Team:Penn/MaGellinToolbox

From 2013.igem.org

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<b>Constructing a Toolbox</b>Our goal was to create a toolbox for developing customized site-specific methylases. Like any good toolbox, it includes three components: the tool, the assay, and the automation.
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<li>The Tool: a fusion between a DNA binding domain and a methylase enzyme</li>
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<li>The Assay: a digestion based assay, called MaGellin, to measure both methylase activity and sequence specificity</li>
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<li>The Automation: a unique software package that predicts experimental outcomes and analyzes gel electrophoresis images to measure methylase functionality</li>
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Our toolbox satisfies 6 requirements:
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<li>Robust – includes functional fusion proteins for comparison</li>
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<li>Standardized – all inclusive in one-plasmid with simple multiple cloning sites, standard bisulfite sequencing primers, and a digestion based methylation assay built in</li>
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<li>Easy to Use – we programmed a software package to predict experimental outcomes and automate gel electrophoresis analysis</li>
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<li>Inexpensive – methylase activity and specificity can be screened by simply digesting and running a gel</li>
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<li>Noiseless – the bacterial chassis has no background CpG methylation</li>
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<li>Open Source – we BioBrick’ed the full plasmid and the methylases</li>
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Revision as of 04:55, 27 October 2013

Penn iGEM

Toolbox




Constructing a ToolboxOur goal was to create a toolbox for developing customized site-specific methylases. Like any good toolbox, it includes three components: the tool, the assay, and the automation.
  1. The Tool: a fusion between a DNA binding domain and a methylase enzyme
  2. The Assay: a digestion based assay, called MaGellin, to measure both methylase activity and sequence specificity
  3. The Automation: a unique software package that predicts experimental outcomes and analyzes gel electrophoresis images to measure methylase functionality
Our toolbox satisfies 6 requirements:
  1. Robust – includes functional fusion proteins for comparison
  2. Standardized – all inclusive in one-plasmid with simple multiple cloning sites, standard bisulfite sequencing primers, and a digestion based methylation assay built in
  3. Easy to Use – we programmed a software package to predict experimental outcomes and automate gel electrophoresis analysis
  4. Inexpensive – methylase activity and specificity can be screened by simply digesting and running a gel
  5. Noiseless – the bacterial chassis has no background CpG methylation
  6. Open Source – we BioBrick’ed the full plasmid and the methylases





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