Difference between revisions of "Part:BBa K3202059:Design"

 
 
Line 7: Line 7:
  
 
===Design Notes===
 
===Design Notes===
−
Arac-pC-pBAD-lacI-B0034-PhiC31-T500-T1/TE-MicC sRNA-sRNA Binding site-PA1/04
+
N/A
  
 +
===Source===
  
 +
Synthesized
  
 +
===References===
  
−
===Source===
+
【1】LWOFF, A. Lysogeny. Bacteriol. Rev. 17, 269–337 (1953)
  
−
Arac-pC-pBAD-lacI-B0034-PhiC31-T500-T1/TE-MicC sRNA-sRNA Binding site-PA1/04
+
【2】Campbell A. (2006) in The Bacteriophages, General aspects of lysogeny, ed Calendar R. (Oxford University Press, Oxford), 2nd edn, pp 66–73.
  
 +
【3】Myers, C. J. Engineering Genetic Circuits. 306 (CRC Press, 2009)
  
−
===References===
+
【4】Campbell A. (1962) Episomes. Adv. Genet. 11:101–145.Web of Science
 +
 
 +
【5】Azaro M.A., Landy A. (2002) in Mobile DNA II, λ integrase and the λ Int family, eds Craig N.L., Craigie R., Gellert M., Lambowitz A.M. (ASM Press, Washington, DC), pp 118–148.
 +
 
 +
【6】Yueju Wang. Recombinase technology: applications and possibilities. Plant Cell Rep. 2011 Mar; 30(3): 267–285.
 +
 
 +
【7】Gretchen Meinke. Cre Recombinase and Other Tyrosine Recombinases. Chem. Rev., 2016, 116 (20), pp 12785–12820.
 +
 
 +
【8】Grindley N D F, Whiteson K L, Rice P A. Mechanisms of site-specific recombination. Annu Rev Biochem, 2006, 75: 567—605
 +
 
 +
【9】Hsu P L, Ross W, Landy A. The λ-phage att site: functional limits and interaction with Int protein. Nature, 1980, 285: 85—91
 +
 
 +
【10】Abremski K, Gottesman S. Site-specific recombination: Xis-independent excisive recombination of bacteriophage λ. J Mol Biol, 1981, 153: 67—78
 +
 
 +
【11】Abremski K, Hoess R. Bacteriophage P1 site-specific recombination: purification and properties of the Cre recombinase protein. J Biol Chem, 1984, 259: 1509—1514
 +
 
 +
【12】Decapentaplegic and growth control in the developing Drosophila wing. Takuya Akiyama  & Matthew C. Gibson. Nature 527, 375–378 (19 November 2015) doi:10.1038/nature15730
 +
 
 +
【13】Alexandra Pokhilko et al. The mechanism of ϕC31 integrase directionality: experimental analysis and computational modelling. Nucleic Acids Research, pp. gkw616, 2016, ISSN
 +
0305-1048.
 +
 
 +
【14】Nathaniel Roquet1, Ava P. Soleimany, Alyssa C. Ferris, Scott Aaronson, Timothy K. Lu. Synthetic recombinase-based state machines in living cells. Science 22 Jul 2016: Vol. 353, Issue 6297
 +
 
 +
【15】Piro Siuti, John Yazbek, Timothy K Lu. Synthetic circuits integrating logic and memory in living cells. Nature Biotechnology 31, 448–452 (2013)
 +
 
 +
【16】Benjamin H Weinberg et al. Large-scale design of robust genetic circuits with multiple inputs and outputs for mammalian cells. Nature Biotechnology 35, 453–462 (2017) doi:10.1038/nbt.3805
 +
 
 +
【17】Jesus Fernandez-Rodriguez，Lei Yang，Thomas E. Gorochowski，D. Benjamin Gordon，Christopher A. Voigt. Memory and Combinatorial Logic Based on DNA Inversions: Dynamics and Evolutionary Stability. ACS Synth. Biol., 2015, 4 (12), pp 1361–1372.
 +
 
 +
【18】Aiba H (2007) Mechanism of RNA silencing by Hfq-binding small RNAs. Current Opinion in Microbiology
 +
 
 +
【19】Anthony LC, Suzuki H, Filutowicz M (2004) Tightly regulated vectors for the cloning and expression of toxic genes. Journal of Microbiological Methods 58: 243-250
 +
 
 +
【20】Aparicio T, de Lorenzo V, Martínez-García E (2017) Broadening the SEVA Plasmid Repertoire to Facilitate Genomic Editing of Gram-Negative Bacteria. In Hydrocarbon and Lipid Microbiology Protocols: Genetic, Genomic and System Analyses of Pure Cultures
 +
 
 +
【21】McGenity TJ, Timmis KN, Nogales B (eds), pp 9-27. Berlin, Heidelberg: Springer Berlin Heidelberg Balzer S, Kucharova V, Megerle J, Lale R, Brautaset T, Valla S (2013) A comparative analysis of the properties of regulated promoter systems commonly used for recombinant gene expression in Escherichia coli. Microbial cell factories
 +
 
 +
【22】Bervoets I, Charlier D (2019) Diversity, versatility and complexity of bacterial gene regulation mechanisms: opportunities and drawbacks for applications in synthetic biology.
 +
 
 +
【23】Lopez-Walle B, Gauthier M, Chaillet N (2008) Principle of a submerged freeze gripper for micro-assembly. IEEE Trans Robotics 24(4):897–902
 +
 
 +
【24】Rakotondrabe M, Haddab Y, Lutz P (2009) Development, modelling and control of micro/nano positionning 2 dof stick-slip device, IEEE/ASME Trans. Mechatronics 14(6):733–745
 +
 
 +
【25】M. Rakotondrabe Y. Haddab and P. Lutz, "Design, development and experiments of a high stroke-precision 2DoF (linear-angular) microsystem" in Proc. 2006 IEEE Int. Conf. on Robotics and Automation: pp. 669 - 674.

