The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the likelihood of an identical or similar DNA sequence on a sister chromatid is high. Thus, the timing of repair prevents recombination between non-identical sequences. This is a critical feature of HR, particularly during the recombination of parental DNA sequences in an offspring, where faulty HR can lead to loss of the entire gene and the surrounding chromosomal region.

The accurate repair ensured by HR has been applied in gene-editing techniques. HR is the earliest method that has been used to edit genomes in living cells. The CRISPR-Cas9 system is used to create targeted double-strand breaks to correct disease-causing mutations in the genome. The isolated fragments are taken up by cells, where they can recombine with cellular DNA and replace the targeted region of the genome. HR mechanisms govern the repair of the breaks and their accurate recombination with the cellular genome. To help the HR proteins localize precisely at double-strand breaks, Cas9 proteins are fused with HR effector proteins that can recruit repair proteins at the damaged sites. Studies have shown that fusing Cas9 with proteins such as CtIP, Rad52, and Mre11 can increase HR events in the cell by two-folds while discouraging Non-homologous end joining. Such applications of HR in genome editing can revolutionize gene therapy and provide treatment for genetic diseases that are currently considered incurable.