Genomic Mining of Prokaryotic Repressors for Orthogonal Logic Gates
By Brynne C. Stanton, Alec A. K. Nielsen, Alvin Tamsir, Kevin Clancy, T. Peterson, Christopher A. Voigt. Nature Chemical Biology, 2013
394 citations recorded by the source corpus.
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 do not interact with other promoters. Each repressor:promoter pair was converted to a NOT gate and characterized. Used as a set of 16 NOR gates, there are >1054 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.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/016ee71d545c269382f691a04fc0980844b14164
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Citations in the corpus
- Genetic circuit design automation (2016, methodology): “Within this paradigm, the regulators performing the gate biochemistry could be transcrip-tionfactors( 21 , 63 ),RNA-basedregulation( 64 – 66 ), protein-protein interactions ( 19 , 67 ), CRISPR/ Cas-based regulation ( 68 – 71 ), or recombinases ( 25 , 26 , 72 ).”
- Large-scale de novo DNA synthesis: technologies and applications (2014, neutral): “The Voigt lab has also applied synthetic metagenomics for part mining to find libraries of orthogonal repressors (73 synthetic genes) 105 and transcription factors (62 synthetic genes) 106 .”