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Nucleic Acids Research, 1983, Vol. 11, No. 24 8825-8839
© 1983

CHEMISTRY

Theoretical studies of the selective binding to DNA of two non-intercalating ligands: netropsin and SN 18071

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 September 12, 1983. Revised October 28, 1983. Accepted November 17, 1983.

A theoretical study of the binding to DNA of netropsin and a bisquaternary ammonium heterocycle, SN 18071, is undertaken with an energy minimizing program based on empirical potential functions. The positionning of the ligand is achieved by force and torque calculations and its internal flexibility is taken into account. The binding preference of both drugs studied for the AT minor groove of B-DNA is shown to depend on both the electrostatic potential generated by the base sequence and the quality of the steric fit of the ligand in the groove. Ligand-DNA hydrogen bonds are shown to aid binding, but not to be essential in establishing binding preferences.


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