Difference between revisions of "Team:BostonU/App 2/Results"

 
(12 intermediate revisions by 2 users not shown)
Line 18: Line 18:
  
 
<h3>Results</h3>
 
<h3>Results</h3>
−
<p>Unfortunately, the system we designed had some errors, and we were unable to gather any useful data on our split SaCas9 experiment. We tested the full SaCas9 on the traffic light reporter, and there was no fluorescence at all, so we concluded that no double stranded break had been made. We realize that there may have been an issue with our choice of target sequence within the traffic light reporter. For future analysis, we can test the SpCas9 on the traffic light reporter to see how feasible the system is before moving on to SaCas9 and split SaCas9 halves.</p>
+
<p>We were excited to have identified 16 candidate split sites, and cloned most of these split saCas9 constructs into the FKBP-FRB dimerizable domain backbones, in both orientations. We set up our flow cytometry experiments similarly to our integrase and RDF ones, except used our traffic light reporter and new guide RNA designs.</p>
 +
 +
<p>When performing flow cytometry, we measured mCherry (NHEJ) and GFP (HDR) fluorescence values in arbitrary units. Each transfection condition was performed in triplicate on every plate, and thus we were able to obtain the mean and standard deviation across three replicates. However, the results that we obtained using flow cytometry were not optimal. Below is a result of our conditionally dimerizable saCas9 variants (in both domain orientations). </p>
  
−
<p>Towards the end of our project, the Feng Zhang group at MIT published the crystal structure of saCas9 in Cell<sup>1</sup>. The paper demonstrated the development of a conditionally dimerizable saCas9 system using the FKBP-FRB domain pairs and PYL-ABI domain pairs, which is what we wanted to accomplish. </p>
+
<center><img style="height:50%; width:40%;" src="https://static.igem.org/mediawiki/2015/thumb/d/dd/Sacas9_gfp_finalized_.png/800px-Sacas9_gfp_finalized_.png" />
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 +
<img style= "height:50%; width:40%;" src="https://static.igem.org/mediawiki/2015/thumb/2/2d/Sacas9_mcherry_finalized.png/800px-Sacas9_mcherry_finalized.png" />
 +
<center>
  
−
<p>One facet worth noting is that the Zhang group used the 3D structure of the saCas9 protein to target flexible linker regions that would serve as potential split sites. Out of the three split sites that they chose, the one that worked best was almost identical (one amino acid away) to one of the split sites that we identified using our model. Furthermore, the other two split sites that they chose which were not as successful happened to be located in regions with secondary structural elements. </p>
+
<p>We noticed that we got a low raw fluorescence signal using this reporting system, even with the intact saCas9. Because of this, we did not calculate or plot normalized % GFP or % mCherry for this system. We believe that our negative results are likely due to our modified gRNAs using the traffic light reporter system - these might not have optimally functioned, thus resulting in minimal saCas9 activity. We would debug our initial experimental workflow by adding in an additional control - characterizing how spCas9 (for which the traffic light reporter system was initially designed) functioned. If we had a functional reporter system, we could properly characterize our split saCas9 variants and identify any viable splits and interesting trends.</p>
  
−
<center><img style="height:75%; width:75%; padding:30px;" src="https://static.igem.org/mediawiki/2015/thumb/e/e8/SaCas9_plasmids_with_split_sites_ours_vs_zhang.png/799px-SaCas9_plasmids_with_split_sites_ours_vs_zhang.png" /></center>
+
<p>Despite unsuccessful flow cytometry results, we had another interesting finding to share. Towards the end of our project (at the very end of August), the Feng Zhang group at MIT published the crystal structure of saCas9 in the journal Cell7. The paper demonstrated the development of a conditionally dimerizable saCas9 system using the FKBP-FRB domain pairs and PYL-ABI domain pairs, which is what we originally wanted to accomplish.</p>
  
