Site-specific recombinases and their essential role in synthetic biology

Site-specific recombinases, enzymes that bind to specific DNA attachment sites and catalyze DNA rearrangement reactions resulting in permanent and heritable genetic modifications, have emerged as powerful tools in synthetic biology. Their broad applications in genome engineering, genetic circuit design, DNA assembly, and computational design have significantly advanced the field over the past decades. To provide a systematic overview of both fundamental concepts and recent progress, this review comprehensively summarizes site-specific recombinases across enzyme categories, structural mechanisms, key characteristics of individual recombinases, recombination models, engineering strategies, and diverse functional applications. We anticipate that continued discovery, characterization, and engineering of site-specific recombinases will further accelerate the development of synthetic biology and support the establishment of more robust, versatile, and practical genetic toolboxes for future applications.