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

✓ 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.