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.
Kostjukov
V V
VV
Department of Physics, Sevastopol National Technical University, Sevastopol 99053, Crimea, Ukraine.
Khomytova
N M
NM
Davies
D B
DB
Evstigneev
M P
MP
D004247:DNA / Q000737:chemistry*; D006841:Hydrocarbons, Aromatic / Q000737:chemistry*; D007364:Intercalating Agents / Q000737:chemistry; D008024:Ligands; D009692:Nucleic Acid Heteroduplexes; D009841:Oligonucleotides / Q000737:chemistry; D055672:Static Electricity; D013816:Thermodynamics
D006841:Hydrocarbons, Aromatic; D007364:Intercalating Agents; D008024:Ligands; D009692:Nucleic Acid Heteroduplexes; D009841:Oligonucleotides; D004247:DNA