Latest revision as of 22:10, 20 October 2019


Xyls-Pc-Pm-TetR-RBS1-PhiC31-T500-T1/TE-MicCsRNA-sRNA Binding site-PLtetO


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 999
    Illegal NheI site found at 1022
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 930
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 208
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 1775
    Illegal SapI site found at 2118
    Illegal SapI site found at 2223
    Illegal SapI site found at 2281
    Illegal SapI.rc site found at 1972


Design Notes

N/A

Source

Synthesized

References

【1】LWOFF, A. Lysogeny. Bacteriol. Rev. 17, 269–337 (1953)

【2】Campbell A. (2006) in The Bacteriophages, General aspects of lysogeny, ed Calendar R. (Oxford University Press, Oxford), 2nd edn, pp 66–73.

【3】Myers, C. J. Engineering Genetic Circuits. 306 (CRC Press, 2009)

【4】Campbell A. (1962) Episomes. Adv. Genet. 11:101–145.Web of Science

【5】Azaro M.A., Landy A. (2002) in Mobile DNA II, λ integrase and the λ Int family, eds Craig N.L., Craigie R., Gellert M., Lambowitz A.M. (ASM Press, Washington, DC), pp 118–148.

【6】Yueju Wang. Recombinase technology: applications and possibilities. Plant Cell Rep. 2011 Mar; 30(3): 267–285.

【7】Gretchen Meinke. Cre Recombinase and Other Tyrosine Recombinases. Chem. Rev., 2016, 116 (20), pp 12785–12820.

【8】Grindley N D F, Whiteson K L, Rice P A. Mechanisms of site-specific recombination. Annu Rev Biochem, 2006, 75: 567—605

【9】Hsu P L, Ross W, Landy A. The λ-phage att site: functional limits and interaction with Int protein. Nature, 1980, 285: 85—91

【10】Abremski K, Gottesman S. Site-specific recombination: Xis-independent excisive recombination of bacteriophage λ. J Mol Biol, 1981, 153: 67—78

【11】Abremski K, Hoess R. Bacteriophage P1 site-specific recombination: purification and properties of the Cre recombinase protein. J Biol Chem, 1984, 259: 1509—1514

【12】Decapentaplegic and growth control in the developing Drosophila wing. Takuya Akiyama & Matthew C. Gibson. Nature 527, 375–378 (19 November 2015) doi:10.1038/nature15730

【13】Alexandra Pokhilko et al. The mechanism of ϕC31 integrase directionality: experimental analysis and computational modelling. Nucleic Acids Research, pp. gkw616, 2016, ISSN 0305-1048.

【14】Nathaniel Roquet1, Ava P. Soleimany, Alyssa C. Ferris, Scott Aaronson, Timothy K. Lu. Synthetic recombinase-based state machines in living cells. Science 22 Jul 2016: Vol. 353, Issue 6297

【15】Piro Siuti, John Yazbek, Timothy K Lu. Synthetic circuits integrating logic and memory in living cells. Nature Biotechnology 31, 448–452 (2013)

【16】Benjamin H Weinberg et al. Large-scale design of robust genetic circuits with multiple inputs and outputs for mammalian cells. Nature Biotechnology 35, 453–462 (2017) doi:10.1038/nbt.3805

【17】Jesus Fernandez-Rodriguez，Lei Yang，Thomas E. Gorochowski，D. Benjamin Gordon，Christopher A. Voigt. Memory and Combinatorial Logic Based on DNA Inversions: Dynamics and Evolutionary Stability. ACS Synth. Biol., 2015, 4 (12), pp 1361–1372.

【18】Aiba H (2007) Mechanism of RNA silencing by Hfq-binding small RNAs. Current Opinion in Microbiology

【19】Anthony LC, Suzuki H, Filutowicz M (2004) Tightly regulated vectors for the cloning and expression of toxic genes. Journal of Microbiological Methods 58: 243-250

【20】Aparicio T, de Lorenzo V, Martínez-García E (2017) Broadening the SEVA Plasmid Repertoire to Facilitate Genomic Editing of Gram-Negative Bacteria. In Hydrocarbon and Lipid Microbiology Protocols: Genetic, Genomic and System Analyses of Pure Cultures

【21】McGenity TJ, Timmis KN, Nogales B (eds), pp 9-27. Berlin, Heidelberg: Springer Berlin Heidelberg Balzer S, Kucharova V, Megerle J, Lale R, Brautaset T, Valla S (2013) A comparative analysis of the properties of regulated promoter systems commonly used for recombinant gene expression in Escherichia coli. Microbial cell factories

【22】Bervoets I, Charlier D (2019) Diversity, versatility and complexity of bacterial gene regulation mechanisms: opportunities and drawbacks for applications in synthetic biology.

【23】Lopez-Walle B, Gauthier M, Chaillet N (2008) Principle of a submerged freeze gripper for micro-assembly. IEEE Trans Robotics 24(4):897–902

【24】Rakotondrabe M, Haddab Y, Lutz P (2009) Development, modelling and control of micro/nano positionning 2 dof stick-slip device, IEEE/ASME Trans. Mechatronics 14(6):733–745

【25】M. Rakotondrabe Y. Haddab and P. Lutz, "Design, development and experiments of a high stroke-precision 2DoF (linear-angular) microsystem" in Proc. 2006 IEEE Int. Conf. on Robotics and Automation: pp. 669 - 674.