Difference between revisions of "Part:BBa M50048:Design"

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===Design Notes===
 
===Design Notes===
−
We replaced the aptamer in the original riboswitch with an aptamer that would target our molecule of interest, atrazine.
+
We replaced the aptamer in the original riboswitch with an aptamer that would target our molecule of interest, atrazine. Because the atrazine aptamer that we found was meant to function as single-stranded DNA, we used its sequence in the coding strand of our plasmid so that the RNA transcript would have similar chemical properties to the original DNA design.
  
 
===Source===
 
===Source===
Line 13: Line 13:
 
Riboswitch components: https://parts.igem.org/Part:BBa_K784005
 
Riboswitch components: https://parts.igem.org/Part:BBa_K784005
  
−
Atrazine aptamer:
+
Atrazine aptamer: In Vitro Selection of a Single-Stranded DNA Molecular Recognition Element against Atrazine, IJMS International Journal of Molecular Sciences
−
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
+
  
 
===References===
 
===References===
  
 
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
 
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
 +
<BR>
 
<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
 
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>
 
<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
 
Park, M., Tsai, S., & Chen, W. (2013). Microbial Biosensors: Engineered Microorganisms as the Sensing Machinery. Sensors, 13(5), 5777-5795. doi:10.3390/s130505777
 +
<BR>
 
<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
 
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 08:34, 12 December 2016


Atrazine riboswitch


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
    COMPATIBLE WITH RFC[1000]


Design Notes

We replaced the aptamer in the original riboswitch with an aptamer that would target our molecule of interest, atrazine. Because the atrazine aptamer that we found was meant to function as single-stranded DNA, we used its sequence in the coding strand of our plasmid so that the RNA transcript would have similar chemical properties to the original DNA design.

Source

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

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

References

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