Difference between revisions of "Part:BBa K3431023"
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<partinfo>BBa_K3431023 short</partinfo>
 
<partinfo>BBa_K3431023 short</partinfo>
  
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Toehold Switch with Invertase as Expression Protein (zr31) is an RNA-based device that is to apply as a biosensor for miRNA. This biosensor is designed to detect and reflect the amount of miRNA-31 through the expression of Beta-Fructosidase (Thermotoga Maritima MSB8) (BBa_K3431000), which can convert sucrose into glucose in a time-saving process and its result can be easily represented in the readout of glucose meter. The mechanism for detection relied on the following part - Toehold Switch for miRNA-31 (zr31) (BBa_K3431007) - whose restriction on the expression of invertase can be liberated upon binding with miRNA-31. Furthermore, we include T7 promoter (BBa_I719005) and terminator (BBa_K731721) to ensure that our device can transcribe and translate in the environment of PURExpress in vitro protein synthesis kit.
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===Description===
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===Experiment result===
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zr31_ToeholdSwitch-Regulated Invertase is a genetic device that can be applied as a biosensor for miR-31, which is a biomarker of oral squamous cell carcinoma (OSCC)<sup>[1][2][3][4]</sup>.This part consists of 4 basic parts: T7 promoter (BBa_I719005), zr31 Toehold Switch (BBa_K3431007), <i>Thermotoga maritima</i> Invertase (BBa_K3431000), and T7 terminator (BBa_K731721).
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The mechanism of the detection is mainly based on the regulatory part, zr31 Toehold Switch for miR-31 Detection (BBa_K3431007). When the miR-31 binds with the trigger binding site of the toehold, the hairpin structure can be opened up and the ribosomes can bind with the RBS, triggering the translation of the downstream reporter, invertase (BBa_K3431000). The invertase can convert sucrose to glucose, which can be easily measured by a personal glucose meter (PGM).
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As for the T7 promoter (BBa_I719005) and T7 terminator (BBa_K731721), they are the essential genetic elements for the in vitro gene expression with PURExpress® In Vitro Protein Synthesis Kit (New England Biolabs).
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<br><br>
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===Construction===
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The construction process of the composite part is shown below.
 
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<div style="width=100%; display:flex; align-items: center; justify-content: center">
 
<div style="width=100%; display:flex; align-items: center; justify-content: center">
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<img src="https://static.igem.org/mediawiki/parts/0/05/T--CSMU_Taiwan--EXP_4-1_31.png" style="width:100%">
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<img src="https://static.igem.org/mediawiki/parts/3/37/T--CSMU_Taiwan--Fig._6_%28In_fusion_cloning%29.png" style="width:50%">
 
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Figure. 1. Gene cloning of the toehold switch regulated invertase. (A) Using PCR to produce the target insert, which includes invertase and T7 terminator sequences. The forward primer contained XbaI and overlapped with the 5’ end of the invertase; while the reverse primer contained PstI and was complementary to the 3’ end of the T7 terminator. (B) Lane 1 to 8 are the toehold switch vectors digested with XbaI and PstI, whose length is about 2000 bp. Lane 9 is the Insert containing invertase and T7 terminator, whose length is 1358 bp. (C) Ligate the invertase sequence with the toehold switches we designed.
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<br><br>
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</html>
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===Response in different miRNA===
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To further understand the functionality of the genetic device, 2020 iGEM CSMU-Taiwan conducted a series of tests.
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The plasmids were transcribed and translated with the PURExpress® In Vitro Protein Synthesis Kit (New England Biolabs) at 37℃ for 2 hours. We would then add 5μl of 0.5M sucrose, and measured the glucose concentration with Bionime Rightest™ GM550 glucose meter after 30 minutes of enzymatic reaction time.
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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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<div style="width=100%; display:flex; align-items: center; justify-content: center">
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<img src="https://static.igem.org/mediawiki/parts/3/3d/T--CSMU_Taiwan--zr31_%28BBa_K3431023%29.png" style="width:50%">
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</div>
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Figure 2. The glucose productions of the zr31 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-31 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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<b>Results</b><br>
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The glucose concentration in the ON state with miR-31 is 310.67 mg/dL, indicating the high sensitivity of the toehold switch. The ON/OFF ratio with miR-31 is 2.65, which suggested the regulatory function of the toehold switch. By contrast, in the experiment of negative selection, the ON/OFF ratios with miR-191 and miR-223 are 1.46 and 1.21, respectively. These ratios are close to 1, meaning the zr31 toehold switch has high specificity. As a result, zr31_ToeholdSwitch-Regulated Invertase has been proven to be useful for miR-31 detection.<br><br>
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===Response under different amounts of trigger ===
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To understand the correlation of the trigger amount and the glucose production, we added different amounts of miR-31 to the protein synthesis kit and produced the proteins at 37℃ for 2 hours. We would then add 5μl of 0.5M sucrose and measured the glucose concentration with the glucose meter after 30 minutes.
 
