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Serine Integrase Directional Recombination

The natural function of the large serine integrases (such as φC31 Integrase) is to integrate circular DNA into a bacterial host chromosome, by recombining attP with attB.

Recombination is highly directional. In the presence of the integrase alone, attP recombines efficiently with attB to form attL and attR which do not recombine further. However, in the presence of a recombination directionality factor (RDF) attL and attR recombine to re-form attP and attB.

This directional recombination can be used for a variety Synthetic Biology Applications

such as:

  • counting [1]
  • logic gates [2, 3]
  • metabolic pathway assembly (SIRA) [4]


  1. Bonnet J, Subsoontorn P, and Endy D. Rewritable digital data storage in live cells via engineered control of recombination directionality. Proc Natl Acad Sci U S A. 2012 Jun 5;109(23):8884-9. DOI:10.1073/pnas.1202344109 | PubMed ID:22615351 | HubMed [Bonnet-12]
  2. Siuti P, Yazbek J, and Lu TK. Synthetic circuits integrating logic and memory in living cells. Nat Biotechnol. 2013 May;31(5):448-52. DOI:10.1038/nbt.2510 | PubMed ID:23396014 | HubMed [Siuti]
  3. Bonnet J, Yin P, Ortiz ME, Subsoontorn P, and Endy D. Amplifying genetic logic gates. Science. 2013 May 3;340(6132):599-603. DOI:10.1126/science.1232758 | PubMed ID:23539178 | HubMed [Bonnet-13]
  4. Colloms SD, Merrick CA, Olorunniji FJ, Stark WM, Smith MC, Osbourn A, Keasling JD, and Rosser SJ. Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination. Nucleic Acids Res. 2014 Feb;42(4):e23. DOI:10.1093/nar/gkt1101 | PubMed ID:24225316 | HubMed [Colloms]
All Medline abstracts: PubMed | HubMed