Homologous recombination is vital for life. In eukaryotic meiosis, it ensures proper separation of homologous chromosomes by locking them together and promotes genetic diversity in offspring by scrambling parental genes. In all life forms, it plays a crucial role in managing DNA damage.

In E. coli, homologous recombination via the RecBCD pathway starts with the invasion of duplex DNA by single-stranded DNA from another duplex that has undergone a double-stranded break. This process begins with RecBCD's nuclease and helicase activities, which generate a free end by preferentially nicking DNA at Chi sites. The invading strand is then coated with RecA and SSB. RecA facilitates the pairing of the invading strand with its complementary homologous DNA, forming a D-loop, while SSB enhances recombination by melting secondary structures and preventing RecA from trapping such structures, which could inhibit subsequent strand exchange. Following this, RecBCD likely nicks the D-loop strand, creating a branched intermediate known as a Holliday junction. The RuvA–RuvB helicase catalyzes branch migration, moving the crossover of the Holliday junction to a favorable resolution site. Finally, RuvC resolves the Holliday junction by nicking two of its strands, producing either noncrossover recombinants with heteroduplex patches or two crossover recombinant DNAs.

Meiotic recombination in yeast begins with double-stranded breaks (DSBs) created by two Spo11 molecules. These molecules work together to cleave both DNA strands at closely spaced sites through transesterification reactions involving active site tyrosines. This reaction forms covalent bonds between Spo11 and the newly created DSBs. Spo11 is subsequently released.