Energetics of Base Pairs in B-DNA in Solution: An Appraisal of Potential Functions and Dielectric Treatments

The energetics of base pairs in B-DNA in solution has been estimated via recently reported versions of some empirical potential energy functions, namely, AMBER, CHARMM, GROMOS, and OPLS used commonly in biomolecular simulations. The electrostatic component of the interaction energy between bases involved in Watson-Crick pairing in B-DNA in aqueous environment, evaluated via the finite difference PoissonBoltzmann methodology with all the above force fields, is in the range of -2 to -3 kcal/mol per H-bond. An examination of different dielectric functions used in conjunction with the above force fields suggests that a sigmoidal function, with an estimate of -2 kcal/mol per H-bond, comes closest to mimicking the electrostatics of AT and GC base pairs under aqueous conditions.