<html>
 
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<div style="width=100%; display:flex; align-items: center; justify-content: center">
 
<div style="width=100%; display:flex; align-items: center; justify-content: center">
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<img src="https://static.igem.org/mediawiki/parts/8/86/T--CSMU_Taiwan--EXP_4-2_31.png" style="width:100%">
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<img src="https://static.igem.org/mediawiki/parts/b/b7/T--CSMU_Taiwan--EXP_5_zr31_.png" style="width:50%">
 
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Fig. 3. Glucose production under different amounts of miR-31.
 
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<b>Results</b><br>
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As shown above, the glucose concentration rose as the miR-31 triggers increased, representing a positive correlation.<br><br>
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===Reference===
 
===Reference===
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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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1. Liu, C.-J., Lin, S.-C., Yang, C.-C., Cheng, H.-W., & Chang, K.-W. (2011). Exploiting salivary miR-31 as a clinical biomarker of oral squamous cell carcinoma. Head & Neck, 34(2), 219–224. https://doi.org/10.1002/hed.21713<br>
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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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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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2. Mazumder, S., Datta, S., Ray, J. G., Chaudhuri, K., & Chatterjee, R. (2019). Liquid biopsy: miRNA as a potential biomarker in oral cancer. Cancer epidemiology, 58, 137–145. https://doi.org/10.1016/j.canep.2018.12.008<br>
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3. Min, A., Zhu, C., Peng, S., Rajthala, S., Costea, D. E., & Sapkota, D. (2015). MicroRNAs as Important Players and Biomarkers in Oral Carcinogenesis. BioMed Research International, 2015, 1–10. https://doi.org/10.1155/2015/186904<br>
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4. Momen-Heravi, F., Trachtenberg, A. J., Kuo, W. P., & Cheng, Y. S. (2014). Genomewide Study of Salivary MicroRNAs for Detection of Oral Cancer. Journal of Dental Research, 93(7_suppl), 86S-93S. https://doi.org/10.1177/0022034514531018<br>
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Latest revision as of 01:33, 28 October 2020


zr31_ToeholdSwitch-Regulated Invertase

Description

zr31_ToeholdSwitch-Regulated Invertase is a genetic device that can be applied as a biosensor for miR-31, which is a biomarker of oral squamous cell carcinoma (OSCC)[1][2][3][4].This part consists of 4 basic parts: T7 promoter (BBa_I719005), zr31 Toehold Switch (BBa_K3431007), Thermotoga maritima Invertase (BBa_K3431000), and T7 terminator (BBa_K731721). The mechanism of the detection is mainly based on the regulatory part, zr31 Toehold Switch for miR-31 Detection (BBa_K3431007). When the miR-31 binds with the trigger binding site of the toehold, the hairpin structure can be opened up and the ribosomes can bind with the RBS, triggering the translation of the downstream reporter, invertase (BBa_K3431000). The invertase can convert sucrose to glucose, which can be easily measured by a personal glucose meter (PGM). As for the T7 promoter (BBa_I719005) and T7 terminator (BBa_K731721), they are the essential genetic elements for the in vitro gene expression with PURExpress® In Vitro Protein Synthesis Kit (New England Biolabs).

