The formation of paranemic and plectonemic joints between DNA molecules by the recA and single-stranded DNA-binding proteins of Escherichia coli.

During the initial pairing events in the transfer of a strand from a linear duplex to a homologous single-stranded circular DNA by the recA and single-stranded DNA-binding proteins of Escherichia coli, two types of structure are formed that are distinguishable by their stability in the presence of protein denaturants. One type which is resistant to 5.2 M guanidinium chloride is most likely a D-loop that depends only on heteroduplex base pairing for its stability. These D-loops form rapidly when the ends of the linear duplex are homologous with the single-stranded DNA but do not form when the ends are heterologous. The second type appears to require protein, in addition to base pairing, for stability since it is rapidly dissociated by treatment with 5.2 M guanidinium chloride. These unstable structures form even when the ends of the duplex are not homologous with the circular single-stranded DNA. The stability and topological properties of the stable and unstable structures are consistent with those of plectonemic and paranemic joints, respectively (Bianchi, M., Das Gupta, C., and Radding, C. M. (1983) Cell 34, 931-939). The plectonemic joints can be generated in situ from paranemic joints by the addition of a restriction enzyme that cleaves in the region of homology, thus producing free homologous ends. Omission of single-stranded DNA-binding protein results in a large decrease in the rate of formation of both paranemic and plectonemic joints.