The thermodynamics of binding of low-molecular-weight ligands at extreme tetrads of telomeric G-quadruplexes

Ligand binding constants at the 3'- and 5'-ends of a fluorophore-labelled telomeric G-quadruplex structure were determined. The temperature dependence of the fluorescence quenching reflected that of the binding constants, which in turn was determined by the thermodynamic parameters of the formation of a DNA–ligand complex. Since the quenching of fluorescence can only be mediated by proximal ligand binding, this method allows the characterization of complexes at different ligand-binding sites.