Difference between revisions of "Part:BBa K3431032"

(→‎Experiment result)
Line 3: Line 3:
 
<partinfo>BBa_K3431032 short</partinfo>
 
<partinfo>BBa_K3431032 short</partinfo>
  
−
===Description===
+
===Introduction===
−
This toehold switch has been designed to open up its hairpin loop structure upon binding with miRNA-21, resulting in the translation of downstream reporter protein. The design of toehold switch can be separated into the following 5 regions from its 5' end: trigger binding sites, stem region, loop region with RBS, complimentary stem region with start codon, and linker amino acids. In our constructions of toehold switches for miRNA-21, we optimised the loop region with RBS and linker amino acids based on three articles: the original work on toehold switch (Green, A.A. et al., 2014), the adaptation of toehold switch to detect zika virus (Pardee, K. et al., 2016), and novel toehold switch design for detection of miRNA in mammalian cells (Wang, S. et al., 2019) . The loop structure from the article of Pardee, K. et al. has been truncated to 12 base pairs compared to the work from Green, A.A. et al. in order to reduce the leakage of output expression. We chose to test the 3 different loop structures and 2 different linker structures (Pardee, K. et al. and Wang, S. et al.) from the above-mentioned studies.
+
zz21_B toehold switch is a regulatory part for the downstream reporter gene. With this part, the protein expression can be controlled by the miR-21. The sequence of the toehold switch can be separated into the following 5 regions from its 5&#39; end: TBS (trigger binding site), stem region, loop region with RBS(ribosome binding site), complimentary stem region with a start codon, and linker. Upon binding with miR-21, its hairpin structure can be opened up and the ribosomes can bind with its RBS (ribosome binding site), triggering the
 +
translation of the downstream reporter.
  
−
For this particular toehold switch (zz21_B), we incorporate the loop and linker structure from the work of Pardee, K. et al.
+
===Design===
 +
The design of the toehold switch was mainly based on the previous research. 1 2 3 4 5 6 For the zz21_B toehold switch, we adopted the loop and the linker structure from Green et al., 2016 7 . Using NUPACK analysis and Vienna binding models, we designed the sequence of the toehold switch.  
 +
(See our model page: https://2020.igem.org/Team:CSMU_Taiwan/Model )
  
 
===Model===
 
===Model===
 
<html>
 
<html>
 
<br>
 
<br>
−
NUPACK ANALYSIS <br>
+
<figure style="mirgin-right: 1em; float:left; width:40%; border:1px solid black">
−
<div style="width=100%; display:flex; align-items: center; justify-content: center;">
+
<img src="https://static.igem.org/mediawiki/parts/a/a1/T--CSMU_Taiwan--zz21_B_NU.png" style="display: block;margin-left: auto;margin-right: auto; width: 70%">
−
<img src="https://static.igem.org/mediawiki/parts/a/a1/T--CSMU_Taiwan--zz21_B_NU.png" style="width:50%;">
+
<figcaption style="text-align: center;">
 +
Figure 1. NUPACK analysis result
 +
</figcaption>
 +
</figure>
 
</div>
 
</div>
−
<br>
+
<figure style="mirgin-right: 1em; float:left; width:40%; border:1px solid black">
−
</html>
+
<img src="https://static.igem.org/mediawiki/parts/2/20/T--CSMU_Taiwan--zz21_B_Ve.png" style="display: block;margin-left: auto;margin-right: auto; width: 100%">
−
VIENNA RNA PACKAGE <br>
+
<figcaption style="text-align: center;">
−
<html>
+
Figure 2. ViennaRNA Package result
−
<div style="width=100%; display:flex; align-items: center; justify-content: center;">
+
</figcaption>
−
<img src="https://static.igem.org/mediawiki/parts/2/20/T--CSMU_Taiwan--zz21_B_Ve.png" style="width:50%;">
+
</figure>
−
</div>
+
−
<br>
+
 
</html>
 
</html>
−
Link to our model page: https://2020.igem.org/Team:CSMU_Taiwan/Model
+
<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
  
−
===Experiment result===
+
===Characrterization using invertase===
 +
The 2020 iGEM CSMU-Taiwan characterized the toehold switch with invertase (BBa_K3431000) reporter protein. The plasmid would be transcribed and translated with the protein synthesis kit at 37℃ for 2 hours. We would then add 5μl of 0.5M sucrose and measured the glucose concentration with Rightest TM GS550 glucose meter after 30 minutes. In our
 +
experiments, the ON state refers to the conditions with miRNA triggers; while the OFF state means that there was no miRNA in the environment. We calculated the ON/OFF ratio of the toehold switch, which is defined as “the glucose concentration of the ON state/ the glucose concentration of the OFF state”.
 
