Difference between revisions of "Part:BBa K3431003"
 
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<partinfo>BBa_K3431003 short</partinfo>
 
<partinfo>BBa_K3431003 short</partinfo>
  
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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 region of loop 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) . 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.
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===Introduction===
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zp21_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.
  
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NUPACK ANALYSIS  <br>
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===Design===
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https://static.igem.org/mediawiki/parts/4/49/T--CSMU_Taiwan--zp21_B_NU.png
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The design of the toehold switch was mainly based on the previous research<sup>[1][2][3][4][5][6]</sup>. For the zp21_B toehold switch, we adopted the loop structure from
 +
Green et al., 2016<sup>[7]</sup>, and the linker structure is from Wang et al., 2019<sup>[8]</sup>. 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) 
  
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VIENNA RNA PACKAGE <br>
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<html>
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https://static.igem.org/mediawiki/parts/8/8c/T--CSMU_Taiwan--zp21_B_Ve.png  
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<br>
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<figure style="mirgin-right: 1em; float:left; width:40%; border:1px solid black">
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<img src="https://static.igem.org/mediawiki/parts/4/49/T--CSMU_Taiwan--zp21_B_NU.png" style="display: block;margin-left: auto;margin-right: auto; width: 70%">
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<figcaption style="text-align: center;">
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Figure 1. NUPACK analysis result
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</figcaption>
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</figure>
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</div>
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<figure style="mirgin-right: 1em; float:left; width:40%; border:1px solid black">
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<img src="https://static.igem.org/mediawiki/parts/8/8c/T--CSMU_Taiwan--zp21_B_Ve.png" style="display: block;margin-left: auto;margin-right: auto; width: 100%">
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<figcaption style="text-align: center;">
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Figure 2. ViennaRNA Package result
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</figcaption>
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</figure>
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</html>
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<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
  
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Link to our model page: https://2020.igem.org/Team:CSMU_Taiwan/Model
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===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”.
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<html>
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<br>
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<div style="width=100%; display:flex; align-items: center; justify-content: center">
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<img src="https://static.igem.org/mediawiki/parts/d/d1/T--CSMU_Taiwan--zp21_B_%28BBa_K3431018%29.png" style="width:50%">
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</div>
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Figure 3. The glucose productions of the zp21_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).
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<br>
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</html>
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<br>
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<b>Results</b> The ON/OFF ratio with miR-21 is 0.99, which suggested the leakage problem. The regulatory function of the zp21_B toehold switch was not good
 +
enough. Thus, zp21_B toehold switch-regulated invertase cannot be well controlled by the miR-21.
  
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References:
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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.
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===Information contributed by City of London UK (2021)===
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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.
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[[File:ToeholdTools.png|x200px|center]]
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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.
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This toehold switch was characterized <i>in silico</i> using the ToeholdTools project that our team developed.
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See https://github.com/lkn849/thtools for more information.
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 +
Metadata:
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*'''Group:''' City of London UK 2021
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*'''Author:''' Lucas Ng
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*'''Summary:''' Used our software ToeholdTools to investigate the target miRNA specificity and activation of this part.
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Raw data:
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*[[Media:BBa_K3431003_thtest.txt]]
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*[[Media:BBa_K3431003_crt.txt]]
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This contribution was autogenerated by the script '''contrib.py''', available at https://github.com/lkn849/thtools/tree/master/registry.
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 +
----
 +
 
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This switch was designed to detect the miRNA hsa-miR-21-5p at a temperature of 37°C.
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We tested it against every mature <i>Homo sapiens</i> miRNA in miRBase and our analysis shows that at this temperature it is best used to detect hsa-miR-4729.
 +
 
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With hsa-miR-4729 at 37°C, the switch has a specificity of 35 ± Infinity % and an activation of 0.0 ± 0.3 %.
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These values represent 95% confidence limits (z=1.96).
 +
 
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The temperature&ndash;activation&ndash;specificity relationship is shown here.
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CRT is an acronym for CelsiusRangeTest, the class in our Python library responsible for the following graph:
 +
 
 +
[[File:BBa_K3431003_graph.png|500px|center]]
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Error bars represent the standard deviation.
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The line of best fit was calculated using a univariate cubic spline weighted inverse to each point's standard error.
 +
 
 +
'''Caveats:'''
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*As per the above, we cannot confirm that this switch accurately detects the desired miRNA sequence.
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We do not recommend this part for future usage.
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<!-- Add more about the biology of this part here
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===Usage and Biology===
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===References===
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1. Green, A. A., Silver, P. A., Collins, J. J., &amp; Yin, P. (2014).Toehold switches: de-novo-designed regulators of gene expression. Cell, 159(4), 925–939.
 +
https://doi.org/10.1016/j.cell.2014.10.002
 +
 
