Difference between revisions of "Part:BBa K2587000:Design"
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<h2><b>Experimental design</b></h2> | <h2><b>Experimental design</b></h2> | ||
| − | Part of our project was to design a synthetic promoter, able to induce expression of a reporter gene, which is activated upon synthesis of the Quorum sensing molecule acyl homoserine lactone synthase, by LuxI. Therefore we codon | + | Part of our project was to design a synthetic promoter, able to induce expression of a reporter gene, which is activated upon synthesis of the Quorum sensing molecule acyl homoserine lactone synthase, by LuxI. Therefore we codon optimized this sequence for the organism <i>S.cerervisiae</i> and implemented this in our construct. With this we did not only apply this sequence into our project, but also improved a previous part by codon optimizing a gene, usually not used for <i>S.cerevisiae</i>. |
__NOTOC__ | __NOTOC__ | ||
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===Design Notes=== | ===Design Notes=== | ||
| − | This part is codon | + | This part is codon optimized for <i>S.cerevisiae</i> and TypeII S restriction sites (on both sides) are added to the sequence for special use in the YTK toolbox but also for general Golden Gate cloning, a trending becoming cloning method. This construct was built using the MoClo YTK Toolbox (1). As an example, our final construct containing the <i>LuxI</i> gene is shown here: <br> |
https://static.igem.org/mediawiki/parts/3/37/T--Duesseldorf--syntheticpromoter.PNG | https://static.igem.org/mediawiki/parts/3/37/T--Duesseldorf--syntheticpromoter.PNG | ||
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===Source=== | ===Source=== | ||
| − | The source of this part is the organism Alivibrio fischeri which was retrieved from Genbank ( and is codon | + | The source of this part is the organism <i>Alivibrio fischeri</i> which was retrieved from Genbank (and is codon optimized for <i>S. cerevisiae</i>.) |
===References=== | ===References=== | ||
| − | (1) <b>A Highly-characterized Yeast Toolkit for Modular, Multi-part Assembly.</b> Lee ME, DeLoache, WC A, Cervantes B, Dueber, JE. ACS Synthetic Biology 2015. DOI: 10.1021/sb500366v. | + | (1) <b>A Highly-characterized Yeast Toolkit for Modular, Multi-part Assembly.</b> Lee ME, DeLoache, WC A, Cervantes B, Dueber, JE. <i>ACS Synthetic Biology</i> 2015. DOI: 10.1021/sb500366v. |
Latest revision as of 16:45, 17 October 2018
Experimental design
Part of our project was to design a synthetic promoter, able to induce expression of a reporter gene, which is activated upon synthesis of the Quorum sensing molecule acyl homoserine lactone synthase, by LuxI. Therefore we codon optimized this sequence for the organism S.cerervisiae and implemented this in our construct. With this we did not only apply this sequence into our project, but also improved a previous part by codon optimizing a gene, usually not used for S.cerevisiae.
luxI_codon optimized S.cerevisiae
- 10COMPATIBLE WITH RFC[10]
- 12INCOMPATIBLE WITH RFC[12]Illegal NotI site found at 6
- 21INCOMPATIBLE WITH RFC[21]Illegal BamHI site found at 689
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000INCOMPATIBLE WITH RFC[1000]Illegal BsaI site found at 30
Illegal BsaI.rc site found at 673
Design Notes
This part is codon optimized for S.cerevisiae and TypeII S restriction sites (on both sides) are added to the sequence for special use in the YTK toolbox but also for general Golden Gate cloning, a trending becoming cloning method. This construct was built using the MoClo YTK Toolbox (1). As an example, our final construct containing the LuxI gene is shown here:
Source
The source of this part is the organism Alivibrio fischeri which was retrieved from Genbank (and is codon optimized for S. cerevisiae.)
References
(1) A Highly-characterized Yeast Toolkit for Modular, Multi-part Assembly. Lee ME, DeLoache, WC A, Cervantes B, Dueber, JE. ACS Synthetic Biology 2015. DOI: 10.1021/sb500366v.