Quantitative Transcription Factor Binding Kinetics at the Single-Molecule Level

We investigated the binding interaction between the bacteriophage A-repressor Cl and its target DNA using total internal reflection fluorescence microscopy. Large stepwise changes in the intensity of the red fluorescent protein fused to Cl were observed as it associated with and dissociated from individually labeled single-molecule DNA targets. The stochastic association and dissociation were characterized by Poisson statistics. Dark and bright intervals were measured for thousands of individual events. The exponential distribution of the intervals allowed direct determination of the association and dissociation rate constants (k(a) and k(d), respectively). We resolved in detail how ka and kd varied as a function of three control parameters: the DNA length L, the Cl dimer concentration, and the binding affinity. Our results show that although interactions with nonoperator DNA sequences are observable, Cl binding to the operator site is not dependent on the length of flanking nonoperator DNA.