Duplex-duplex interactions catalyzed by RecA protein allow strand exchanges to pass double-strand breaks in DNA.

Using gapped circular DNA and homologous duplex DNA cut with restriction nucleases, we show that E. coli RecA protein promotes strand exchanges past double-strand breaks. The products of strand exchange are heteroduplex DNA molecules that contain nicks, which can be sealed by DNA ligase, thereby effecting the repair of double-strand breaks in vitro. These results show that RecA protein can promote pairing interactions between homologous DNA molecules at regions where both are duplex. Moreover, pairing leads to strand exchanges and the formation of heteroduplex DNA. In contrast, strand exchanges are unable to pass a double-strand break in the gapped substrate. This apparent paradox is discussed in terms of a model for RecA-DNA interactions in which we propose that each RecA monomer contains two nonequivalent DNA-binding sites.