Difference between revisions of "Team:Bielefeld-CeBiTec/Demonstrate"
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| − | Our goal was to introduce <b><a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/unnatural_base_pair">unnatural bases</a></b> into the genetic code of <i>E.coli</i> to create new blank codons for the translational incorporation of <b><a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/toolbox">non-canonical amino acids</a></b>. To demonstrate that the incorporation of unnatural base pairs is possible and that <i>E. coli</i> can take up iso-dGTP and iso-CmTP from the media through a <b><a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/unnatural_base_pair/uptake_and_biosynthesis">nucleotide transporter</a></b>. Further we showed that certain Taq polymerases can incorporate these bases <i>in vitro</i>. To sequence the unnatural base pairs, we also developed a <b><a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Software">nanopore software</a></b> modification and were able to proof the presence of unnatural base pairs using our modified software and by a simple <b>restriction experiment</b> developed by us. <br><br> | + | Our goal was to introduce <b><a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/unnatural_base_pair">unnatural bases</a></b> into the genetic code of <i>E.coli</i> to create new blank codons for the translational incorporation of <b><a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/toolbox">non-canonical amino acids</a></b>. To demonstrate that the incorporation of unnatural base pairs is possible and that <i>E. coli</i> can take up iso-dGTP and iso-CmTP from the media through a <b><a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/unnatural_base_pair/uptake_and_biosynthesis">nucleotide transporter</a></b>. Further we showed that certain Taq polymerases can incorporate these bases <i>in vitro</i>. To sequence the unnatural base pairs, we also developed a <b><a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Software">nanopore software</a></b> modification and were able to proof the presence of unnatural base pairs using our modified software and by a simple <b>restriction experiment</b> developed by us. <br><br> |
| − | To use these new blank codons, we developed a <b><a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/translational_system/library_and_selection">library</a></b> over hundred-thousand synthetase sequences and a positive/negative <b><a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/translational_system/library_and_selection">selection system</a></b> to obtain new <b><a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Project/toolbox">aminoacyl-tRNA-synthetases</a></b>. These can be applied to couple non-canonical amino acids to the tRNA and to turn <b>semi-synthetic codons</b> functional. <br><br> | + | To use these new blank codons, we developed a <b><a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/translational_system/library_and_selection">library</a></b> over hundred-thousand synthetase sequences and a positive/negative <b><a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/translational_system/library_and_selection">selection system</a></b> to obtain new <b><a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Project/toolbox">aminoacyl-tRNA-synthetases</a></b>. These can be applied to couple non-canonical amino acids to the tRNA and to turn <b>semi-synthetic codons</b> functional. <br><br> |
| − | To demonstrate the benefits of non-canonical amino acids to the synthetic biology community, we worked on five <b><a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/toolbox">applications</a></b> utilizing non-canonical amino acids. Furthermore, we designed and synthetized our own fully <b><a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/toolbox/fusing">synthetic non-canonical amino acid</a></b> and <b><a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Model">modeled</a></b> possible synthetase-sequences for its incorporation. We also improved a <b><a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Improve">test system</a></b> and defined a ranking system for aminoacyl-tRNA synthetases<br><br> | + | To demonstrate the benefits of non-canonical amino acids to the synthetic biology community, we worked on five <b><a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/toolbox">applications</a></b> utilizing non-canonical amino acids. Furthermore, we designed and synthetized our own fully <b><a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Results/toolbox/fusing">synthetic non-canonical amino acid</a></b> and <b><a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Model">modeled</a></b> possible synthetase-sequences for its incorporation. We also improved a <b><a target="_blank" href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Improve">test system</a></b> and defined a ranking system for aminoacyl-tRNA synthetases<br><br> |
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! <b>Expand</b>! | 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! <b>Expand</b>! | ||
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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> | + | <b>Establishment of two orthogonal methods for the detection of unnatural base pairs in a target sequence via <a target="_blank" 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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Revision as of 17:28, 29 October 2017
Demonstrate Your Work
To use these new blank codons, we developed a library over hundred-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!
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
Proof that certain Taq-polymerases can efficiently incorporate unnatural nucleotides
Construction of a toolkit consisting of five aminoacyl-tRNA synthetases for incorporation of non-canonical amino acids
Development of a photoswitchable lycopene pathway
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”
