STRUCTURE AND STABILITY OF DNA-BASE TRIMERS - AN ELECTROSTATIC APPROACH

Triplexes involving major groove binding of a third oligomer to the DN A duplex structure have gathered much interest in recent years. The st udy of base trimer interactions in the gas phase is expected to provid e useful information regarding orientational preferences and inherent stabilities. A recently developed electrostatic potential for intermol ecular 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 o f 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 m odel. The overall good agreement of the trimer interaction energies wi th the corresponding single-point SCF values made at the model-predict ed geometries reveals the suitability of the EPIC model for studying D NA base complexes.