<html>
 
<html>
 
<br>
 
<br>
Line 32: Line 38:
 
<img src="https://static.igem.org/mediawiki/parts/6/68/T--CSMU_Taiwan--zz21_B_(BBa_K3431041).png" style="width:50%">
 
<img src="https://static.igem.org/mediawiki/parts/6/68/T--CSMU_Taiwan--zz21_B_(BBa_K3431041).png" style="width:50%">
 
</div>
 
</div>
 +
Figure 3. The glucose productions of the zz21_B toehold switch-regulated invertase in different states. The blue bar refers to the OFF state (not added with miRNA). The green bar refers to the ON state (added with miR-21 trigger). The yellow bar refers to the state with non-related RNAs (added with miR-191). The pink bar refers to the state with non-related RNAs (added with miR-223).
 
<br>
 
<br>
 
</html>
 
</html>
 +
<br>
 +
<b>Results</b>  The ON/OFF ratio with miR-21 is 1.32, which suggested the regulatory function of the toehold switch. Thus, zz21_B toehold switch-regulated invertase can be controlled by the miR-21.
  
 
===References===
 
===References===

Revision as of 17:21, 25 October 2020


zz21_B Toehold Switch for miR-21 Detection

Introduction

zz21_B toehold switch is a regulatory part for the downstream reporter gene. With this part, the protein expression can be controlled by the miR-21. The sequence of the toehold switch can be separated into the following 5 regions from its 5' end: TBS (trigger binding site), stem region, loop region with RBS(ribosome binding site), complimentary stem region with a start codon, and linker. Upon binding with miR-21, its hairpin structure can be opened up and the ribosomes can bind with its RBS (ribosome binding site), triggering the translation of the downstream reporter.

Design

The design of the toehold switch was mainly based on the previous research. 1 2 3 4 5 6 For the zz21_B toehold switch, we adopted the loop and the linker structure from Green et al., 2016 7 . Using NUPACK analysis and Vienna binding models, we designed the sequence of the toehold switch. (See our model page: https://2020.igem.org/Team:CSMU_Taiwan/Model )

Model


Figure 1. NUPACK analysis result
Figure 2. ViennaRNA Package result

















Characrterization using invertase

The 2020 iGEM CSMU-Taiwan characterized the toehold switch with invertase (BBa_K3431000) reporter protein. The plasmid would be transcribed and translated with the protein synthesis kit at 37℃ for 2 hours. We would then add 5μl of 0.5M sucrose and measured the glucose concentration with Rightest TM GS550 glucose meter after 30 minutes. In our experiments, the ON state refers to the conditions with miRNA triggers; while the OFF state means that there was no miRNA in the environment. We calculated the ON/OFF ratio of the toehold switch, which is defined as “the glucose concentration of the ON state/ the glucose concentration of the OFF state”.

Figure 3. The glucose productions of the zz21_B toehold switch-regulated invertase in different states. The blue bar refers to the OFF state (not added with miRNA). The green bar refers to the ON state (added with miR-21 trigger). The yellow bar refers to the state with non-related RNAs (added with miR-191). The pink bar refers to the state with non-related RNAs (added with miR-223).

Results The ON/OFF ratio with miR-21 is 1.32, which suggested the regulatory function of the toehold switch. Thus, zz21_B toehold switch-regulated invertase can be controlled by the miR-21.

References

Green, A. A., Silver, P. A., Collins, J. J., & Yin, P. (2014). Toehold switches: de-novo-designed regulators of gene expression. Cell, 159(4), 925-939. Pardee, K., Green, A. A., Takahashi, M. K., Braff, D., Lambert, G., Lee, J. W., ... & Daringer, N. M. (2016). Rapid, low-cost detection of Zika virus using programmable biomolecular components. Cell, 165(5), 1255-1266. Wang, S., Emery, N. J., & Liu, A. P. (2019). A novel synthetic toehold switch for microRNA detection in mammalian cells. ACS synthetic biology, 8(5), 1079-1088

Sequence and Features


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]