 John Wiley & Sons, Inc. [References: 46]