Physics of RecA-mediated homologous recognition

Abstract

Most proteins involved in processing DNA accomplish their activities as a monomer or as a component of a multimer containing a relatively small number of other elements. They generally act locally, binding to one or a few small regions of the DNA substrate. Striking exceptions are the \textit{E. coli} protein RecA and its homologues in other species, whose activities are associated with homologous DNA recombination. The active form of RecA in DNA recombination is a stiff nucleoprotein filament formed by RecA and DNA, within which the DNA is extended by 50%. Invoking physical and geometrical ideas, we show that the filamentary organization greatly enhances the rate of homologous recognition while preventing the formation of topological traps originating from multi-site recognition.