DNA strand exchange in the absence of homologous pairing

The strand exchange reaction that is widely used for in vitro studies on recombination of DNA molecules is generally presumed to result from a preceding homologous pairing step. With the use of a single-stranded circular DNA and a short homologous linear duplex fragment as substrates in a model strand exchange reaction, it was found that modest concentrations of polyethylene glycol or salt promote formation of heteroduplex molecules and strand exchange. When the duplex fragment was partially resected with an exonuclease exposing a short single-stranded stretch on the ends, the reaction was promoted by the addition of commercial bovine serum albumin. The transcription factor TFIIIA promoted strand exchange when the DNA substrates contained the cognate DNA binding sequence recognized by the protein. These observations suggest that detection of strand exchange in vitro does not necessarily imply a preceding homologous pairing step.