Biopolymers and cell. 2009; 25 (2): 133 - 141

Hydrophobic contribution to the free energy of complexation of aromatic ligands with DNA

V. V. Kostjukov, N. M. Khomutova, A. O. Lantushenko, M. P. Evstigneev

Sevastopol state technical university Sevastopil, Ukraine, 99053

The hydrophobic component of complexation energy of double-stranded DNA with biologically active aromatic compounds was calculated using two semi-empirical methods – correlations of hydrophobic energy with changes of a heat capacity (DCp) and solvent-accessible surface area (SASA). These surface areas were calculated for free ligands and DNA oligomers, unwound DNA duplexes and DNA-ligand complexes. The changes of polar and non-polar SASAs of molecules upon binding ligands to DNA were found. The hydrophobic contribution at both complexation stages were calculated. It was shown that the calculation of hydrophobic energy by SASA method is more correct than (DCp) method for DNA-binding ligands.

Keywords: double-stranded DNA, aromatic ligand, hydropho- bic contribution, solvent-accessible surface area.