Electrostatic contribution to the energy of binding of aromatic ligands with DNA

The method of solution of the nonlinear Poisson–Boltzmann equation was used to calculate electrostatic energy of binding of various aromatic ligands with DNA oligomers of different length. Analysis of the electrostatic contribution was made in terms of a two‐step DNA binding process: formation of the intercalation cavity and insertion of the ligand. The total electrostatic energy was also partitioned into components: the energy of atom–atom coulombic interactions and the energy of interaction with surrounding water. The results indicate that electrostatic interactions are, as a whole, unfavorable to the intercalation process and that a correct analysis of structure‐energy interrelation for Ligand‐DNA interactions should only be accomplished at the level of the components rather than at the level of total electrostatic energy. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 680–690, 2008. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com