Team:BostonU/FusionProteins

From 2014.igem.org

Revision as of 01:17, 14 October 2014

• TEAM
• PROJECT
  • Overview
  • Priority Encoder
  • MoClo Assembly Method
  • Low Copy Backbones
  • Tandem Promoters
  • Fusion Proteins
  • Repressor Proteins
  • Multiplexing
  • BioDesign Automation Tools
  • Future Work
• ACHIEVEMENTS
  • Data Collected
  • Parts Submitted
  • Chimera Workflow
  • Chimera Example
  • Medal Fulfillment
• NOTEBOOK
  • Training
  • Protocols
  • Backbones
  • Tandem Promoters and Repressors
  • Fusion Proteins
• CONSIDERATIONS
  • Collaborations
  • Measurement Track
  • Safety
  • Interlab Study
  • NEGEM
  • Policy and Practices
• ACKNOWLEDGEMENTS

Fusion Proteins

Why Fusion Proteins? As described here, our main goal last summer was to come up with an efficient workflow to design, build and test large genetic devices. To demonstrate the efficacy of our workflow , we started building a priority encoder. In order to test the individual transcriptional units and the regulatory arcs associated with them, we needed the output for the individual parts of the device to be fluorescence. One way to do this is by using the bicystronic design - Bicystronic Design that could be used as an alternative to fusion proteins A peculiar effect was observed in relation to this design. When ribosomes bind to the genes sequentially, the ribosome that binds before might block the next ribosome from binding to the mRNA and translating the gene. So, the later genes are expressed less than the genes before. This problem is solved with fused proteins as only one ribosome will then be required to translate the entire sequence, eliminating any possible problems during translation. [REFERENCE NEEDED] Another way to measure function by fluorescence is by using consecutive transcriptional units - This design drives up the cloning cost as it usually takes more time cloning multiple transcriptional units. Fusion Proteins are fused coding sequences that allow us more direct measurement of fluorescence than either of the other designs. They reduce order effect seen with the bicystronic design and also, should theoretically be much easier to build as compared to cloning multiple TUs. Assembly To make fusion proteins, we used the Modular Cloning method that we have used for most digestion-ligation reactions. First, we added a new MoClo fusion site (I - TCTA) to the genes (at the end of repressors and before the reporter proteins). The fusion site, I (TCTA) was then added to another 2-nucleotide sequence (GA) to make the XbaI site. This was done to allow the two proteins made by the two gene to split up after translation. Phusion Polymerase Chain reaction was performed on the basic MoClo Level 0 parts using primers designed based on the fusion sites. We ended up with repressors with TCTAGA sequence at their ends and reporter proteins with the same sequence at the start. These can be treated as standard Level 0 parts which can then be assembled and tested using MoClo. Testing It is important that the fusion proteins made aren’t drastically inferior to the individual action of the repressor or the fusion proteins. In order to test this, the following Level 2 constructs were assembled using MoClo - J00-C12_AE - R10-C40-E40m_EF - R40-E10_FG J00-C12_AE - R10-C40-E30_EF - R40-E10_FG J00-C12_AE - R10-C80-E40m_EF - I13-E10_FG J00-C12_AE - R10-C80-E30_EF - I13-E10_FG Here onwards, all constructs made were to compare with those above. Simply put, all 6 Level 2s below were used a controls. J00-C12_AE - R10-C80_EF - I13-E10_FG J00-C12_AE - R10-E30_EF - I13-E10_FG J00-C12_AE - R10-E40m_EF - I13-E10_FG J00-C12_AE - R10-C40_EF - R40-E10_FG J00-C12_AE - R10-E30_EF - R40-E10_FG J00-C12_AE - R10-E40m_EF - R40-E10_FG * All constructs contain BCD2_BC as 5' UTRs and B0015 as terminators. Detailed progress on the construction of fusion proteins can be found in the Fusion Proteins notebook.

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