Difference between revisions of "Part:BBa M50055:Design"

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===Design Notes===
 
===Design Notes===
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We added an eGFP sequence downstream of our atrazine riboswitch so the the riboswitch would control translation of the eGFP.
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We added an eGFP sequence taken from BBa_K598009 downstream of our atrazine riboswitch (BBa_M50048) so that the riboswitch would control translation of the eGFP. When we ordered the construct, DNA 2.0 also added an IPTG-inducible promoter to the beginning of our sequence. Typically, an RBS follows the promoter that is added to a plasmid. However, in this situation an RBS would be redundant and interfere with our riboswitch function; if there is an RBS before the UTR and aptamer, a ribosome could bind there and disrupt the shape of the riboswitch. For this reason, it was necessary to request a custom plasmid design that did not include the standard RBS.
  
 
===Source===
 
===Source===
  
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Riboswitch components: BBa_J89000
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Riboswitch components: BBa_K784005
  
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Atrazine aptamer: Williams, R., Crihfield, C., Gattu, S., Holland, L., & Sooter, L. (2014). In Vitro Selection of a Single-Stranded DNA Molecular Recognition Element against Atrazine. IJMS International Journal of Molecular Sciences, 15(8), 14332-14347. doi:10.3390/ijms150814332
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Atrazine aptamer: In Vitro Selection of a Single-Stranded DNA Molecular Recognition Element against Atrazine, IJMS International Journal of Molecular Sciences
  
 
eGFP sequence: BBa_K598009
 
eGFP sequence: BBa_K598009
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https://parts.igem.org/Part:BBa_K598009
 
https://parts.igem.org/Part:BBa_K598009
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<BR>
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<BR>
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https://parts.igem.org/Part:BBa_K784005
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Williams, R., Crihfield, C., Gattu, S., Holland, L., & Sooter, L. (2014). In Vitro Selection of a Single-Stranded DNA Molecular Recognition Element against Atrazine. IJMS International Journal of Molecular Sciences, 15(8), 14332-14347. doi:10.3390/ijms150814332
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<BR>
 +
<BR>
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Wang, X. C., Wilson, S. C., & Hammond, M. C. (2016). Next-generation RNA-based fluorescent biosensors enable anaerobic detection of cyclic di-GMP. Nucleic Acids Research, 44(17). doi:10.1093/nar/gkw580
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<BR>
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<BR>
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Wang L, Chen W, Xu D, Shim BS, Zhu Y, Sun F, Liu L, Peng C, Jin Z, Xu C, Kotov N. Nano Lett. 2009, 9(12), 4147-4152
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<BR>
 +
<BR>
 +
Song, Y., Zhang, D., Polizzi, K., Zhang, E., Li, G., & Huang, W. (2012). Bacterial Whole Cell Bioreporters in Environmental Health. Biosensors and Environmental Health, 127-148. doi:10.1201/b12775-9
 +
<BR>
 +
<BR>
 +
Park, M., Tsai, S., & Chen, W. (2013). Microbial Biosensors: Engineered Microorganisms as the Sensing Machinery. Sensors, 13(5), 5777-5795. doi:10.3390/s130505777
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<BR>
 +
<BR>
 +
Rai, N., Ferreiro, A., Neckelmann, A., Soon, A., Yao, A., Siegel, J., . . . Tagkopoulos, I. (2015). RiboTALE: A modular, inducible system for accurate gene expression control. Sci. Rep. Scientific Reports, 5, 10658. doi:10.1038/srep10658
 +
<BR>
 +
<BR>
 +
Williams, R., Crihfield, C., Gattu, S., Holland, L., & Sooter, L. (2014). In Vitro Selection of a Single-Stranded DNA Molecular Recognition Element against Atrazine. IJMS International Journal of Molecular Sciences, 15(8), 14332-14347. doi:10.3390/ijms150814332

Latest revision as of 01:32, 12 December 2018


Atrazine biosensor


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 760


Design Notes

We added an eGFP sequence taken from BBa_K598009 downstream of our atrazine riboswitch (BBa_M50048) so that the riboswitch would control translation of the eGFP. When we ordered the construct, DNA 2.0 also added an IPTG-inducible promoter to the beginning of our sequence. Typically, an RBS follows the promoter that is added to a plasmid. However, in this situation an RBS would be redundant and interfere with our riboswitch function; if there is an RBS before the UTR and aptamer, a ribosome could bind there and disrupt the shape of the riboswitch. For this reason, it was necessary to request a custom plasmid design that did not include the standard RBS.

Source

Riboswitch components: BBa_K784005

Atrazine aptamer: In Vitro Selection of a Single-Stranded DNA Molecular Recognition Element against Atrazine, IJMS International Journal of Molecular Sciences

eGFP sequence: BBa_K598009

References

https://parts.igem.org/Part:BBa_K598009

https://parts.igem.org/Part:BBa_K784005

Wang, X. C., Wilson, S. C., & Hammond, M. C. (2016). Next-generation RNA-based fluorescent biosensors enable anaerobic detection of cyclic di-GMP. Nucleic Acids Research, 44(17). doi:10.1093/nar/gkw580

Wang L, Chen W, Xu D, Shim BS, Zhu Y, Sun F, Liu L, Peng C, Jin Z, Xu C, Kotov N. Nano Lett. 2009, 9(12), 4147-4152

Song, Y., Zhang, D., Polizzi, K., Zhang, E., Li, G., & Huang, W. (2012). Bacterial Whole Cell Bioreporters in Environmental Health. Biosensors and Environmental Health, 127-148. doi:10.1201/b12775-9

Park, M., Tsai, S., & Chen, W. (2013). Microbial Biosensors: Engineered Microorganisms as the Sensing Machinery. Sensors, 13(5), 5777-5795. doi:10.3390/s130505777

Rai, N., Ferreiro, A., Neckelmann, A., Soon, A., Yao, A., Siegel, J., . . . Tagkopoulos, I. (2015). RiboTALE: A modular, inducible system for accurate gene expression control. Sci. Rep. Scientific Reports, 5, 10658. doi:10.1038/srep10658

Williams, R., Crihfield, C., Gattu, S., Holland, L., & Sooter, L. (2014). In Vitro Selection of a Single-Stranded DNA Molecular Recognition Element against Atrazine. IJMS International Journal of Molecular Sciences, 15(8), 14332-14347. doi:10.3390/ijms150814332