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Biophys J, February 2000, p. 600-607, Vol. 78, No. 2
Center for Studies in Physics and Biology, Rockefeller University, 1230 York Avenue, New York, New York 10021, U.S.A. and Department of Physics, Warwick University, Coventry, CV4 7AL, United Kingdom
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-ATP
s system, for which the nucleation
time is 4.7 × 104 min per recA binding site and the
total growth rate of each domain is 1400 recA/min.
Biophys J, February 2000, p. 600-607, Vol. 78, No. 2
© 2000 by the Biophysical Society 0006-3495/00/02/600/08 $2.00
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