Recombinases

Recombinases are enzymes that catalyze DNA rearrangements at defined sequence motifs, enabling inversion, excision, integration, or translocation of genetic material. They operate by recognizing short DNA sites and mediating controlled strand breakage and rejoining, thereby altering genome structure without relying on broad homologous regions. Recombinases are essential tools in genetics and biotechnology for precise genome engineering.

Most recombinases are grouped into two mechanistic classes. Tyrosine recombinases, including Cre and lambda integrase, cut and rejoin DNA through a Holliday junction intermediate and typically act on defined sites such as loxP or attB/attP. Serine recombinases, such as Flp and related enzymes, perform a concerted double-strand exchange that often yields products without Holliday junctions, and can function in diverse genomic contexts.

Prominent members in research and biotechnology include Cre recombinase (loxP), FLP recombinase (FRT), lambda integrase (attB/attP), and XerC/XerD (bacterial chromosome dimer resolution). In eukaryotes, site-specific recombinases enable conditional gene knockouts, marker removal, and lineage tracing. By contrast, homologous recombination relying on RecA or Rad51 uses long homologous sequences rather than defined target motifs.

Applications span conditional gene inactivation, reporter systems, transgene integration, and genome editing in model organisms and mammalian cells. Recombinase systems can be engineered to be inducible or tissue-specific, and multiple orthogonal recombinases permit complex genetic circuits. Limitations include dependence on precise recognition sites, potential off-target activity, and variable efficiency across cell types and chromatin context.