Latest revision as of 03:57, 29 October 2011

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Wiki Highlights

Read our project description and summary on our Project page: more details on how team members completed work for the three sections of our project are on Design, Synthesize, and Test pages, respectively.

Results of all parts of our project (including our biobricks) are located on our Results page, along with an Attributions and Acknowledgments section.

Human practices can be found on our Human Practices page.

Please be sure to stop by our poster during the poster session with any questions.

Accomplishments

Experimental Results

✓ Researched zinc finger proteins and choose 6 novel, clinically relevant target sequences
✓ Generated 55,000 zinc finger protein sequences using bioinformatics
✓ Used three recently developed technologies together for the first time: a foundational advance
✓ Expressed those 55,000 sequences in E.coli, with a sub-library for each target
✓ Created a genomic one-hybrid selection system sensitive enough to detect one hit in a million
✓ Found at least 15 novel zinc finger proteins

Biobricks and Protocols

✓ Submitted 5 Biobricks to the registry, including our one-hybrid selection strain
✓ Created several chassis for our Biobricks, including our one-hybrid selection strain
✓ Used and shared our easy-to-follow protocols
✓ Made protocols, Biobricks, and source code freely available, so that others can adapt them for other projects

Human Practices

✓ [http://www.youtube.com/watch?feature=player_embedded&v=eBT8SaBAm80 Interviewed] zinc finger researchers Dr. Keith Joung and Dr. George Church
✓ Interviewed chip-based DNA synthesis researcher Dr. Sriram Kosuri
✓ Researched intellectual property and how it applies to zinc finger proteins
✓ Created a timeline and case study of zinc finger intellectual property
✓ Reached out to our elected representatives about the potential effects of IP on zinc finger research and synthetic biology generally
✓ Handed out IP pamphlets and chassis data sheets at our poster presentation
✓ Educated local high school students about synthetic biology to provide accurate information from sources other than the media.

Foundational Advance

Combining Computational Design, High-throughput Synthesis, and Selection

We brought together 3 new technologies to create a working pipeline that allows scientists to engineer novel protein-DNA interactions. Our methods represents a fundamentally different way of building new biological parts and devices: using selection to identify working members of a large computationally predicted library of potential designs.

Putting parts and devices directly onto the genome

The genome is the next frontier in synthetic biology. Our project has made use of genome modification in order to design a new device that allows the testing of DNA-protein interactions. We want iGEM and the broader synthetic biology community to use these techniques as an alternative to plasmids. To encourage their adoption, we have submitted new E. coli chassis that allow easy genome modification, and we have provided detailed protocols for their use.

@@ Line 25: / Line 25: @@
 '''✓''' [https://2011.igem.org/Team:Harvard/Project/Synthesize Expressed] those 55,000 sequences <html><x>in E.coli</x></html>, with a sub-library for each target <br>
 '''✓''' [https://2011.igem.org/Team:Harvard/Project/Test#Fine-tuning_the_one-hybrid_selection_system Created] a <html><x>genomic one-hybrid selection system</x></html> sensitive enough to detect <html><x>one hit in a million </x></html> <br>
-'''✓''' [https://2011.igem.org/Team:Harvard/Results#Novel_Zinc_Fingers Found] up to <html><x>15 novel zinc finger proteins</x></html> <br>
+'''✓''' [https://2011.igem.org/Team:Harvard/Results#Novel_Zinc_Fingers Found] at least <html><x>15 novel zinc finger proteins</x></html> <br>
 ==Biobricks and Protocols==
@@ Line 35: / Line 35: @@
 ==Human Practices==
 '''✓''' [http://www.youtube.com/watch?feature=player_embedded&v=eBT8SaBAm80 Interviewed] <html><x>zinc finger researchers</x></html> Dr. Keith Joung and Dr. George Church<br>
+'''✓''' [https://2011.igem.org/Team:Harvard/Technology/Chip_Synthesis#The_Man_Behind_the_Research:_Sriram_Kosuri_on_Chip-Based_DNA_Synthesis Interviewed] chip-based DNA synthesis researcher Dr. Sriram Kosuri  <br>
 '''✓''' [https://2011.igem.org/Team:Harvard/Human_Practices Researched] <html><x>intellectual property</x></html> and how it applies to zinc finger proteins<br>
 '''✓''' [https://2011.igem.org/Team:Harvard/Human_Practices Created] a <html><x>timeline and case study</x></html> of zinc finger intellectual property<br>
@@ Line 43: / Line 44: @@
 =Foundational Advance=
 ==Combining Computational Design, High-throughput Synthesis, and Selection==
-We <html><x>brought together 3 new technologies</x></html> to create a working pipeline that allows scientists to <html><x>engineer novel protein-DNA interactions</x></html>. Our methods represents a <html><x>fundamentally different way of building new biological parts and devices</x></html>: using selection on a large computationally designed library of potential designs.
+We <html><x>brought together 3 new technologies</x></html> to create a working pipeline that allows scientists to <html><x>engineer novel protein-DNA interactions</x></html>. Our methods represents a <html><x>fundamentally different way of building new biological parts and devices</x></html>: using selection to identify working members of a large computationally predicted library of potential designs.
 ==Putting parts and devices directly onto the genome==
-<html><x>The genome is the next frontier in synthetic biology</x></html>. Our project has made use of genome modification in order to design a new device that allows the testing of DNA-protein interactions. We want the iGEM and the broader synthetic biology community to use these techniques as an alternative to plasmids. To encourage their adoption, <html><x>we have submitted new E. coli chassis that allow easy genome modification</x></html>, and <html><x>we have provided detailed protocols</x></html> for their use.
+<html><x>The genome is the next frontier in synthetic biology</x></html>. Our project has made use of genome modification in order to design a new device that allows the testing of DNA-protein interactions. We want iGEM and the broader synthetic biology community to use these techniques as an alternative to plasmids. To encourage their adoption, <html><x>we have submitted new E. coli chassis that allow easy genome modification</x></html>, and <html><x>we have provided detailed protocols</x></html> for their use.
 </div>

Team:Harvard/Judging

From 2011.igem.org