A general method of analysis of ligand-macromolecule equilibria using a spectroscopic signal from the ligand to monitor binding. Application to Escherichia coli single-strand binding protein-nucleic acid interactions

Abstract

We describe a general method for the analysis of ligand-macromolecule binding equilibria for cases in which the interaction is monitored by a change in a signal originating from the ligand. This method allows the absolute determination of the average degree of ligand binding per macromolecule without any assumptions concerning the number of modes or states for ligand binding or the relationship between the fractional signal change and the fraction of bound ligand. Although this method is generally applicable to any type of signal, we discuss the details of the method as it applies to the analysis of binding data monitored by a change in fluorescence of a lignad upon binding to a nucleic acid. We apply the analysis to the equilibrium binding of Escherichia coli single-strand binding (SSB) protein to single-stranded nucleic acids, which is monitored by the quenching to the intrinsic tryptophan fluorescence of the SSB protein. With this method, one can quantitatively determine the relationship between the fractional signal change of the ligand and the fraction of bound ligand, LB/LT, and rigorously test whether the signal change is directly porportional to LB/LT. For E. coli SSB protein binding to single-stranded mucleic acids in its (SSB)65 binding mode [Lohman, T. M. and Overmans, L. B. (1985) J. Biol. Chem. 260, 3594; Chrysogelos, S., and Griffith, J. (1982) Proc Natl. Acad. Sci. USA 79, 5803], we show that the fractional quenching of the SSB fluorescence is equal to the fraction of bound SSB.