Benzimidazoles: a minor groove-binding ligand-induced stabilization of triple helix.

Nonintercalating minor groove-binding ligands netropsin, Hoechst 33258, and DAPI are reported to destabilize the triplex. Ligands with different substitutions on the phenyl ring of bis- and terbenzimidazoles were evaluated for their effect on the stability of C+.GC triplex and Hoogsteen duplex. We found that newly synthesized benzimidazoles stabilize the triplex as shown by fluorescence and melting studies. Modeling studies showed that these molecules bind in the Watson-Crick minor groove of triplex, which can exert a profound impact on the properties of the host triplex. Circular dichroism-binding studies indicate 5.77 base triplets/ligand as an apparent binding site for bis- and 8.66 for terbenzimidazoles. The stabilization of triplex can be attributed to the protonation of nitrogens and amines of benzimidazoles at pH 5.2 that compensate the negative charge of phosphate backbone to reduce the repulsion between the strands resulting in the stabilization.