A Theoretical and Experimental Study of Competition Between Solution and Surface Receptors for Ligand in a Biacore Flow Cell

Abstract Rate constants that characterize the kinetics of binding and dissociation between biomolecules carry fundamental information about the biological processes these molecules are involved in. An instrument that is widely used to determine these rate constants is the Biacore. In a Biacore experiment, one of the reactants, which we will call the receptor, is immobilized on a sensor chip. During the binding phase of the experiment the other reactant flows past the chip. After binding, buffer alone is introduced into the flow cell and dissociation is monitored. Often surface-based binding assays are influenced by the transport of the reactant in solution, complicating the determination of the chemical rate constants from the observed binding kinetics. We propose a new way to determine the dissociation rate constant by adding soluble receptor during dissociation. The method is tested first on simulated data and then on Biacore experiments where the lac repressor protein binds and dissociates from a stretch of double stranded DNA containing the lac repressor binding site. With this method we find a dissociation rate constant kd=0.075 ± 0.005s-1, a value that is faster than previously obtained from Biacore experiments. In developing our method to analyze these experiments we obtain an expression for the transport limited rate constant for a Biacore experiment when soluble receptor is present during dissociation.