Homologous pairing can occur before DNA strand separation in general genetic recombination.

In the presence of ATP and Mg2+, purified Escherichia coli recA protein promotes the formation of joint molecules between closed circular duplex DNA and homologous circular single-stranded DNA carrying a short annealed fragment. The presence of this fragment is essential for pairing between molecules. In similar conditions recA protein is unable to act as a helicase and does not cause strand separation of the fragment from the single-stranded circle. Thus, homologous pairing between DNA molecules can take place without prior unwinding of a free end.