Difference between revisions of "Team:ETH Zurich/Parts"

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<section class="design">
 
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    <h1>Design</h1>
 
  
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<p>All parts were codon-optimized for expression in <span class="bacterium">E. coli</span> Nissle via Geneious software and modified to remove forbidden restriction sites.</p>
 
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    <div class="multi-summary">
 
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<details>
 
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<summary>BBa_K2500000: Bacterioferritin</summary>
 
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<p><strong>Organism:</strong> <span class="bacterium">Escherichia coli</span> Nissle</p>
 
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<p><strong>Based on:</strong> <a href="http://parts.igem.org/Part:BBa_K1438001">BBa_K1438001</a></p>
 
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<p><strong>Source:</strong> gBlock</p>
 
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<p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500000">BBa_K2500000</a></p>
 
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</details>
 
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<details>
 
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<summary>BBa_K2500001: Azurin</summary>
 
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<p><strong>Design notes:</strong> Native signalling peptide removed.</p>
 
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<p><strong>Organism:</strong> <span class="bacterium">Pseudomonas aeruginosa</span></p>
 
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<p><strong>Based on:</strong> <a href="http://parts.igem.org/Part:BBa_K835004">BBa_K835004</a></p>
 
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<p><strong>Source:</strong> gBlock</p>
 
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<p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500001">BBa_K2500001</a></p>
 
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</details>
 
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<details>
 
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<summary>BBa_K2500002: p28</summary>
 
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<p><strong>Design notes:</strong> Designed by taking aminoacids 50 to 77 from azurin and adding a start codon (ATG) at the beginning and two stop codons (TAA TAA) at the end.</p>
 
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<p><strong>Organism:</strong> <span class="bacterium">Pseudomonas aeruginosa</span></p>
 
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<p><strong>Based on:</strong> <a href="http://parts.igem.org/Part:BBa_K2500001">BBa_K2500001</a></p>
 
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<p><strong>Source:</strong> gBlock</p>
 
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<p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500002">BBa_K2500002</a></p>
 
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</details>
 
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<details>
 
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<summary>BBa_K2500003: p<sub>TlpA</sub></summary>
 
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<p><strong>Organism:</strong> <span class="bacterium">Salmonella typhimurium</span></p>
 
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<p><strong>Based on:</strong> <a href="https://doi.org/10.1038/nchembio.2233">Piraner, Dan I., et al. <cite>Nature chemical biology</cite> 13.1 (2017): 75-80.</a></p>
 
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<p><strong>Source:</strong> oligonucleotide sequence</p>
 
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<p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500003">BBa_K2500003</a></p>
 
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</details>
 
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<details>
 
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<summary>BBa_K2500004: TlpA</summary>
 
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<p><strong>Organism:</strong> <span class="bacterium">Salmonella typhimurium</span></p>
 
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<p><strong>Based on:</strong> <a href="https://doi.org/10.1038/nchembio.2233">Piraner, Dan I., et al. <cite>Nature chemical biology</cite> 13.1 (2017): 75-80.</a></p>
 
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<p><strong>Source:</strong> gBlock</p>
 
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<p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500004">BBa_K2500004</a></p>
 
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</details>
 
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<details>
 
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<summary>BBa_K2500005: RBS_TlpA</summary>
 
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<p><strong>Design notes:</strong> FIXME FIXME FIXME RBS info</p>
 
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<p><strong>Organism:</strong> <span class="bacterium">Salmonella typhimurium</span></p>
 
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<p><strong>Based on:</strong> <a href="https://doi.org/10.1038/nchembio.2233">Piraner, Dan I., et al. <cite>Nature chemical biology</cite> 13.1 (2017): 75-80.</a></p>
 
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<p><strong>Source:</strong> gBlock</p>
 
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<p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500005">BBa_K2500005</a></p>
 
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</details>
 
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<details>
 
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<summary>BBa_K2500006: Protein E</summary>
 
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<p><strong>Organism:</strong> phage Phi X 174</p>
 
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<p><strong>Based on:</strong> provided by dr. Irene Wüthrich from Panke lab at the D-BSSE of ETH Zurich</p>
 
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<p><strong>Source:</strong> plasmid provided by dr. Irene Wüthrich from Panke lab at the D-BSSE of ETH Zurich</p>
 
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<p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500006">BBa_K2500006</a></p>
 
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</details>
 
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<details>
 
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<summary>BBa_K2500007: RBS<sub>eng</sub>_TlpA</summary>
 
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<p><strong>Design notes:</strong> FIXME FIXME FIXME RBS info</p>
 
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<p><strong>Organism:</strong> <span class="bacterium">Salmonella typhimurium</span></p>
 
