Play of molecular host: guest assembly on a G-quadruplex binder

Benzimidazoles are known G-quadruplex binding molecules. G-quadruplex-selective binding is relevant in the target-based design of the molecules for treating certain diseases, including cancer. Herein, we present the synthesis of a new benzimidazolyl guanidine and its binding association with various nucleic acids viz., calf thymus DNA (duplex), kit22, myc22, and telo (G-quadruplexes). The synthesized compound is characterized by IR, NMR, and mass spectrometric techniques. The binding titration is carried out utilizing UV–vis and fluorescence spectroscopy. The conformational changes of DNAs on the ligand binding are monitored using circular dichroism. Further, the compound inclusion complex with a porphyrin-β-cyclodextrin host molecule. The binding strengths of the guanidine and its Ppy-CD inclusion complex are compared. The inclusion complexes bind stronger to G-quadruplexes than CT-DNA. The binding constants value is the largest for the interaction of the guanidine: porphyrin-β-cyclodextrin inclusion complex with the G-quadruplex kit22, which possesses a parallel conformation. The difference in the binding strengths is articulated and compared between duplex and G-quadruplex bindings.