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Biophysical Journal 87:1466-1477 (2004)
© 2004 The Biophysical Society

Physics of RecA-Mediated Homologous Recognition

Kevin Klapstein *, Tom Chou * and Robijn Bruinsma {dagger}

* Department of Biomathematics, {dagger} Department of Physics, University of California-Los Angeles, Los Angeles, California

Correspondence: Address reprint requests to Tom Chou, Dept. of Biomathematics, UCLA, Box 951766, Los Angeles, CA 90095-1766. Tel.: 310-206-2787; E-mail: tomchou{at}ucla.edu.

To accomplish its DNA strand exchange activities, the Escherichia coli protein RecA polymerizes onto DNA to form a stiff helical nucleoprotein filament within which the DNA is extended by 50%. Homology search and recognition occurs between ssDNA within the filament and an external dsDNA molecule. We show that stretching the internal DNA greatly enhances homology recognition by increasing the probability that the homologous regions of a stretched DNA molecule and a parallel, unstretched DNA molecule will be "in register" at some position. We also show that the stretching and stiffness of the filament act together to ensure that initiation of homologous exchange between the substrate DNA molecules at one position precludes initiation of homologous exchange at any other position. This prevents formation of multiple exchange site "topological traps" which would prevent completion of the exchange reaction and resolution of the products.




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R. Fulconis, M. Dutreix, and J.-L. Viovy
Numerical Investigation of Sequence Dependence in Homologous Recognition: Evidence for Homology Traps
Biophys. J., June 1, 2005; 88(6): 3770 - 3779.
[Abstract] [Full Text] [PDF]


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