Difference between revisions of "Team:ETH Zurich/Basic Part"

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<h1>Design</h1>
 
<h1>Design</h1>
  
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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>
 +
<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>
 +
<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>
 +
<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>
 +
<p><strong>Based on:</strong> <a href="http://parts.igem.org/Part:BBa_K2500001">BBa_K2500001</a></p>
 +
<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>
 +
<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>
 +
<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>
 +
<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>
 +
<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>
 +
<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>
 +
<p><strong>Based on:</strong> provided by dr. Irene Wüthrich from Panke lab at the D-BSSE of ETH Zurich</p>
 +
<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>
  
  

Revision as of 12:11, 30 October 2017

Basic Parts

FIXME

Overview

All parts were codon-optimized for expression in E. coli Nissle with Geneious and modified to remove forbidden restriction sites.

Part Description BioBrick
Best Basic Part:
AND Gate B		 Synthetic promoter responsive to LldR and luxR BBa_K2500011
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
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 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

Design

BBa_K2500000: Bacterioferritin

Organism: Escherichia coli Nissle

Based on: BBa_K1438001

Source: gBlock

Registry: BBa_K2500000

BBa_K2500001: Azurin

Design notes: Native signalling peptide removed.

Organism: Pseudomonas aeruginosa

Based on: BBa_K835004

Source: gBlock

Registry: BBa_K2500001

BBa_K2500002: p28

Design notes: 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.

Organism: Pseudomonas aeruginosa

Based on: BBa_K2500001

Source: gBlock

Registry: BBa_K2500002

BBa_K2500003: pTlpA

Organism: Salmonella typhimurium

Based on: Piraner, Dan I., et al. Nature chemical biology 13.1 (2017): 75-80.

Source: oligonucleotide sequence

Registry: BBa_K2500003

BBa_K2500004: TlpA

Organism: Salmonella typhimurium

Based on: Piraner, Dan I., et al. Nature chemical biology 13.1 (2017): 75-80.

Source: gBlock

Registry: BBa_K2500004

BBa_K2500005: RBS_TlpA

Design notes: FIXME FIXME FIXME RBS info

Organism: Salmonella typhimurium

Based on: Piraner, Dan I., et al. Nature chemical biology 13.1 (2017): 75-80.

Source: gBlock

Registry: BBa_K2500005

BBa_K2500006: Protein E

Organism: phage Phi X 174

Based on: provided by dr. Irene Wüthrich from Panke lab at the D-BSSE of ETH Zurich

Source: plasmid provided by dr. Irene Wüthrich from Panke lab at the D-BSSE of ETH Zurich

Registry: BBa_K2500006

BBa_K2500007: RBSeng_TlpA

Design notes: FIXME FIXME FIXME RBS info

Organism: Salmonella typhimurium

Based on: Piraner, Dan I., et al. Nature chemical biology 13.1 (2017): 75-80.

Source: FIXME RedLibs + gBlock

Registry: BBa_K2500007

BBa_K2500008: pConst_RBSeng_TlpA

Design notes: FIXME FIXME FIXME RBS info

Organism: Salmonella typhimurium

Based on: BBa_J23104 (promoter) and Piraner, Dan I., et al. Nature chemical biology 13.1 (2017): 75-80. (TlpA)

Source: FIXME RedLibs + gBlock

Registry: BBa_K2500008

BBa_K2500009: RBSeng_ProteinE

Design notes: FIXME FIXME FIXME RBS info

Organism: phage Phi X 174

Based on: provided by dr. Irene Wüthrich from Panke lab at the D-BSSE of ETH Zurich

Source: FIXME RedLibs + plasmid provided by dr. Irene Wüthrich from Panke lab at the D-BSSE of ETH Zurich

Registry: BBa_K2500009

BBa_K2500010: AND Gate A

Design notes: In the absence of high concentrations of L-lactate, LldR inhibitor proteins bind to the binding sites O1 and O2 surrounding the pLux promoter leading to the formation of a DNA loop. The pLux promoter is sequestered and inaccessible for transcription. In design A, the distances between the intercalated promoter and the binding sites were taken from BBa_K1847007.

FIXME

Organism: FIXME FIXME FIXME

Based on: BBa_K1847007 (O1 and O2) and BBa_R0062 (pLux)

Source: gBlock

Registry: BBa_K2500010

BBa_K2500011: AND Gate B

Design notes: 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.

FIXME

Organism: FIXME FIXME FIXME

Based on: BBa_K1847007 (O1 and O2) and BBa_R0062 (pLux)

Source: gBlock

Registry: BBa_K2500011

BBa_K2500012: AND Gate C

Design notes: In design C, an artificial spacer was embedded between the pLux promoter and the O2 binding site in order to influence the looping dynamics.

FIXME

Organism: FIXME FIXME FIXME

Based on: BBa_K1847007 (O1 and O2) and BBa_R0062 (pLux)

Source: gBlock

Registry: BBa_K2500012

BBa_K2500013: pConst1_RBS_LldP/LldR_pConst2_RBS_LuxR

Design notes:FIXME FIXME FIXME

Organism: FIXME FIXME FIXME

Based on: FIXME BBa_J23118 (pConst1), BBa_J23100 (pConst2), BBa_K1847007 (LldP/LldR) and BBa_C0062 (LuxR)

Source: FIXME

Registry: BBa_K2500013