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<p><strong>Based on:</strong> <a href="https://doi.org/10.1038/nchembio.2233">Piraner, Dan I., et al. <cite>Nature chemical biology</cite> 13.1 (2017): 75-80.</a></p>
 
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<p><strong>Source:</strong> FIXME RedLibs + gBlock</p>
 
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<p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500007">BBa_K2500007</a></p>
 
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</details>
 
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<details>
 
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<summary>BBa_K2500008: p<sub>Const</sub>_RBS<sub>eng</sub>_TlpA</summary>
 
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<p><strong>Design notes:</strong> FIXME FIXME FIXME RBS info</p>
 
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<p><strong>Organism:</strong> <span class="bacterium">Salmonella typhimurium</span></p>
 
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<p><strong>Based on:</strong> <a href="http://parts.igem.org/Part:BBa_J23104">BBa_J23104</a> (promoter) and <a href="https://doi.org/10.1038/nchembio.2233">Piraner, Dan I., et al. <cite>Nature chemical biology</cite> 13.1 (2017): 75-80.</a> (TlpA)</p>
 
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<p><strong>Source:</strong> FIXME RedLibs + gBlock</p>
 
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<p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500008">BBa_K2500008</a></p>
 
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</details>
 
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<details>
 
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<summary>BBa_K2500009: RBS<sub>eng</sub>_ProteinE</summary>
 
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<p><strong>Design notes:</strong> FIXME FIXME FIXME RBS info</p>
 
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<p><strong>Organism:</strong> phage Phi X 174</p>
 
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<p><strong>Based on:</strong> provided by dr. Irene Wüthrich from Panke lab at the D-BSSE of ETH Zurich</p>
 
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<p><strong>Source:</strong> FIXME RedLibs + plasmid provided by dr. Irene Wüthrich from Panke lab at the D-BSSE of ETH Zurich</p>
 
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<p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500009">BBa_K2500009</a></p>
 
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</details>
 
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<details>
 
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<summary>BBa_K2500010: AND Gate A</summary>
 
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<p><strong>Design notes:</strong> In the absence of high concentrations of L-lactate, LldR inhibitor proteins bind to the binding sites O1 and O2 surrounding the p<sub>Lux</sub> promoter leading to the formation of a DNA loop. The p<sub>Lux</sub> promoter is sequestered and inaccessible for transcription. In design A, the distances between the intercalated promoter and the binding sites were taken from <a href="http://parts.igem.org/Part:BBa_K1847007">BBa_K1847007</a>.</p>
 
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<figure class="A">
 
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<img src="https://static.igem.org/mediawiki/2017/7/72/T--ETH_Zurich--ANDgateA.png" alt="FIXME">
 
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</figure>
 
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<p><strong>Organism:</strong> <span class="bacterium">FIXME FIXME FIXME</span></p>
 
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<p><strong>Based on:</strong> <a href="http://parts.igem.org/Part:BBa_K1847007">BBa_K1847007</a> (O1 and O2) and <a href="http://parts.igem.org/Part:BBa_R0062">BBa_R0062</a> (p<sub>Lux</sub>)</p>
 
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<p><strong>Source:</strong> gBlock</p>
 
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<p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500010">BBa_K2500010</a></p>
 
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</details>
 
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<details>
 
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<summary>BBa_K2500011: AND Gate B</summary>
 
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<p><strong>Design notes:</strong> In design B, each binding site was duplicated in order to achieve a potential zipper mechanism and stronger inhibition due to binding more LldR inhibitor proteins.</p>
 
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<figure class="B">
 
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<img src="https://static.igem.org/mediawiki/2017/6/6a/T--ETH_Zurich--ANDgateB.png" alt="FIXME">
 
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</figure>
 
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<p><strong>Organism:</strong> <span class="bacterium">FIXME FIXME FIXME</span></p>
 
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<p><strong>Based on:</strong> <a href="http://parts.igem.org/Part:BBa_K1847007">BBa_K1847007</a> (O1 and O2) and <a href="http://parts.igem.org/Part:BBa_R0062">BBa_R0062</a> (p<sub>Lux</sub>)</p>
 
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<p><strong>Source:</strong> gBlock</p>
 
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<p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500011">BBa_K2500011</a></p>
 
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</details>
 
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<details>
 
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<summary>BBa_K2500012: AND Gate C</summary>
 
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<p><strong>Design notes:</strong> In design C, an artificial spacer was embedded between the pLux promoter and the O2 binding site in order to influence the looping dynamics.</p>
 
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<figure class="C">
 
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<img src="https://static.igem.org/mediawiki/2017/c/c2/T--ETH_Zurich--ANDgateC.png" alt="FIXME">
 
