Kinetic Studies of Lambda Repressor-Mediated DNA Looping Suggest Physiological Role for Non-Specific Binding

Abstract

The kinetics of DNA loop formation and breakdown by the λ repressor or CI protein was characterized using the tether particle motion technique (TPM) and a novel method of analysis with increased time resolution. The kinetics of loop formation was described by a stretch exponential, while the kinetics of loop breakdown was found to be more complex and only the distribution of the long dwell times could be described by a power law. Comparison with the kinetics of loop formation and breakdown induced in DNA with mutated operators, shows that repressor bound at these sites may act as a nucleation site for further binding and loop stabilization, and may contribute to broaden the rate constants distribution. A model is suggested by which nonspecific binding of CI along the inter-operator distance may shorten the effective separation between the specific sites which mediate looping thereby lowering the potential energy necessary for loop formation. Finally, CI-mediated looping kinetics also shows that the frequency of transition between the looped and unlooped DNA conformation does not vary with CI concentration, despite the fact that the loop becomes thermodynamically more stable. The relevance of this feature to the robustness of the system is discussed.