Difference between revisions of "Team:Edinburgh OG/Parts"

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<p>This year the iGEM Edinburgh_OG team focused on developing a modular toolkit using CRISPR systems and phages to re-sensitise antibiotic-resistant bacteria. As a BioBrick we submit the <em>E. coli </em>codon-optimised <em>Staphylococcus aureus Cas9</em>.</p>
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<p>Each team will make new parts during iGEM and will submit them to the Registry of Standard Biological Parts. The iGEM software provides an easy way to present the parts your team has created. The <code>&lt;groupparts&gt;</code> tag (see below) will generate a table with all of the parts that your team adds to your team sandbox.</p>
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<p><strong>&lt;groupparts&gt;iGEM17 Edinburgh_OG&lt;/groupparts&gt;</strong></p>
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<p>Remember that the goal of proper part documentation is to describe and define a part, so that it can be used without needing to refer to the primary literature. Registry users in future years should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.</p>
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<p><br /><br /><br /></p>
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<p>http://www.nature.com/news/genome-editing-revolution-my-whirlwind-year-with-crispr-1.19063</p>
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<h2>How does this part work?</h2>
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<h5>Note</h5>
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<p>Note that parts must be documented on the <a href="http://parts.igem.org/Main_Page"> Registry</a>. This page serves to <i>showcase</i> the parts you have made. Future teams and other users and are much more likely to find parts by looking in the Registry than by looking at your team wiki.</p>
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<h5>Adding parts to the registry</h5>
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<p>You can add parts to the Registry at our <a href="http://parts.igem.org/Add_a_Part_to_the_Registry">Add a Part to the Registry</a> link.</p>
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<p>We encourage teams to start completing documentation for their parts on the Registry as soon as you have it available. The sooner you put up your parts, the better you will remember all the details about your parts. Remember, you don't need to send us the DNA sample before you create an entry for a part on the Registry. (However, you <b>do</b> need to send us the DNA sample before the Jamboree. If you don't send us a DNA sample of a part, that part will not be eligible for awards and medal criteria.)</p>
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<h5>What information do I need to start putting my parts on the Registry?</h5>
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<p>The information needed to initially create a part on the Registry is:</p>
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<li>Part Name</li>
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<li>Our SaCas9 can be programmed to cleave specific target sequence followed by the PAM sequence (5&rsquo;-NNGRRT-3&rsquo;).</li>
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<li>Part type</li>
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<li>Creator</li>
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<li>Sequence</li>
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<li>Short Description (60 characters on what the DNA does)</li>
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<li>Long Description (Longer description of what the DNA does)</li>
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<li>Design considerations</li>
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We encourage you to put up <em>much more</em> information as you gather it over the summer. If you have images, plots, characterization data and other information, please also put it up on the part page. </p>
 
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<h5>Inspiration</h5>
 
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<p>We have a created  a <a href="http://parts.igem.org/Well_Documented_Parts">collection of well documented parts</a> that can help you get started.</p>
 
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<p> You can also take a look at how other teams have documented their parts in their wiki:</p>
 
 
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<li><a href="https://2014.igem.org/Team:MIT/Parts"> 2014 MIT </a></li>
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<li>To express SaCas9, it requires suitable machinery such as promoter, RBS,and terminator.</li>
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<li><a href="https://2014.igem.org/Team:Heidelberg/Parts"> 2014 Heidelberg</a></li>
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<li>To programme SaCas9, you need to design guide RNA (tracrRNA [2], 21 bp spacer flanked by direct repeats [2] ).</li>
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<li><a href="https://2014.igem.org/Team:Tokyo_Tech/Parts">2014 Tokyo Tech</a></li>
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<h3>Advantages of SaCas9 compared with the conventional <em>Streptococcus pyogenes</em> Cas9:</h3>
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<h5>Part Table </h5>
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<li>Smaller size (1053 amino acids against 1368) resulting in an easier expression/delivery</li>
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<li>Different PAM sequence recognised (5&rsquo;-NNGRRT-3&rsquo; ) increasing the usability</li>
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<p>Please include a table of all the parts your team has made during your project on this page. Remember part characterization and measurement data must go on your team part pages on the Registry. </p>
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<li>Higher efficiency of SaCas9 over SpCas9 [2]</li>
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<p>[1] Ran, F. A., Cong, L., Yan, W. X., Scott, D. A., Gootenberg, J. S., Kriz, A. J., Zetsche, B., Shalem, O., Wu, X., Makarova, K. S., Koonin, E. V. Sharp, P.A., Zhang, F. 2015. In vivo genome editing using Staphylococcus aureus Cas9. Nature. 520 (7546). pp.186-191.</p>
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<p>[2] Friedland AE, Baral R, Singhal P, et al. Characterization of Staphylococcus aureus Cas9: a smaller Cas9 for all-in-one adeno-associated virus delivery and paired nickase applications. Genome Biology. 2015;16:257. doi:10.1186/s13059-015-0817-8.</p>
  
  
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Revision as of 01:04, 30 October 2017

PhagED: a molecular toolkit to re-sensitise ESKAPE pathogens

Parts

This year the iGEM Edinburgh_OG team focused on developing a modular toolkit using CRISPR systems and phages to re-sensitise antibiotic-resistant bacteria. As a BioBrick we submit the E. coli codon-optimised Staphylococcus aureus Cas9.

<groupparts>iGEM17 Edinburgh_OG</groupparts>




http://www.nature.com/news/genome-editing-revolution-my-whirlwind-year-with-crispr-1.19063



How does this part work?

  • Our SaCas9 can be programmed to cleave specific target sequence followed by the PAM sequence (5’-NNGRRT-3’).
  • To express SaCas9, it requires suitable machinery such as promoter, RBS,and terminator.
  • To programme SaCas9, you need to design guide RNA (tracrRNA [2], 21 bp spacer flanked by direct repeats [2] ).




Advantages of SaCas9 compared with the conventional Streptococcus pyogenes Cas9:

  • Smaller size (1053 amino acids against 1368) resulting in an easier expression/delivery
  • Different PAM sequence recognised (5’-NNGRRT-3’ ) increasing the usability
  • Higher efficiency of SaCas9 over SpCas9 [2]



[1] Ran, F. A., Cong, L., Yan, W. X., Scott, D. A., Gootenberg, J. S., Kriz, A. J., Zetsche, B., Shalem, O., Wu, X., Makarova, K. S., Koonin, E. V. Sharp, P.A., Zhang, F. 2015. In vivo genome editing using Staphylococcus aureus Cas9. Nature. 520 (7546). pp.186-191.

[2] Friedland AE, Baral R, Singhal P, et al. Characterization of Staphylococcus aureus Cas9: a smaller Cas9 for all-in-one adeno-associated virus delivery and paired nickase applications. Genome Biology. 2015;16:257. doi:10.1186/s13059-015-0817-8.

<groupparts>iGEM17 Edinburgh_OG</groupparts>