−
<p style="padding-bottom:60px;">This important result gave us some experimental validation that our model could offer scientists insights into choosing promising viable split sites for proteins, without only relying on 3D structures of proteins.</p>
+
<p>One facet worth noting is that the Zhang group used the 3D structure of the saCas9 protein to target flexible linker regions that would serve as potential split sites. Out of the three split sites that they chose, the one that worked best was almost identical (one amino acid away) to one of the split sites that we identified using our model. Furthermore, another split sites that they chose happened to be fairly close to one that we chose. Finally, the third split that they created was intended to be a negative control - we did not pick any split sites near this split, and it happened to be located in a region with secondary structural elements.</p>
  
 +
<center><img style="height:75%; width:75%; padding:30px;" src="https://static.igem.org/mediawiki/2015/thumb/3/39/New_sacas9_plasmids_w_split_sites.png/799px-New_sacas9_plasmids_w_split_sites.png" /></center>
 +
 +
<p>This important result gave us some experimental validation that our model could offer scientists insights into choosing promising viable split sites for proteins, without only relying on 3D structures of proteins. We also predict that our two split saCas9 constructs chosen near the Zhang lab sites would likely be viable, though we would need to experimentally confirm this.
 +
</p>
  
 
<h4 style="font-size:16px; text-align:center;">Citations</h4>
 
<h4 style="font-size:16px; text-align:center;">Citations</h4>

Latest revision as of 23:21, 18 September 2015

Motivation Design Results

Results

We were excited to have identified 16 candidate split sites, and cloned most of these split saCas9 constructs into the FKBP-FRB dimerizable domain backbones, in both orientations. We set up our flow cytometry experiments similarly to our integrase and RDF ones, except used our traffic light reporter and new guide RNA designs.

When performing flow cytometry, we measured mCherry (NHEJ) and GFP (HDR) fluorescence values in arbitrary units. Each transfection condition was performed in triplicate on every plate, and thus we were able to obtain the mean and standard deviation across three replicates. However, the results that we obtained using flow cytometry were not optimal. Below is a result of our conditionally dimerizable saCas9 variants (in both domain orientations).

               

We noticed that we got a low raw fluorescence signal using this reporting system, even with the intact saCas9. Because of this, we did not calculate or plot normalized % GFP or % mCherry for this system. We believe that our negative results are likely due to our modified gRNAs using the traffic light reporter system - these might not have optimally functioned, thus resulting in minimal saCas9 activity. We would debug our initial experimental workflow by adding in an additional control - characterizing how spCas9 (for which the traffic light reporter system was initially designed) functioned. If we had a functional reporter system, we could properly characterize our split saCas9 variants and identify any viable splits and interesting trends.

Despite unsuccessful flow cytometry results, we had another interesting finding to share. Towards the end of our project (at the very end of August), the Feng Zhang group at MIT published the crystal structure of saCas9 in the journal Cell7. The paper demonstrated the development of a conditionally dimerizable saCas9 system using the FKBP-FRB domain pairs and PYL-ABI domain pairs, which is what we originally wanted to accomplish.

One facet worth noting is that the Zhang group used the 3D structure of the saCas9 protein to target flexible linker regions that would serve as potential split sites. Out of the three split sites that they chose, the one that worked best was almost identical (one amino acid away) to one of the split sites that we identified using our model. Furthermore, another split sites that they chose happened to be fairly close to one that we chose. Finally, the third split that they created was intended to be a negative control - we did not pick any split sites near this split, and it happened to be located in a region with secondary structural elements.

This important result gave us some experimental validation that our model could offer scientists insights into choosing promising viable split sites for proteins, without only relying on 3D structures of proteins. We also predict that our two split saCas9 constructs chosen near the Zhang lab sites would likely be viable, though we would need to experimentally confirm this.

Citations

  1. Nureki, Osamu et al., “Crystal structure of staphylococcus aureus Cas9”, Cell, 2015.