Studies on the torsions of nucleic acids using ABEEMσπ/MM method

The biological functions of DNA are related to its conformation. In this work, potential energy profiles of nucleic acid torsions associated with the sugar-phosphate backbone and the glycosyl linkage were studied using the ab initio and ABEEM sigma pi/MM methods. The ABEEM sigma pi/MM well reproduced the entire potential energy profiles (not just minima) of the torsion of model compounds. The ABEEM sigma pi/MM method also gives reasonable results about the structures and dipole moments of DNA bases and interactions between bases and one water molecule. The torsions of four deoxyribonucleosides were investigated in aqueous solution through molecular dynamics simulations based on the ABEEM sigma pi/MM. Reasonable distributions of the torsional angles were observed with the pseudorotation angles in south, glycosyl torsion chi in anti conformation, and g(+) conformations for torsion gamma. The reasonable results on simulating DNA fragments in gas and aqueous solution suggest that the newly constructed ABEEM sigma pi/MM method would be robust for simulating nucleic acids. (C) 2009 Elsevier B.V. All rights reserved.