Difference between revisions of "Team:Bielefeld-CeBiTec"

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iGEM Bielefeld-CeBiTec 2017
 
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<h2> Expanding the Genetic Code </h2>
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<article> We are exploring the application of unnatural base pairs as an expansion of the genetic code. To prevent loss of unnatural base pairs during replication, we will utilize several systems including CRISPR/Cas9. The expanded genetic code allows for the ribosomal incorporation of multiple non-canonical amino acids (ncAAs) into peptides. With their broad chemical and functional diversity, ncAAs provide a variety of promising applications including protein labeling, photocaging, structure analysis, and specific protein interactions. Therefore, our innovative toolkit for the translational incorporation of ncAAs in E. coli is a valuable contribution to iGEM. Directed evolution of tRNA/aminoacyl-tRNA synthetase pairs enables the site-specific incorporation of ncAAs into peptides. This approach results in an optimal orthogonality to the autologous translation apparatus and a high flexibility concerning the incorporation of multiple ncAAs. As proof of concept, we are developing a rapid test for prions and a new chromatography method for mild protein elution.
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For more information visit our <b><a href="https://www.researchgate.net/publication/318084694_Expansion_of_the_genetic_code_for_the_translational_incorporation_of_non-canonical_amino_acids">project poster</a></b> on reasearch gate
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<h2>Achievements</h2>
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<b>Establishment of two orthogonal methods for the detection of unnatural base pairs in a target sequence via <a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Software">Oxford Nanopore sequencing</a> and an enzyme based detection method</b>
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<b>Development of a <a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Software">software</a> suite for these orthogonal methods </b>
 
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<b>Integration and characterization of  the <a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/unnatural_base_pair/uptake_and_biosynthesis">nucleotide transporter PtNTT2</a> from <i>P.tricornutum</i> in <i>E.coli</i> for the uptake of  unnatural nucleoside triphosphates</b>
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<b>Proof that certain Taq-polymerases can efficiently <a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/unnatural_base_pair/preservation_system">incorporate unnatural nucleotides</a> </b>
 
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<b>Construction of a <a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/toolbox">toolbox</a> consisting of five aminoacyl-tRNA synthetases for incorporation of non-canonical amino acids</b>
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<b><a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/toolbox/labeling">Colocalization</a> of the RuBisCo using a fluorescent amino acid</b>
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<b>Development of a <a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/toolbox/photoswitching">photoswitchable lycopene pathway</a></b>
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<b>Design, <a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/toolbox/fusing">chemical synthesis</a> and proof of functionality of a novel, fully synthetic amino acid based on cyanonitrobenzothiazol and asparagine</b>
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<b><a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Model">Modeling</a> more than ten new aaRS sequences</b>
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<b><a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/translational_system/library_and_selection">Library development</a> with several hundred thousand sequences for selecting aminoacyl-tRNA synthetases</b>
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<b>Construction of positive and negative <a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/translational_system/library_and_selection">selection plasmids</a> for the evolution of new synthetases for non-canonical amino acids</b>
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<b><a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Improve">Improvement</a> of an aminoacyl-tRNA synthetase test-system by introducing a FRET-system and development of a ranking system</b>
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<b>Construction of an <a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Hardware">LED panel</a> for irradiating 96-well microtiter plates, which can be used to manipulate non-canonical amino acids and much more </b>
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<b>Development of an <a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Software">Android</a> App to control the LED panel with your smartphone via Bluetooth</b>
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<b>Writing a <a target="_blank" href="https://static.igem.org/mediawiki/2017/1/1e/T--Bielefeld-CeBiTec--DKE_Biosafety_Report.pdf">biosafety report</a> titled “Auxotrophy to Xeno-DNA: A Comprehensive Exploration of Combinatorial Mechanisms for a High-Fidelity Biosafety System” </b>
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<img class="start-page-image" src="https://static.igem.org/mediawiki/2017/0/01/T--Bielefeld-CeBiTec--start-page-screen5.png">
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<div class="content">
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<h2>Achievements</h2>
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<div class="contentline">
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<div class="third">
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<div class="sponsor-figure small">
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<img class="sponsor-figure image" src="https://static.igem.org/mediawiki/2017/9/94/T--Bielefeld-CeBiTec--YKE_Bingo.png">
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<p class="sponsor-figure subtitle"></p>
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</div>
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</div>
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<div class="third double">
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<article><br>
 +
<b>Establishment of two orthogonal methods for the detection of unnatural base pairs in a target sequence via <a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Software">Oxford Nanopore sequencing</a> and an enzyme based detection method</b>
 +
</article>
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</div>
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</div>
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 +
<div class="contentline">
 +
<div class="third">
 +
<div class="sponsor-figure small">
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<img class="sponsor-figure image" src="https://static.igem.org/mediawiki/2017/9/94/T--Bielefeld-CeBiTec--YKE_Bingo.png">
 +
<p class="sponsor-figure subtitle"></p>
 +
</div>
 +
</div>
 +
<div class="third double">
 +
<article><br><br>
 +
<b>Development of a <a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Software">software</a> suite for these orthogonal methods </b>
 +
</article>
 +
</div>
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</div>
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 +
<div class="contentline">
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<div class="third">
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<div class="sponsor-figure small">
 +
<img class="sponsor-figure image" src="https://static.igem.org/mediawiki/2017/9/94/T--Bielefeld-CeBiTec--YKE_Bingo.png">
 +
<p class="sponsor-figure subtitle"></p>
 +
</div>
 +
</div>
 +
<div class="third double">
 +
<article><br>
 +
<b>Integration and characterization of  the <a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/unnatural_base_pair/uptake_and_biosynthesis">nucleotide transporter PtNTT2</a> from <i>P.tricornutum</i> in <i>E.coli</i> for the uptake of  unnatural nucleoside triphosphates</b>
 +
</article>
 +
</div>
 +
</div>
 +
 
