Team:Warsaw/Project

From 2011.igem.org

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<h2>Synthetic cloning and expression control</h2>
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<!-- <div class="note">Here goes something about our project</div> -->
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!align="center"|[[Team:Warsaw|Home]]
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!align="center"|[[Team:Warsaw/Team|Team]]
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!align="center"|[https://igem.org/Team.cgi?year=2010&team_name=Warsaw Official Team Profile]
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!align="center"|[[Team:Warsaw/Project|Project]]
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!align="center"|[[Team:Warsaw/Parts|Parts Submitted to the Registry]]
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!align="center"|[[Team:Warsaw/Modeling|Modeling]]
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!align="center"|[[Team:Warsaw/Notebook|Notebook]]
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!align="center"|[[Team:Warsaw/Safety|Safety]]
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!align="center"|[[Team:Warsaw/Attributions|Attributions]]
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This year's goal of iGEM Warsaw team is to develop two foundational
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techniques for synthetic biologists:
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<div class="note">Expression Adapters</div>
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== '''Overall project''' ==
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So far all RBS parts were measured with GFP protein. We have measured the RBS parts with various fluorescent proteins and guess what - they are not as standard as we would like them to be. The strength of a RBS part depends on the protein used. Why - because the beginning of the protein influences the mRNA fold. When mRNA is strongly folded ribosome can not start translation. We came up with the idea of RBS parts fused with short 'protein beginnings'  - we call this expression adapters. We developed a genetic algorithm to design expression adapters that would provide standardized protein expression from each RBS from community collection. Also we are working on adapters that increase expression of your favorite protein. Currently we are testing our design in the wet lab </div>
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<br>
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This year's goal of iGEM Warsaw team is to develop 2 foundational
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<div class="note">Synthetic Cloning</div>
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techniques for synthetic biologists:
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<div align="justify">Our goal is to make easy and efficient protocol for cell free
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Our first goal is to make easy and efficient protocol for cell free
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cloning. It skips most basic step of classical cloning approach -
cloning. It skips most basic step of classical cloning approach -
plasmid propagation in bacteria or yeast. This allows cloning of
plasmid propagation in bacteria or yeast. This allows cloning of
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try to optimize all time consuming steps: DNA digestion, substrate
try to optimize all time consuming steps: DNA digestion, substrate
purification, ligation and product amplification. We'll also try to
purification, ligation and product amplification. We'll also try to
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deal with specificity problems of phiX29 polymerase by designing RNA
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deal with specificity problems of phi29 polymerase by designing RNA
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primers optimized for BioBrick amplification.
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primers optimized for BioBrick amplification.</div>
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<h2>Our project explained in 2 pictures;)</h2>
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<a href="https://static.igem.org/mediawiki/2011/1/1f/Comix.png"><img src="https://static.igem.org/mediawiki/2011/1/1f/Comix.png" width="350" align="middle"></a>
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<a href="https://static.igem.org/mediawiki/2011/5/59/FluoBac.jpg"><img src="https://static.igem.org/mediawiki/2011/5/59/FluoBac.jpg" width="300" align="top"></a>
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Our second goal is to provide BioBrick community standardized method
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of insertion of large constructs into E. coli genome via landingPad
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mediated homologous recombination. To achieve this we are going to
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develop BioBrick-compatible landingPad vectors and at least one
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recombination proficient host strain with LPs already in genome. We
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are also going to utilize the power of flippase to achieve very tight
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expression regulation and allow induced genome editing
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(deletions/substitutions).
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Latest revision as of 22:17, 21 September 2011

Example Tabs

Synthetic cloning and expression control

This year's goal of iGEM Warsaw team is to develop two foundational techniques for synthetic biologists:

Expression Adapters
So far all RBS parts were measured with GFP protein. We have measured the RBS parts with various fluorescent proteins and guess what - they are not as standard as we would like them to be. The strength of a RBS part depends on the protein used. Why - because the beginning of the protein influences the mRNA fold. When mRNA is strongly folded ribosome can not start translation. We came up with the idea of RBS parts fused with short 'protein beginnings' - we call this expression adapters. We developed a genetic algorithm to design expression adapters that would provide standardized protein expression from each RBS from community collection. Also we are working on adapters that increase expression of your favorite protein. Currently we are testing our design in the wet lab

Synthetic Cloning
Our goal is to make easy and efficient protocol for cell free cloning. It skips most basic step of classical cloning approach - plasmid propagation in bacteria or yeast. This allows cloning of constructs that are toxic to host cells (i.e. nucleases or lysins) and speeds up the whole procedure at least three times. The cell free cloning process involves rolling circle amplification of ligation products by phi29 polymerase. Our protocol is speed-oriented so we'll try to optimize all time consuming steps: DNA digestion, substrate purification, ligation and product amplification. We'll also try to deal with specificity problems of phi29 polymerase by designing RNA primers optimized for BioBrick amplification.

Our project explained in 2 pictures;)

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