Quantitative analysis of ligand-macromolecule interactions using differential dynamic quenching of the ligand fluorescence to monitor the binding

Quantitative analyses of the thermodynamics and kinetics of ligand-macromolecule interactions in biological systems rely predominately on monitoring changes in the spectroscopic properties of the ligand or macromolecule, particularly fluorescence changes, which accompany the formation of the studied complexes. However, in many instances the interactions do not affect the fluorescence properties of interacting species and do not provide a resolution high enough to perform quantitative and rigorous measurements of the thermodynamic and/or kinetic parameters. In this communication, we describe the theoretical and experimental aspects of a method of studying complex, multiple ligand-macromolecule interactions by the fluorescence titration technique, when the intrinsic fluorescence changes accompanying binding do not provide a resolution necessary to perform quantitative analyses. The method is based on the fact that a fluorescent ligand, or binding sites of the macromolecule, can have different accessibility to the collisional (dynamic) quencher, when involved in the complex, rather than in the free, unbound state. The presence of an external dynamic quencher in solution, i.e., the presence of an extra collisional quenching process, transforms the fluorescence of the ligand or macromolecule, intrinsically independent of the complex formation, into a property which is dramatically different in the free state than in the bound state of the fluorophore. The approach is applicable to any model of noncooperative or cooperative ligand binding to a macromolecule and allows for the optimization of the resolution of the binding or kinetic studies for a given ligand-macromolecule system. The application of the method is illustrated by applying it to the study of the binding of the fluorescent derivative of a nucleotide cofactor, epsilon ADP, to the six interacting sites of the E. coli primary replicative helicase DnaB protein hexamer.