 +
<div class="contentline">
 +
<div class="third">
 +
<div class="sponsor-figure small">
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<img class="sponsor-figure image" src="https://static.igem.org/mediawiki/2017/9/94/T--Bielefeld-CeBiTec--YKE_Bingo.png">
 +
<p class="sponsor-figure subtitle"></p>
 +
</div>
 +
</div>
 +
<div class="third double">
 +
<article><br><br>
 +
<b>Proof that certain Taq-polymerases can efficiently <a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/unnatural_base_pair/preservation_system">incorporate unnatural nucleotides</a> </b>
 +
</article>
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</div>
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</div>
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 +
<div class="contentline">
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<div class="third">
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<div class="sponsor-figure small">
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<img class="sponsor-figure image" src="https://static.igem.org/mediawiki/2017/9/94/T--Bielefeld-CeBiTec--YKE_Bingo.png">
 +
<p class="sponsor-figure subtitle"></p>
 +
</div>
 +
</div>
 +
<div class="third double">
 +
<article><br><br>
 +
<b>Construction of a <a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/toolbox">toolbox</a> consisting of five aminoacyl-tRNA synthetases for incorporation of non-canonical amino acids</b>
 +
</article>
 +
</div>
 +
</div>
 +
 
 +
<div class="contentline">
 +
<div class="third">
 +
<div class="sponsor-figure small">
 +
<img class="sponsor-figure image" src="https://static.igem.org/mediawiki/2017/9/94/T--Bielefeld-CeBiTec--YKE_Bingo.png">
 +
<p class="sponsor-figure subtitle"></p>
 +
</div>
 +
</div>
 +
<div class="third double">
 +
<article><br><br>
 +
<b><a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/toolbox/labeling">Colocalization</a> of the RuBisCo using a fluorescent amino acid</b>
 +
</article>
 +
</div>
 +
</div>         
 +
 +
<div class="contentline">
 +
<div class="third">
 +
<div class="sponsor-figure small">
 +
<img class="sponsor-figure image" src="https://static.igem.org/mediawiki/2017/9/94/T--Bielefeld-CeBiTec--YKE_Bingo.png">
 +
<p class="sponsor-figure subtitle"></p>
 +
</div>
 +
</div>
 +
<div class="third double">
 +
<article><br><br>
 +
<b>Development of a <a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/toolbox/photoswitching">photoswitchable lycopene pathway</a></b>
 +
</article>
 +
</div>
 +
</div>
 +
 
