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

Research paper by V V VV Kostjukov, N M NM Khomytova, D B DB Davies, M P MP Evstigneev

Indexed on: 21 Mar '08Published on: 21 Mar '08Published in: Biopolymers



Abstract

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.