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

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<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.</p>
 
<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.</p>
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<h4>Citations</h4>
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<li>Sander, Jeffry D., Joung, J. Keith, “CRISPR-Cas systems for editing, regulating, and targeting genomes”, Nature Biotechnology, 2013.</li>
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<li>Zetsche, Bernd, Volz, Sara E., Zhang, Feng, “A split-Cas9 architecture for inducible genome editing and transcription modulation”, Nature Biotechnology, 2015.</li>
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<li>Daya, Shyam, Berns, Kenneth I., “Gene Therapy using Adeno-Associated Virus Vectors”, Clinical Microbiology Reviews, 2008.</li>
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<li>Zhang, Feng et al., “In vivo genome editing using Staphylococcus aureus Cas9”, Nature, 2015.</li>
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<li>Scharenberg, Andrew M. et al., “Tracking genome engineering outcome at individual DNA breakpoints”, Nature Methods, 2011.</li>
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<li>Cox, David Benjamin Turitz, Platt, Randall Jeffrey, Zhang, Feng, “Therapeutic Genome Engineering: prospects and challenges”, Nature Medicine, 2015.</li>
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<li>Nureki, Osamu et al., “Crystal structure of staphylococcus aureus Cas9”, Cell, 2015.</li>
 
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Revision as of 15:46, 17 September 2015

Motivation Design Results

Results

Towards the end of our project, the Feng Zhang group at MIT published the crystal structure of saCas9 in 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 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, the other two split sites that they chose which were not as successful happened to be located in regions 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.

Citations

  1. Sander, Jeffry D., Joung, J. Keith, “CRISPR-Cas systems for editing, regulating, and targeting genomes”, Nature Biotechnology, 2013.
  2. Zetsche, Bernd, Volz, Sara E., Zhang, Feng, “A split-Cas9 architecture for inducible genome editing and transcription modulation”, Nature Biotechnology, 2015.
  3. Daya, Shyam, Berns, Kenneth I., “Gene Therapy using Adeno-Associated Virus Vectors”, Clinical Microbiology Reviews, 2008.
  4. Zhang, Feng et al., “In vivo genome editing using Staphylococcus aureus Cas9”, Nature, 2015.
  5. Scharenberg, Andrew M. et al., “Tracking genome engineering outcome at individual DNA breakpoints”, Nature Methods, 2011.
  6. Cox, David Benjamin Turitz, Platt, Randall Jeffrey, Zhang, Feng, “Therapeutic Genome Engineering: prospects and challenges”, Nature Medicine, 2015.
  7. Nureki, Osamu et al., “Crystal structure of staphylococcus aureus Cas9”, Cell, 2015.