Site-specificity of bis-benzimidazole Hoechst 33258 in A-tract recognition of the DNA dodecamer duplex d(GCAAAATTTTGC)2

Fluorescence titration measurements and NMR spectroscopy have identified a single molecule of Hoechst 33258 bound within the long A-tract of the dodecamer duplex d(GCAAAATTTTGC)(2): despite the possibility of multiple binding sites, and the apparent requirement from previous studies for the drug N-methylpiperazine ring to bind close to GC base pairs at the end of an A-tract (leading to an off-set asymmetric complex with this sequence), we identify a binding site that spans the central AAATTT sequence with the planar aromatic rings of the drug binding in the narrowest part of the minor groove.