The design, synthesis, and DNA binding properties of azaHx-PI or p-anisyl-4-aza-benzimidazole-pyrrole-imidazole (5) are described. AzaHx, 2-(p-anisyl)-4-aza-benzimidazole-5-carboxamide, is a novel, fluorescent DNA recognition element, derived from Hoechst 33258 to recognize G·C base pairs. Supported by theoretical data, the results from DNase I footprinting, CD, ΔTM, and SPR studies provided evidence that an azaHx/IP pairing, formed from antiparallel stacking of two azaHx-PI molecules in a side-by-side manner in the minor groove, selectively recognized a C-G doublet. AzaHx-PI was found to target 5′-ACGCGT-3′, the Mlu1 Cell Cycle Box (MCB) promoter sequence with specificity and significant affinity (Keq 4.0 ± 0.2 × 107 M-1).
Satam, V., Babu, B., Patil, P., Brien, K. A., Olson, K., Savagian, M., … Kiakos, K. (2015). AzaHx, a novel fluorescent, DNA minor groove and G·C recognition element: Synthesis and DNA binding properties of a p-anisyl-4-aza-benzimidazole-pyrrole-imidazole (azaHx-PI) polyamide. Bioorganic and Medicinal Chemistry Letters, 25(17), 3681–3685. https://doi.org/10.1016/j.bmcl.2015.06.055