Supramolecular complex binding to G-quadruplex DNA: Berberine encapsulated by a planar side arm-tethered β-cyclodextrin.

G-quadruplex-binders have the plausible potential to act as anticancer agents. Herein, the mode of binding of a synthesized fluorenyl derivative of β-cyclodextrin with a duplex and G-quadrulex DNAs has been investigated. Moreover, the loading of the well-known G-quadruplex binder, berberine, in the β-cyclodextrin derivative using 2-dimensional rotating-frame Overhauser effect spectroscopy is studied. The intensity of proton NMR signals is weakened on the β-cyclodextrin derivative's interaction with the quadruplexes. Binding constants are reported for each binding of the ligands to calf thymus DNA, , , and employing fluorescence spectroscopy. A general trend of fluorescence response (quenching) on the β-cyclodextrin derivative to the DNAs is modified when the berberine molecule is loaded in the host structure. Despite berberine binds to the macromolecular target strongly, its host-guest association with the cavity of β-cyclodextrin diminishes the binding strength. A significant difference between the binding strengths of the ligands with duplex and quadruplex structures is observed. Communicated by Ramaswamy H. Sarma.