Difference between revisions of "Part:BBa K3431006"
| Line 3: | Line 3: | ||
<partinfo>BBa_K3431006 short</partinfo> | <partinfo>BBa_K3431006 short</partinfo> | ||
| + | ===Description=== | ||
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. | 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. | ||
For this particular toehold switch (oz21_A), we incorporate the loop structure from Green, A.A. et al. and the linker structure from Pardee, K. et al.. | For this particular toehold switch (oz21_A), we incorporate the loop structure from Green, A.A. et al. and the linker structure from Pardee, K. et al.. | ||
| + | ===Model=== | ||
| + | <html> | ||
| + | <br> | ||
NUPACK ANALYSIS <br> | NUPACK ANALYSIS <br> | ||
| − | https://static.igem.org/mediawiki/parts/1/1e/T--CSMU_Taiwan--oz21_A_NU.png | + | <div style="width=100%; display:flex; align-items: center; justify-content: center;"> |
| − | + | <img src="https://static.igem.org/mediawiki/parts/1/1e/T--CSMU_Taiwan--oz21_A_NU.png" style="width:50%;"> | |
| + | </div> | ||
| + | <br> | ||
| + | </html> | ||
VIENNA RNA PACKAGE <br> | VIENNA RNA PACKAGE <br> | ||
| − | https://static.igem.org/mediawiki/parts/0/06/T--CSMU_Taiwan--oz21_A_Ve.png | + | <html> |
| + | <div style="width=100%; display:flex; align-items: center; justify-content: center;"> | ||
| + | <img src="https://static.igem.org/mediawiki/parts/0/06/T--CSMU_Taiwan--oz21_A_Ve.png" style="width:50%;"> | ||
| + | </div> | ||
| + | <br> | ||
| + | </html> | ||
| + | Link to our model page: https://2020.igem.org/Team:CSMU_Taiwan/Model | ||
| − | + | ===Experiment result=== | |
| + | <html> | ||
| + | <br> | ||
| + | <div style="width=100%; display:flex; align-items: center; justify-content: center"> | ||
| + | <img src="https://static.igem.org/mediawiki/parts/c/c6/T--CSMU_Taiwan--oz21_A_%28BBa_K3431022%29.png" style="width:50%"> | ||
| + | </div> | ||
| + | <br> | ||
| + | </html> | ||
| − | References | + | ===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. | 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. | 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. | ||
Revision as of 16:00, 24 October 2020
oz21_A Toehold Switch for miR-21 Detection
Description
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.
For this particular toehold switch (oz21_A), we incorporate the loop structure from Green, A.A. et al. and the linker structure from Pardee, K. et al..
Model
NUPACK ANALYSIS
VIENNA RNA PACKAGE
Link to our model page: https://2020.igem.org/Team:CSMU_Taiwan/Model
Experiment result
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
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]