Structure and stability of DNA base trimers: an electrostatic approach

Abstract

Triplexes involving major groove binding of a third oligomer to the DNA duplex structure have gathered much interest in recent years. The study of base trimer interactions in the gas phase is expected to provide useful information regarding orientational preferences and inherent stabilities. A recently developed electrostatic potential for intermolecular complexation (EPIC) model has been found to be quite useful for exploring the structures and energetics in base pairs [Gadre, S. R.; Pundlik, S. S. J. Phys. Chem. 1996, 101, 3298]. This model makes use of complementary electrostatic features of the interacting species that are determined by ab initio theory. We report here the investigations on various trimers including TAT, TAG, ATG, CGG, and TCG using this model. The overall good agreement of the trimer interaction energies with the corresponding single-point SCF values made at the model-predicted geometries reveals the suitability of the EPIC model for studying DNA base complexes.