combinase

Combinase refers to an enzyme that catalyzes recombination between DNA sequences, enabling rearrangements of genetic elements. These enzymes recognize defined DNA recognition sites and promote cutting and rejoining of DNA to invert, excise, integrate, or swap segments. They are widely used in molecular biology to perform site-specific recombination and differ from enzymes that require extensive sequence homology for recombination.

Most combinases are site-specific recombinases, which can be grouped into two main mechanistic families. Tyrosine recombinases, such as Cre, Flp, and lambda integrase, typically produce a four-stranded Holliday junction intermediate and can mediate reversible or directional recombination depending on the arrangement of sites and cofactors. Serine recombinases, including Tn3 resolvase and related enzymes, perform concerted double-strand breaks and exchanges, often yielding rapid and directional rearrangements. Some systems require additional factors, such as directionality or integrative elements, to control the outcome.

Common examples include the Cre-loxP system from a bacteriophage, used to excise, invert, or activate genes; the Flp-FRT system from yeast for similar edits; and the PhiC31 integrase system that mediates unidirectional integration of DNA at attP and attB sites. Other well-known systems include Dre-rox and XerC/XerD in bacterial chromosome maintenance. These tools enable conditional gene knockouts, lineage tracing, and targeted genome engineering.

Design considerations include ensuring specificity of recognition sites, controlling the timing and location of recombinase expression, and avoiding unintended recombination at off-target sites. Combinases are fundamental tools in genetics and synthetic biology for precise genome manipulation with minimal homology requirements.