Recombinase-Based Genetic Diversification Schemes

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List of publications using the transcription and translation system called shufflonSchematic of the 4-color shufflon constructs for assessing flipping efficiencies. a) unflipped, b) flipped, and c) schematic of the gBlock (all flipped amplicons) cloned into pSET152
Professor Timothy Lu
Department of Electrical Engineering and Computer Science, MIT
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Sara Cleto
Department of Biological Engineering, MIT
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Jon Gilbert
MIT Technology Licensing Officer
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Recombinase-Based Genetic Diversification Schemes

PCT Patent Application WO 2017-044476


A recombinase-based scheme to create a system that generates its own genetic diversity could be used to create novel antibiotics with minimal labor.

Problem Addressed

Currently, common approaches to antibiotic discovery are slow. One must screen for novel bacterial isolates, mix and match genes by traditional cloning, and chemically resynthesize the discovered compounds. A new approach that is less labor-intensive and increases the yield of novel compounds would greatly improve upon current methods.


This invention comprises biological system that generates its own genetic diversity by taking advantage of shufflon, a site-specific recombination system which consists of four DNA segments and seven separate recombination sites. This system was previously reported as a single piece of DNA that has the ability to recombine to create seven different open reading frames, which means that it codes for seven different combinations of proteins. The shufflon system was adapted to generate biological diversity in the pikromycin pathway, a pathway coding for enzymes that modify antibiotic synthesis. Four genes were selected from three different species of bacteria co-synthesized with shufflon in yeast artificial chromosomes. This system is currently being tested for integration into S. coelicolor bacteria, with the ultimate goal of producing new antibiotics.


  • Hands-free engineering
  • Maximization of number of possible pathways for antibiotic synthesis
  • Can undergo multiple rounds of engineering with minimal labor