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Nat Chem Biol. 2014 Feb;10(2):99-105. doi: 10.1038/nchembio.1411. Epub 2013 Dec 8.

Genomic mining of prokaryotic repressors for orthogonal logic gates.

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Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Department of Biochemistry and Biophysics, University of California-San Francisco, San Francisco, California, USA.
Synthetic Biology R&D Unit, Life Technologies, Carlsbad, California, USA.


Genetic circuits perform computational operations based on interactions between freely diffusing molecules within a cell. When transcription factors are combined to build a circuit, unintended interactions can disrupt its function. Here, we apply 'part mining' to build a library of 73 TetR-family repressors gleaned from prokaryotic genomes. The operators of a subset were determined using an in vitro method, and this information was used to build synthetic promoters. The promoters and repressors were screened for cross-reactions. Of these, 16 were identified that both strongly repress their cognate promoter (5- to 207-fold) and exhibit minimal interactions with other promoters. Each repressor-promoter pair was converted to a NOT gate and characterized. Used as a set of 16 NOT/NOR gates, there are >10(54) circuits that could be built by changing the pattern of input and output promoters. This represents a large set of compatible gates that can be used to construct user-defined circuits.

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