Recombinase

A recombinase is an enzyme that catalyzes rearrangements of DNA by recognizing specific short DNA sequences. Site-specific recombinases mediate precise rearrangements such as deletions, inversions, insertions, or translocations of a DNA segment between defined recognition sites. In biology and biotechnology they are used to manipulate genomes in a controlled way, enabling conditional gene modification and cassette exchange. Naturally, recombinases participate in bacteriophage integration and excision, plasmid maintenance, and chromosomal rearrangements.

Two major mechanistic classes exist: tyrosine recombinases and serine recombinases. Tyrosine recombinases, including Cre from bacteriophage P1, Flp from yeast, and lambda integrase, operate via a covalent bond between a tyrosine residue and DNA ends to perform sequential strand exchanges. Serine recombinases, such as PhiC31 and Bxb1, cut all four DNA strands simultaneously and rejoin them to achieve rearrangements. Each class recognizes distinct target sequences and has characteristic reaction orders and requirements for cofactors or accessory proteins.

Examples of widely used systems include Cre-LoxP, Flp-FRT, and XerCD-mediated events in bacteria. Cre-LoxP and Flp-FRT enable conditional gene knockouts, tissue- or time-controlled gene modification, and targeted cassette exchange. Integrases and recombinases are employed for site-specific integration of transgenes, genome editing, and complex genetic engineering in a range of organisms from bacteria to mammals.

Applications extend to basic research, functional genomics, and therapeutic strategies. Limitations include incomplete or leaky recombination, potential off-target activity on pseudo-sites, and the need for careful design of recognition sites and expression control to minimize unintended effects. Inducible and tissue-specific variants (for example, Cre-ERT2) improve temporal and spatial specificity.