 +
<div class="contentline">
 +
<div class="third">
 +
<div class="sponsor-figure small">
 +
<img class="sponsor-figure image" src="https://static.igem.org/mediawiki/2017/9/94/T--Bielefeld-CeBiTec--YKE_Bingo.png">
 +
<p class="sponsor-figure subtitle"></p>
 +
</div>
 +
</div>
 +
<div class="third double">
 +
<article><br>
 +
<b>Design, <a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/toolbox/fusing">chemical synthesis</a> and proof of functionality of a novel, fully synthetic amino acid based on cyanonitrobenzothiazol and asparagine</b>
 +
</article>
 +
</div>
 +
</div>
 +
 
 +
<div class="contentline">
 +
<div class="third">
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<div class="sponsor-figure small">
 +
<img class="sponsor-figure image" src="https://static.igem.org/mediawiki/2017/9/94/T--Bielefeld-CeBiTec--YKE_Bingo.png">
 +
<p class="sponsor-figure subtitle"></p>
 +
</div>
 +
</div>
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<div class="third double">
 +
<article><br><br>
 +
<b><a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Model">Modeling</a> more than ten new aaRS sequences</b>
 +
</article>
 +
</div>
 +
</div>
 +
 
 +
<div class="contentline">
 +
<div class="third">
 +
<div class="sponsor-figure small">
 +
<img class="sponsor-figure image" src="https://static.igem.org/mediawiki/2017/9/94/T--Bielefeld-CeBiTec--YKE_Bingo.png">
 +
<p class="sponsor-figure subtitle"></p>
 +
</div>
 +
</div>
 +
<div class="third double">
 +
<article><br><br>
 +
<b><a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/translational_system/library_and_selection">Library development</a> with several hundred thousand sequences for selecting aminoacyl-tRNA synthetases</b>
 +
</article>
 +
</div>
 +
</div>
 +
 
 +
<div class="contentline">
 +
<div class="third">
 +
<div class="sponsor-figure small">
 +
<img class="sponsor-figure image" src="https://static.igem.org/mediawiki/2017/9/94/T--Bielefeld-CeBiTec--YKE_Bingo.png">
 +
<p class="sponsor-figure subtitle"></p>
 +
</div>
 +
</div>
 +
<div class="third double">
 +
<article><br>
 +
<b>Construction of positive and negative <a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/translational_system/library_and_selection">selection plasmids</a> for the evolution of new synthetases for non-canonical amino acids</b>
 +
</article>
 +
</div>
 +
</div>
 +
 
 +
<div class="contentline">
 +
<div class="third">
 +
<div class="sponsor-figure small">
 +
<img class="sponsor-figure image" src="https://static.igem.org/mediawiki/2017/9/94/T--Bielefeld-CeBiTec--YKE_Bingo.png">
 +
<p class="sponsor-figure subtitle"></p>
 +
</div>
 +
</div>
 +
<div class="third double">
 +
<article><br><br>
 +
<b><a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Improve">Improvement</a> of an aminoacyl-tRNA synthetase test-system by introducing a FRET-system and development of a ranking system</b>
 +
</article>
 +
</div>
 +
</div>
 +
 
 +
<div class="contentline">
 +
<div class="third">
 +
<div class="sponsor-figure small">
 +
<img class="sponsor-figure image" src="https://static.igem.org/mediawiki/2017/9/94/T--Bielefeld-CeBiTec--YKE_Bingo.png">
 +
<p class="sponsor-figure subtitle"></p>
 +
</div>
 +
</div>
 +
<div class="third double">
 +
<article><br><br>
 +
<b>Construction of an <a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Hardware">LED panel</a> for irradiating 96-well microtiter plates, which can be used to manipulate non-canonical amino acids and much more </b>
 +
</article>
 +
</div>
 +
</div>
 +
 
