The Binding of Prototype Lexitropsins to the Minor Groove of DNA: Quantum Chemical Studies

Abstract

Ab initio calculations (Hartree-Fock) using the 6–31G basis set have been performed on two prototype lexitropsins or information-reading molecules. The latter are DNA minor groove binding agents related to the A·T recognizing netropsin in which each of the two N-methylpyrrole moieties is replaced in turn by 1-methylimidazole and which thereby confers the property of recognizing G·C sites. Ab initio treatment was possible by examining composites of separate non-conjugated segments of the molecules. Geometry optimized conformations, energies and distribution of electrostatic charges within the molecules were derived. The ab initio derived parameters of the geometry optimized conformations of these lexitropsins were used to interpret their interaction with different sequences within the minor groove of B-DNA.