Difference between revisions of "Team:Waterloo/Design"
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<p>Kleinstiver et al. recently demonstrated modified spCas9 with altered PAM specificity <cite ref="Kleinstiver2015"></cite>. | <p>Kleinstiver et al. recently demonstrated modified spCas9 with altered PAM specificity <cite ref="Kleinstiver2015"></cite>. | ||
| − | Their results motivated us to explore computational methods of assessing spCas9 mutants for altered PAM specificity profiles. We created an analysis pipeline using python that makes use of PyRosetta, a well known molecular dynamics toolkit. Our suite of scripts is described in our | + | Their results motivated us to explore computational methods of assessing spCas9 mutants for altered PAM specificity profiles. We created an analysis pipeline using python that makes use of PyRosetta, a well known molecular dynamics toolkit. Our suite of scripts is described in our <a href="https://2015.igem.org/Team:Waterloo/Modeling">modeling</a> and <a href="https://2015.igem.org/Team:Waterloo/Modeling/Software">software</a> pages. |
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Revision as of 03:29, 19 September 2015
Design
Simple sgRNA Exchange
[Lab paragraph]
[Math paragraph]
Cas9 PAM Flexibility
Being able to target DNA at different protospacer adjacent motif (PAM) site will allow scientists to target a larger portion of the genome. "Dead" Cas9 (dCas9) allows for easier analysis of products because the DNA still remains intact. Kleinstiver et al proposed an EQR variant of Cas9 with three amino acid substitutions. This new proposed version of Cas9 targeted an NGAG PAM sequence. Our design was to make these three amino acid substitutions in dCas9 and try to target an NGAG PAM site in GFP.
Kleinstiver et al. recently demonstrated modified spCas9 with altered PAM specificity . Their results motivated us to explore computational methods of assessing spCas9 mutants for altered PAM specificity profiles. We created an analysis pipeline using python that makes use of PyRosetta, a well known molecular dynamics toolkit. Our suite of scripts is described in our modeling and software pages.
CRISPR Plant Defense
[Lab paragraph]
[Math paragraph]
To model antiviral application, looked at the antiviral effects of CRISPR/Cas9 targeting on three scales: CaMV genomes, plant cells and plant leaves. A background primer on Cauliflower Mosaic Virus (CaMV) genetics, replication and spread can be found on the CaMV Biology page.
References
By talking about your design work on this page, there is one medal criterion that you can attempt to meet, and one award that you can apply for. If your team is going for a gold medal by building a functional prototype, you should tell us what you did on this page. If you are going for the Applied Design award, you should also complete this page and tell us what you did.
Note
In order to be considered for the Best Applied Design award and/or the functional prototype gold medal criterion, you must fill out this page.
This is a prize for the team that has developed a synthetic biology product to solve a real world problem in the most elegant way. The students will have considered how well the product addresses the problem versus other potential solutions, how the product integrates or disrupts other products and processes, and how its lifecycle can more broadly impact our lives and environments in positive and negative ways.
If you are working on art and design as your main project, please join the art and design track. If you are integrating art and design into the core of your main project, please apply for the award by completing this page.