Difference between revisions of "Team:Edinburgh OG/Basic Part"

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<h3>★  ALERT! </h3>
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<p>This page is used by the judges to evaluate your team for the <a href="https://2017.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2017.igem.org/Judging/Awards"> award listed above</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://2017.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
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  <h1 class="subtitle text-center">Basic Parts</h1>
  
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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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<h2 align="center"> Table of the Basic Parts BioBricks</h2>
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<tr><th style="width:8px" class="header"></th><th style="width:8px" class="header"></th><th style="width:8px" class="header"></th><th style="width: 87px;" class="header">Name</th><th style="width: 80px" colspan="" class="header">Type</th><th style="width: auto;" colspan="" class="header">Description</th><th style="width: 150px" colspan="" class="header">Designer</th><th style="width: 50px" colspan="" class="header">Length</th>
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<td class="status_cell  "></td><td class="status_cell cell_white">&nbsp;</td><td class="status_cell cell_green">W</td><td><a class="noul_link part_link" href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2330000">BBa_K2330000</a></td><td>Coding</td><td>SaCas9 codon-optimised for E. coli</td><td width="100px">filippo abbondanza</td><td align="right">3183</td>
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<h1>Basic Parts</h1>
 
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A <b>basic part</b> is a functional unit of DNA that cannot be subdivided into smaller component parts. <a href="http://parts.igem.org/wiki/index.php/Part:BBa_R0051">BBa_R0051</a> is an example of a basic part, a promoter regulated by lambda cl.
 
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<p>Most genetically-encoded functions have not yet been converted to BioBrick parts. Thus, there are <b>many</b> opportunities to find new, cool, and important genetically encoded functions, and refine and convert the DNA encoding these functions into BioBrick standard biological parts. </p>
 
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<h3>Best Basic Part Special Prize</h3>
 
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<p>Most genetically-encoded functions have not yet been converted to BioBrick parts. Thus, there are *many* opportunities to find new, cool, and important genetically encoded functions, and refine and convert the DNA encoding these functions into BioBrick standard biological parts. To be eligible for this award, this part must adhere to <a href="http://parts.igem.org/DNA_Submission">Registry sample submission guidelines</a> and have been sent to the Registry of Standard Biological Parts. If you have a part you wish to nominate your team for this <a href="https://2017.igem.org/Judging/Awards">special prize</a>, make sure you add your part number to your <a href="https://2017.igem.org/Judging/Judging_Form">judging form</a> and delete the box at the top of this page.
 
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<b>Please note:</b> Judges will only look at the first part number you list, so please only enter ONE (1) part number in the judging form for this prize. </p>
 
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<p>This page should list all the basic parts your team has made during your project. You must add all characterization information for your parts on the Registry. You should not put characterization information on this page. Remember judges will only look at the first part in the list for the Best Basic Part award, so put your best part first!</p>
 
  
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    <img src="https://static.igem.org/mediawiki/2017/c/c6/T--Edinburgh_OG--cas.png">
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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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    <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>To express SaCas9, it requires suitable machinery such as promoter, RBS,and terminator.</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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  <h3>Advantages of SaCas9 compared with the conventional <em>Streptococcus pyogenes</em> Cas9:</h3>
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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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    <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).
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    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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Latest revision as of 03:00, 2 November 2017

PhagED: a molecular toolkit to re-sensitise ESKAPE pathogens

Basic 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.

Table of the Basic Parts BioBricks

NameTypeDescriptionDesignerLength
 WBBa_K2330000CodingSaCas9 codon-optimised for E. colifilippo abbondanza3183

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.