 +
<div class="contentline">
 +
<div class="third">
 +
<div class="sponsor-figure small">
 +
<img class="sponsor-figure image" src="https://static.igem.org/mediawiki/2017/9/94/T--Bielefeld-CeBiTec--YKE_Bingo.png">
 +
<p class="sponsor-figure subtitle"></p>
 +
</div>
 +
</div>
 +
<div class="third double">
 +
<article><br><br>
 +
<b>Development of an <a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Software">Android</a> App to control the LED panel with your smartphone via Bluetooth</b>
 +
</article>
 +
</div>
 +
</div>
 +
 
 +
<div class="contentline">
 +
<div class="third">
 +
<div class="sponsor-figure small">
 +
<img class="sponsor-figure image" src="https://static.igem.org/mediawiki/2017/9/94/T--Bielefeld-CeBiTec--YKE_Bingo.png">
 +
<p class="sponsor-figure subtitle"></p>
 +
</div>
 +
</div>
 +
<div class="third double">
 +
<article><br>
 +
<b>Writing a <a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/HP/Silver">biosafety report</a> titled “Auxotrophy to Xeno-DNA: A Comprehensive Exploration of Combinatorial Mechanisms for a High-Fidelity Biosafety System” </b>
 +
</article>
 +
</div>
 +
</div>
 +
 
 +
<div class="contentline">
 +
<div class="third">
 +
<div class="sponsor-figure small">
 +
<img class="sponsor-figure image" src="https://static.igem.org/mediawiki/2017/9/94/T--Bielefeld-CeBiTec--YKE_Bingo.png">
 +
<p class="sponsor-figure subtitle"></p>
 +
</div>
 +
</div>
 +
<div class="third double">
 +
<article><br><br>
 +
<b>Writing the <a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/HP/Gold_Integrated">ChImp Report</a> on “Chances and Implications of an Expanded Genetic Code”</b>
 +
</article>
 +
</div>
 +
</div>
 +
 +
</div>
 +
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<div class="contentline">
 
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<img class="figure image" src="https://static.igem.org/mediawiki/2017/9/94/T--Bielefeld-CeBiTec--YKE_Bingo.png">
 
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<p class="figure subtitle"></p>
 
−
</div>
 
−
</div>
 
−
<div class="third double">
 
−
<article><br><br>
 
−
<b>Writing the <a target="_blank" href="https://static.igem.org/mediawiki/2017/1/18/T--Bielefeld-CeBiTec--CMZ-ChImp.pdf">ChImp Report</a> on “Chances and Implications of an Expanded Genetic Code”</b>
 
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Revision as of 00:29, 2 November 2017

Achievements


Establishment of two orthogonal methods for the detection of unnatural base pairs in a target sequence via Oxford Nanopore sequencing and an enzyme based detection method


Development of a software suite for these orthogonal methods

Integration and characterization of the nucleotide transporter PtNTT2 from P.tricornutum in E.coli for the uptake of unnatural nucleoside triphosphates


Construction of a toolbox consisting of five aminoacyl-tRNA synthetases for incorporation of non-canonical amino acids

Design, chemical synthesis and proof of functionality of a novel, fully synthetic amino acid based on cyanonitrobenzothiazol and asparagine


Modeling more than ten new aaRS sequences


Library development with several hundred thousand sequences for selecting aminoacyl-tRNA synthetases

Construction of positive and negative selection plasmids for the evolution of new synthetases for non-canonical amino acids


Improvement of an aminoacyl-tRNA synthetase test-system by introducing a FRET-system and development of a ranking system


Construction of an LED panel for irradiating 96-well microtiter plates, which can be used to manipulate non-canonical amino acids and much more


Development of an Android App to control the LED panel with your smartphone via Bluetooth

Writing a biosafety report titled “Auxotrophy to Xeno-DNA: A Comprehensive Exploration of Combinatorial Mechanisms for a High-Fidelity Biosafety System”


Writing the ChImp Report on “Chances and Implications of an Expanded Genetic Code”