Construction

The construction process of the composite part is shown below.

Figure. 1. Gene cloning of the toehold switch regulated invertase. (A) Using PCR to produce the target insert, which includes invertase and T7 terminator sequences. The forward primer contained XbaI and overlapped with the 5’ end of the invertase; while the reverse primer contained PstI and was complementary to the 3’ end of the T7 terminator. (B) Lane 1 to 8 are the toehold switch vectors digested with XbaI and PstI, whose length is about 2000 bp. Lane 9 is the Insert containing invertase and T7 terminator, whose length is 1358 bp. (C) Ligate the invertase sequence with the toehold switches we designed.

Response in different miRNA

To further understand the functionality of the genetic device, 2020 iGEM CSMU-Taiwan conducted a series of tests. The plasmids were transcribed and translated with the PURExpress® In Vitro Protein Synthesis Kit (New England Biolabs) at 37℃ for 2 hours. We would then add 5μl of 0.5M sucrose, and measured the glucose concentration with Bionime Rightest™ GM550 glucose meter after 30 minutes of enzymatic reaction time. 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 2. The glucose productions of the zr31 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-31 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 glucose concentration in the ON state with miR-31 is 310.67 mg/dL, indicating the high sensitivity of the toehold switch. The ON/OFF ratio with miR-31 is 2.65, which suggested the regulatory function of the toehold switch. By contrast, in the experiment of negative selection, the ON/OFF ratios with miR-191 and miR-223 are 1.46 and 1.21, respectively. These ratios are close to 1, meaning the zr31 toehold switch has high specificity. As a result, zr31_ToeholdSwitch-Regulated Invertase has been proven to be useful for miR-31 detection.

Response under different amounts of trigger

To understand the correlation of the trigger amount and the glucose production, we added different amounts of miR-31 to the protein synthesis kit and produced the proteins at 37℃ for 2 hours. We would then add 5μl of 0.5M sucrose and measured the glucose concentration with the glucose meter after 30 minutes.

Fig. 3. Glucose production under different amounts of miR-31.
Results
As shown above, the glucose concentration rose as the miR-31 triggers increased, representing a positive correlation.

Reference

1. Liu, C.-J., Lin, S.-C., Yang, C.-C., Cheng, H.-W., & Chang, K.-W. (2011). Exploiting salivary miR-31 as a clinical biomarker of oral squamous cell carcinoma. Head & Neck, 34(2), 219–224. https://doi.org/10.1002/hed.21713

2. Mazumder, S., Datta, S., Ray, J. G., Chaudhuri, K., & Chatterjee, R. (2019). Liquid biopsy: miRNA as a potential biomarker in oral cancer. Cancer epidemiology, 58, 137–145. https://doi.org/10.1016/j.canep.2018.12.008

3. Min, A., Zhu, C., Peng, S., Rajthala, S., Costea, D. E., & Sapkota, D. (2015). MicroRNAs as Important Players and Biomarkers in Oral Carcinogenesis. BioMed Research International, 2015, 1–10. https://doi.org/10.1155/2015/186904

4. Momen-Heravi, F., Trachtenberg, A. J., Kuo, W. P., & Cheng, Y. S. (2014). Genomewide Study of Salivary MicroRNAs for Detection of Oral Cancer. Journal of Dental Research, 93(7_suppl), 86S-93S. https://doi.org/10.1177/0022034514531018


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 1426
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 1197
    Illegal BamHI site found at 1327
    Illegal XhoI site found at 1398
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal AgeI site found at 998
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 529