Complementary electrostatics for the study of DNA base-pair interactions

Abstract

The complementary "lock and key" patterns of weakly interacting molecules are explored by mapping the topography of respective molecular electrostatic potentials (MESP). A new model, viz., electrostatic potential for intermolecular complexation (EPIC), which incorporates such MESP features, has been employed for studying interactions between DNA base pairs. A wide variety of pairs of bases involving adenine (A), guanine (G), and cytosine (C) are chosen as test cases. The interaction energy within the EPIC model is expressed as (½){∑V_A,iq_B,i + ∑V_B,iq_A,i}, where V_A,i is the MESP value due to A at the ith atom of molecule B and q_B,i is the MESP-derived charge at this site. The interaction energies and geometrical parameters obtained by this model agree remarkably well with the corresponding literature values obtained by full geometry optimization at the ab initio level. Being intuitively appealing and simple in application, the EPIC model seems to have the potential of being a good predictive tool for investigating weak intermolecular interactions.