Two time constants for the binding of proteins to DNA from micromechanical data.

Recent experimental advances allow the direct measurement of the force/extension behavior for DNA in the presence of strongly binding proteins. Such experiments reveal information about the cooperative mechanism of protein binding. We have studied the irreversible binding of such proteins to DNA using a simple simulation and present a method for estimating quantitative rate constants for the nucleation and growth of linear domains of proteins bound to DNA. Such rate constants also give information about the relative energetics of the two binding processes. We discuss our results in the context of recent data for the DNA-recA-ATPgammas system, for which the nucleation time is 4.7 x 10(4) min per recA binding site and the total growth rate of each domain is 1400 recA/min.