 +
2. Green, A. A., Kim, J., Ma, D., Silver, P. A., Collins, J. J., &amp; Yin, P. (2017).Complex cellular logic computation using ribocomputing devices. Nature,548(7665), 117–121. https://doi.org/10.1038/nature23271
 +
 
 +
3. Pardee, K., Green, A. A., Takahashi, M. K., Braff, D., Lambert, G., Lee, J.W., Ferrante, T., Ma, D., Donghia, N., Fan, M., Daringer, N. M., Bosch, I.,Dudley, D. M., O&#39;Connor, D. H., Gehrke, L., &amp; Collins, J. J. (2016). Rapid,Low-Cost Detection of Zika Virus Using Programmable BiomolecularComponents. Cell, 165(5), 1255–1266.
 +
https://doi.org/10.1016/j.cell.2016.04.059
 +
 
 +
4. Chappell, J., Westbrook, A., Verosloff, M., &amp; Lucks, J. B. (2017).Computational design of small transcription activating RNAs for versatile and
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dynamic gene regulation. Nature communications, 8(1), 1051.https://doi.org/10.1038/s41467-017-01082-6
 +
 
 +
5. Sadat Mousavi, P., Smith, S. J., Chen, J. B., Karlikow, M., Tinafar, A.,Robinson, C., Liu, W., Ma, D., Green, A. A., Kelley, S. O., &amp; Pardee, K.(2020). A multiplexed, electrochemical interface for gene-circuit-based sensors. Nature chemistry, 12(1), 48–55. https://doi.org/10.1038/s41557-019-0366-y
 +
 
 +
6. Hong, F., Ma, D., Wu, K., Mina, L. A., Luiten, R. C., Liu, Y., Yan, H., &amp;Green, A. A. (2020). Precise and Programmable Detection of Mutations Using Ultraspecific Riboregulators. Cell, 180(5), 1018–1032.e16.https://doi.org/10.1016/j.cell.2020.02.011
 +
 
 +
7. Pardee K, Green AA, Takahashi MK, et al. Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components. Cell 2016;165(5): 1255-66. 
 +
 
 +
8. Shue Wang, Nicholas J Emery, Allen P Liu. A Novel Synthetic Toehold Switch for microRNA Detection in Mammalian Cells. ACS Synthetic Biology 2019; 8 (5): 1079-1088.
  
 
<!-- Add more about the biology of this part here
 
<!-- Add more about the biology of this part here

Latest revision as of 19:07, 13 October 2021


zp21_B Toehold Switch for miR-21 Detection

Introduction

zp21_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 zp21_B toehold switch, we adopted the loop structure from Green et al., 2016[7], and the linker structure is from Wang et al., 2019[8]. 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)


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 zp21_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 0.99, which suggested the leakage problem. The regulatory function of the zp21_B toehold switch was not good enough. Thus, zp21_B toehold switch-regulated invertase cannot be well controlled by the miR-21.


Information contributed by City of London UK (2021)

ToeholdTools.png

This toehold switch was characterized in silico using the ToeholdTools project that our team developed. See https://github.com/lkn849/thtools for more information.

Metadata:

  • Group: City of London UK 2021
  • Author: Lucas Ng
  • Summary: Used our software ToeholdTools to investigate the target miRNA specificity and activation of this part.

Raw data:

This contribution was autogenerated by the script contrib.py, available at https://github.com/lkn849/thtools/tree/master/registry.

This switch was designed to detect the miRNA hsa-miR-21-5p at a temperature of 37°C. We tested it against every mature Homo sapiens miRNA in miRBase and our analysis shows that at this temperature it is best used to detect hsa-miR-4729.

With hsa-miR-4729 at 37°C, the switch has a specificity of 35 ± Infinity % and an activation of 0.0 ± 0.3 %. These values represent 95% confidence limits (z=1.96).

The temperature–activation–specificity relationship is shown here. CRT is an acronym for CelsiusRangeTest, the class in our Python library responsible for the following graph:

BBa K3431003 graph.png

Error bars represent the standard deviation. The line of best fit was calculated using a univariate cubic spline weighted inverse to each point's standard error.

Caveats:

  • As per the above, we cannot confirm that this switch accurately detects the desired miRNA sequence.

We do not recommend this part for future usage.

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]