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Construction of a Suppressor Logic Toolkit for Bacterial Quasi-Hash Function

This project aims to build a tRNA suppressor logic gate toolkit with AND, NAND, OR, and NOR functions for use in a bacterial quasi-hash function. The toolkit includes both basic and specific design gates, utilizing cell-to-cell signaling and time-delayed growth mechanisms. Using various suppressor logics, distinct quasi-hash functions will be constructed, enhancing the versatility of genetic circuit design. Key goals include developing new gate designs and integrating different genetic components to achieve desired outputs.

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Construction of a Suppressor Logic Toolkit for Bacterial Quasi-Hash Function

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  1. Construction of a Suppressor Logic Toolkit and its use in a Bacterial Quasi-Hash Function iGEM 2008 Finisher Team Bob Cool, Kin Lau, Xiao Zhu

  2. Goals for 2009 Summer Project • Build tRNA suppressor logic gate tool kit with AND, NAND, OR, and NOR logic gate functions • AND gate is same basic design as in Anderson 2007, but with different parts, including 5-base frameshift suppressor instead of termination suppressor • NAND, OR, and NOR gates are new designs • Use the logic gates to construct two distinct quasi-hash functions using cell-to-cell signaling and time-delayed growth

  3. Suppressor Logic Toolkit Basic design, no specific inputs or outputs

  4. AND Gate Using SSL PoPS Input A Frameshift Suppressor tRNA PoPS Output AGGA OFF to ON PoPS Input B Activator Note: This design was used by Anderson et al. (2007) with a termination suppressor tRNA

  5. NAND Gate Using SSL PoPS Input A Frameshift Suppressor tRNA PoPS Output AGGA ON to OFF PoPS Input B Repressor

  6. OR Gate Using SSL GACC gg CGGA PoPS Input A Frameshift Suppressor 1 Activator PoPS Output OFF to ON Frameshift Suppressor 2 PoPS Input B

  7. NOR Gate Using SSL GACC gg CGGA PoPS Input A Frameshift Suppressor ! Repressor PoPS Output OFF to ON Frameshift Suppressor 2 PoPS Input B

  8. Suppressor Logic Toolkit Specific inputs and outputs

  9. AND Gate Using SSL plac Input A pluxT IPTG 5 bp Frameshift Suppressor tRNA LuxI Output 3OC6 AGCGA OFF to ON ptet Input B aTc Activator luxO • Other Genes Needed • LacI • TetR

  10. NAND Gate Using SSL pluxR Input A 5 bp Frameshift Suppressor tRNA pcI 3OC6 GFP Output AGGA ON to OFF pPrpB Input B Repressor cI Propionate • Other Genes Needed • LuxR • PrpR

  11. OR Gate Using SSL GACC gg CGGA plac Input A 5 bp Frameshift Suppressor 1 pluxT IPTG Activator luxO luxI Output OFF to ON 5 bp Frameshift Suppressor 2 ptet Input B aTc • Other Genes Needed • LacI • TetR

  12. NOR Gate Using SSL GACC gg CGGA pLuxR Input A Frameshift Suppressor ! pcI 3OC6 Repressor cI GFP Output OFF to ON Frameshift Suppressor 2 PprpB Input B Propionate • Other Genes Needed • LuxR • PrpR

  13. Suppressor Logic Toolkit Experimental design

  14. Biological Quasi-Hash Function NAND colony AmpS message Key AND colony AmpR aTc IPTG 3CO6 Growth propionate GFP RFP or Hash Value

  15. Biological Quasi-Hash Function NOR message Key OR colony AmpR aTc IPTG 3CO6 Time- delayed growth propionate colony AmpS GFP RFP or Hash Value

  16. References • Anderson et al. 2007. “Environmental signal integration by a modular AND gate” http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1964800&blobtype=pdf • luxO luxT http://www.jbc.org/cgi/content/full/281/46/34775 • PprpB propionate http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16269719

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