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</figure>
 
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<p><strong>Organism:</strong> <span class="bacterium">FIXME FIXME FIXME</span></p>
 
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<p><strong>Based on:</strong> <a href="http://parts.igem.org/Part:BBa_K1847007">BBa_K1847007</a> (O1 and O2) and <a href="http://parts.igem.org/Part:BBa_R0062">BBa_R0062</a> (p<sub>Lux</sub>)</p>
 
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<p><strong>Source:</strong> gBlock</p>
 
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<p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500012">BBa_K2500012</a></p>
 
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</details>
 
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<details>
 
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<summary>BBa_K2500013: p<sub>Const1</sub>_RBS_LldP/LldR_p<sub>Const2</sub>_RBS_LuxR</summary>
 
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<p><strong>Design notes:</strong>FIXME FIXME FIXME</p>
 
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<p><strong>Organism:</strong> <span class="bacterium">FIXME FIXME FIXME</span></p>
 
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<p><strong>Based on:</strong> FIXME <a href="http://parts.igem.org/Part:BBa_J23118">BBa_J23118</a> (p<sub>Const1</sub>), <a href="http://parts.igem.org/Part:BBa_J23100">BBa_J23100</a> (p<sub>Const2</sub>), <a href="http://parts.igem.org/Part:BBa_K1847007">BBa_K1847007</a> (LldP/LldR) and <a href="http://parts.igem.org/Part:BBa_C0062">BBa_C0062</a> (LuxR)</p>
 
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<p><strong>Source:</strong> FIXME</p>
 
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<p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500013">BBa_K2500013</a></p>
 
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</details>
 
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</div>
 
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</section>
 
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<!--
 
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<section>
 
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    <h1>Inspiration</h1>
 
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    <p>We have a created a <a href="http://parts.igem.org/Well_Documented_Parts">collection of well documented parts</a> that can help you get started. You can also take a look at how other teams have documented their parts in their wiki:</p>
 
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    <ul>
 
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        <li><a href="https://2014.igem.org/Team:MIT/Parts"> 2014 MIT </a></li>
 
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        <li><a href="https://2014.igem.org/Team:Heidelberg/Parts"> 2014 Heidelberg</a></li>
 
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        <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Parts">2014 Tokyo Tech</a></li>
 
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    </ul>
 
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</section>
 
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<section>
 
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    <h1>Part Table </h1>
 
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    <p>Please include a table of all the parts your team has made during your project on this page. Remember part characterization and measurement data must go on your team part pages on the Registry.</p>
 
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    <groupparts>iGEM17 ETH_Zurich</groupparts>
 
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</section>
 
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-->
 
 
</main>
 
</main>
 
</html>
 
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{{ETH_Zurich/Footer_N}}
 
{{ETH_Zurich/Footer_N}}

Revision as of 12:11, 30 October 2017

Parts

FIXME

Overview

We submitted in total 14 new BioBricks to the iGEM registry! You can find them all below in our part collection. For more detailed descriptions, visit Basic Parts and Composite Parts.

Part Collection

Part Description BioBrick
Bacterioferritin Heme-deletion mutant of bacterial iron storage protein functioning as an MRI contrast agent BBa_K2500000
Azurin Redox protein originating from P. aeruginosa with anti-cancer activity BBa_K2500001
p28 Effector domain of azurin BBa_K2500002
pTlpA Temperature-responsive promoter optimized for slight activation above 37°C and full activation at 45 °C BBa_K2500003
TlpA Temperature-dependent transcriptional repressor of pTlpa BBa_K2500004
RBS_TlpA Temperature-dependent transcriptional repressor of pTlpa and synthetic RBS BBa_K2500005
Protein E Bacteria-lysing protein encoded by phage Phi X 17 BBa_K2500006
RBSeng_TlpA Temperature-dependent transcriptional repressor of pTlpa with engineered RBS BBa_K2500007
pConstRBSeng_TlpA Best Composite Part: Constitutively expressed temperature-dependent transcriptional repressor of pTlpa with engineered RBS BBa_K2500008
RBSeng_ProteinE Bacteria-lysing protein encoded by phage Phi X 174 with engineered RBS BBa_K2500009
AND Gate A Synthetic promoter responsive to LldR and luxR BBa_K2500010
AND Gate B Best Basic Part: Synthetic promoter responsive to LldR and luxR BBa_K2500011
AND Gate C Synthetic promoter responsive to LldR and luxR BBa_K2500012
pConst_RBS_LldP/
LldR_pConst_RBS_LuxR		 Expression cassette consisting of LuxR and LldP/LldR BBa_K2500013