Poisson-Boltzmann calculations for nucleic acids and nucleic acids complexes

Abstract

Abstract Numerical solution of Poisson-Boltzmann equation with the finite difference DelPhi program is applied to calculations of the electrostatic energy of nucleic acids and their complexes with ligands. It is shown that this approach improves on the results obtained with a simple distance dielectric function. In the case of DNA-drug complexation, the correct preference for binding mode is observed and complexation energies are brought much closer to the experimental results. The procedure is nevertheless sensitive to the number of parameters and determining correct sequence preferences will probably require geometry optimisation within the PB framework.