Difference between revisions of "Team:Bielefeld-CeBiTec/Demonstrate"

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<b>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</b>
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<b>Establishment of two orthogonal methods for the detection of unnatural base pairs in a target sequence via <a 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 software suite for these orthogonal methods </b>
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<b>Development of a <a 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 nucleotide transporter PtNTT2 from <i>P.tricornutum</i> in <i>E.coli</i> for the uptake of  unnatural nucleoside triphosphates</b>
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<b>Integration and characterization of  the <a 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 incorporate unnatural nucleotides </b>
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<b>Proof that certain Taq-polymerases can efficiently <a 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 toolkit consisting of five aminoacyl-tRNA synthetases for incorporation of non-canonical amino acids</b>
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<b>Construction of a <a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/toolbox">toolkit</a> consisting of five aminoacyl-tRNA synthetases for incorporation of non-canonical amino acids</b>
 
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<b>Development of a photoswitchable lycopene pathway</b>
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<b>Development of a <a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/toolbox/photoswitching">photoswitchable lycopene pathway</a></b>
 
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<b>Design and chemical synthesis of a novel, fully synthetic amino acid based on cyanonitrobenzothiazol and asparagine and proof of its functionality</b>
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<b>Design and <a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/toolbox/fusing">chemical synthesis</a> of a novel, fully synthetic amino acid based on cyanonitrobenzothiazol and asparagine and proof of its functionality</b>
 
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<b>Modeling more than ten new aaRS sequences</b>
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<b><a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Model">Modeling</a> more than ten new aaRS sequences</b>
 
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<b>Library development with several thousand sequences for selecting aminoacyl-tRNA synthetases</b>
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<b><a 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 selection plasmids for the evolution of new synthetases for non-canonical amino acids</b>
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<b>Construction of positive and negative <a 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>Improvement of an aminoacyl-tRNA synthetase test-system by introducing a FRET-system and development of a ranking system</b>
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<b><a 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 LED panel 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>Construction of an <a 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 Android App to control the LED panel with your smartphone via Bluetooth</b>
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<b>Development of an <a 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 of a biosafety report titled “Auxotrophy to Xeno-DNA: A Comprehensive Exploration of Combinatorial Mechanisms for a High-Fidelity Biosafety System” </b>
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<b>Writing of a <a 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>
 
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<b>Writing of the ChImp Report on the “Chances and Implications of an Expanded Genetic Code”</b>
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<b>Writing of the <a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/HP/Gold_Integrated">ChImp Report</a> on the “Chances and Implications of an Expanded Genetic Code”</b>
 
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Revision as of 10:54, 29 October 2017

Demonstrate Your Work
Our goal was to introduce unnatural bases into the genetic code of E.coli to create new blank codons for the translational incorporation of non-canonical amino acids. To demonstrate that the incorporation of unnatural base pairs is possible and that E. coli can take up iso-dGTP and iso-CmTP from the media through a nucleotide transporter. Further we showed that certain Taq polymerases can incorporate these bases in vitro. To sequence the unnatural base pairs, we also developed a nanopore software modification and were able to proof the presence of unnatural base pairs using our modified software and by a simple restriction experiment developed by us.

To use these new blank codons, we developed a library several thousand synthetase sequences and a positive/negative selection system to obtain new aminoacyl-tRNA-synthetases. These can be applied to couple non-canonical amino acids to the tRNA and to turn semi-synthetic codons functional.

To demonstrate the benefits of non-canonical amino acids to the synthetic biology community, we worked on five applications utilizing non-canonical amino acids. Furthermore, we designed and synthetized our own fully synthetic non-canonical amino acid and modeled possible synthetase-sequences for its incorporation. We also improved a test system and defined a ranking system for aminoacyl-tRNA synthetases

While we were not able to incorporate non-canonical amino acids through semi-synthetic codons, we are convinced that we have laid the foundations for a whole new field of synthetic biology for the iGEM community. We would be very honored if future teams would build on our project to further develop this approach and to develop new and exciting applications! Expand!

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 toolkit consisting of five aminoacyl-tRNA synthetases for incorporation of non-canonical amino acids


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



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



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