Difference between revisions of "Team:Imperial College/Measurement"

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<h3>★  ALERT! </h3>
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            <h1>BASIC Method</h1>
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<p>This page is used by the judges to evaluate your team for the <a href="https://2018.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2018.igem.org/Judging/Awards"> award listed below</a>. </p>
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<p> Delete this box in order to be evaluated for this medal criterion and/or award. See more information at <a href="https://2018.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
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<h1>Measurement</h1>
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<p>There are a lot of exciting parts in the Registry, but many parts have still not been characterized. Synthetic Biology needs great measurement approaches for characterizing new parts, and efficient new methods for characterizing many parts at once. If you've done something exciting in the area of Measurement, describe it here!</p>
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<h3>Why do we use BASIC?</h3>
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<p>During the PixCell project we discovered that conventional DNA assembly methods don't always adapt to rapid troubleshooting of some construct parts. As our initial construct was open for improvement, we decided to create a library of transcription factors and promoters and try creating new constructs with them in order to improve our initial system. Hence, we started looking for a more modular method that would allow us to easily vary 1 or 2 components in a construct while keeping everything else the same in order to build our library. So, after previous preliminary research, we found out that BASIC was the perfect technology for this purpose.</p>  
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<h3>Best Innovation in Measurement Special Prize</h3>
 
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<p>If you've done excellent work in measurement, you should consider nominating your team for this special prize. Designing great measurement approaches for characterizing new parts or developing and implementing an efficient new method for characterizing thousands of parts are good examples.
 
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To compete for the <a href="https://2018.igem.org/Judging/Awards">Best Innovation in Measurement prize</a>, please describe your work on this page and also fill out the description on the <a href="https://2018.igem.org/Judging/Judging_Form">judging form</a>.
 
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You must also delete the message box on the top of this page to be eligible for this prize.
 
  
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<h3>BASIC Concept</h3>
  
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<p>BASIC is a modular assembly method in which the different construct parts are made modular linking them to pairs of oligos called linkers. Each linker assembles a part to the previous and subsequent parts. This assembly method allows us to build complex genetic circuits and multipart combinatorial assemblies. Besides, linker oligos are large enough to allow encoding an RBS sequence inside, thus enabling RBS troubleshooting of a construct trying different combinations of RBS without having to change the full structure of the assembly. Furthermore, BASIC includes linkers capable of fusing proteins, making it the best method for rapid assembly and characterization of protein fusion libraries.</p>
  
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<p>BASIC assembly can be divided in four simple steps. First, linkers are prepared and ligated to the corresponding parts. Every part contains a BASIC prefix and suffix, linkers bind to prefix or suffix, and each linker has a homologue linker that binds to the other (prefix or suffix). At the end of this step, all parts have a prefix and a suffix linker. Then parts with linkers are purified with magbead purification. Purified parts are assembled at 50ºC for 45min, each prefix linker will bind to its homologue suffix linker and this will give an order to the construct, allowing us to do the parts assembly in a single step. Finally, constructs are transformed into the desired strain and selected. </p>
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<h3>BASIC Story</h3>
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<p>Developed in 2015 in Baldwin’s lab at Imperial College London no one had used BASIC in iGEM before. From PixCell we want to introduce this versatile technique to the iGEM community and make it compatible with BioBrick assembly, for which we created pSB1C3_BASIC vector (with BioBrick and BASIC sites). Using this method, we were able to assemble a library of 48 different constructs in 3 days, using 6 different transcription factors and 8 promoters.</p>
  
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<h3>Inspiration</h3>
 
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<p>You can look at what other teams did to get some inspiration! <br />
 
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Here are a few examples:</p>
 
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<li><a href="https://2016.igem.org/Team:Stanford-Brown">2016 Stanford-Brown</a></li>
 
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<li><a href="https://2016.igem.org/Team:Genspace">2016 Genspace</a></li>
 
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<li><a href="https://2015.igem.org/Team:William_and_Mary">2015 William and Mary</a></li>
 
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<li><a href="https://2014.igem.org/Team:Aachen">2014 Aachen  </a></li>
 
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<p> In case you want to know more about BASIC check their website:
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<a href="https://www.basic-assembly.org" target="blank">https://www.basic-assembly.org </a> </p>
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          <p><b>Figure 1.</b> BASIC assembly method based on Storch et al. 2015</p>
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Latest revision as of 00:35, 18 October 2018

BASIC Method



Why do we use BASIC?

During the PixCell project we discovered that conventional DNA assembly methods don't always adapt to rapid troubleshooting of some construct parts. As our initial construct was open for improvement, we decided to create a library of transcription factors and promoters and try creating new constructs with them in order to improve our initial system. Hence, we started looking for a more modular method that would allow us to easily vary 1 or 2 components in a construct while keeping everything else the same in order to build our library. So, after previous preliminary research, we found out that BASIC was the perfect technology for this purpose.

BASIC Concept

BASIC is a modular assembly method in which the different construct parts are made modular linking them to pairs of oligos called linkers. Each linker assembles a part to the previous and subsequent parts. This assembly method allows us to build complex genetic circuits and multipart combinatorial assemblies. Besides, linker oligos are large enough to allow encoding an RBS sequence inside, thus enabling RBS troubleshooting of a construct trying different combinations of RBS without having to change the full structure of the assembly. Furthermore, BASIC includes linkers capable of fusing proteins, making it the best method for rapid assembly and characterization of protein fusion libraries.

BASIC assembly can be divided in four simple steps. First, linkers are prepared and ligated to the corresponding parts. Every part contains a BASIC prefix and suffix, linkers bind to prefix or suffix, and each linker has a homologue linker that binds to the other (prefix or suffix). At the end of this step, all parts have a prefix and a suffix linker. Then parts with linkers are purified with magbead purification. Purified parts are assembled at 50ºC for 45min, each prefix linker will bind to its homologue suffix linker and this will give an order to the construct, allowing us to do the parts assembly in a single step. Finally, constructs are transformed into the desired strain and selected.

BASIC Story

Developed in 2015 in Baldwin’s lab at Imperial College London no one had used BASIC in iGEM before. From PixCell we want to introduce this versatile technique to the iGEM community and make it compatible with BioBrick assembly, for which we created pSB1C3_BASIC vector (with BioBrick and BASIC sites). Using this method, we were able to assemble a library of 48 different constructs in 3 days, using 6 different transcription factors and 8 promoters.

In case you want to know more about BASIC check their website: https://www.basic-assembly.org

Figure 1. BASIC assembly method based on Storch et al. 2015