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Nucleic Acids Research, 1984, Vol. 12, No. 16 6559-6574
© 1984

CHEMISTRY

The solvation contribution to the binding energy of DNA with non-intercalating antibiotics

Krystyna Zakrzewska, Richard Lavery and Bernard Pullman

Institut de Biologie Physico-Chimique, Laboratoire de Biochimie Théorique, associé au CNRS 13, rue Pierre et Marie Curie, 75005 Paris, France

Received May 29, 1984. Accepted July 17, 1984.

The Influence of the solvent on the binding energies to DNA of six non-intercalating antibiotics - netropsln. distamycln-3. dlstamycin-2. SN 18071, berenil and stilbamidine - is evaluated by combining the effect of the first hydration shell with that of bulk water. The first effect is computed by a methodology based on a spherical/point dipole model of water and limited to electrostatic interaction energies. Hydration shells are obtained which are energy optimized with respect to both water-solute and water-water interactions for the complexes and for the Isolated DNA oligomers and ligands. The method allows even very large complexes to be studied in reasonable computation times. The second effect is Introduced via a cavity treatment, it is shown that if the vacuum interaction energies already predict correctly the preference of the ilgands for the minor groove of AT squences of B-DNA. the introduction of the soivation effect is indispensable for reproducing the order of affinity of the ligands and for bringing the values of the compiexatlon energies into close agreement with experimental data.


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