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

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Aim. Analysis of the hydration changes at formation of DNA complexes with biologically active aromatic compounds (BAC): antibiotics actinomycin D, daunomycin, nogalamycin, novantrone and mutagens ethidium bromide and proflavine. Methods. Molecular dynamics simulations. Results. The hydration indexes for double-helical DNA and ligands in a free and complexed states were calculated. A critical analysis of modern ideas about changing water environment at binding of aromatic ligands to DNA was performed. Conclusions. It is shown that upon binding of aromatic BAC with DNA a significant (from 2.6 for novantrone to 13.1 for actinomycin D) liberation of water molecules out of hydration shells with the disruption of hydrogen bonds takes place

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