Characterization of the minor groove environment in a drug-DNA complex: bisbenzimide bound to the poly[d(AT)].poly[d(AT)]duplex.

We compare the fluorescence properties of bisbenzimide (also known as Hoechst 33258) bound to the minor groove of the poly[d(AT)].poly[d(AT)] duplex with the corresponding fluorescence properties of bisbenzimide dissolved in neat organic solvents and mixed organic/aqueous solvents. Based on these comparisons, we conclude that the minor groove of the bisbenzimide-poly[d(AT)].poly[d(AT)] complex is quite nonpolar and exhibits a local dielectric constant of approximately 20 D. We discuss how this insight influences our understanding of the molecular forces that dictate and control the binding affinities and specificities of minor groove-directed DNA binding ligands.