Difference between revisions of "Team:Munich/HP/Silver"

Thanks to advances in molecular biology and biochemistry, scientists have been able to consistently detect lower and lower concentration of molecules¹, to the point that single molecules can be reliably recognized with methods such as polymerase chain reaction (PCR)², fluorescence in situ hybridization (FISH)³ and enzyme-linked immunosorbent assays (ELISA)⁴. This has opened doors for synthetic biology to create better and more accurate diagnostic tests that use biomarkers like nucleic acids and proteins as targets^5,6. Through such advances, the field of molecular diagnostics developed. Unfortunately, current standard methods require expensive equipment or trained personnel, which generally limits their usability to hospitals or laboratories. Recently, there has been a push to develop new tests that fuse the reliability of standard methods with affordable platforms such as lab-on-a-chip or paper strips to overcome this restrictions^7-9. We wanted to help close this gap and set out to engineer a diagnosis principle for the detection of a wide array of targets that could be used without difficult-to-meet technical requirements.

Make Munich (6th and 7th May 2017)

Make Munich is the south Germany«s biggest maker and do-it-yourself tech festival. This was a 2-day event where many innovative, technology loving makers had the opportunity to show their skills in their booths, in talks and in various workshops. This year there were a huge variety of booths and workshops from different categories. Also, the audience who visited the event included young kids, students, and seniors. This event was a perfect event for all kinds of audiences fascinated with technological advances.

We are very thankful to the Make Munich team for inviting us to this fascinating tech event. This was our very first public event where we did our first poster presentation and our first public interaction. We got many encouraging comments and ideas on how we could proceed in future. Plus, we also met many tech and synbio geeks who were very kind to give their views on our project development. We also had the opportunity to meet many startups which were based on synthetic biology as well. Plus, we also met some old iGEMers from different countries who gave us more tips on handling our iGEM project.

Picture of the Thermocycler

For RNA extraction from the samples we tested three methods: extraction with silica beads, extraction with silica membrane and heat lysis. We custom-built an affordable thermocycler for signal amplification by RT-PCR to improve the detection limit. We explored recombinase polymerase amplification (RPA), an isothermal amplification procedure, to use over more conventional PCR methods as its simplicity makes it the more attractive option.

Colorimetric read-outs

To couple CascAID with an easy read-out method we explored three colorimetric read-outs:

AeBlue: The RNA strand in a specially designed RNA/DNA dimer is cut by Cas13a's collateral activity. After digestion, the interaction between the two strands is too weak to hold the dimer and it decays. We can then use the DNA-strand as template to translate the chromoprotein aeBlue.

Diagram of aeBlue

Intein-Extein: By binding TEV-protease with a RNA-linker we can use Cas13a's collateral activity to regulate the protease's diffusion and use it to cleave a TEV tag separating the intein regions of a modified chromophore. After the first cleavage, the intein segment excises itself¹³, bringing together the halves of the chromophore. Only then is the chromophore functional and produces the colorimetric read-out.

Diagram of Intein-Extein

Software

To help facilitate the design of crRNA, the sequences that give CascAID its specificity, we developed a software tool that checks crRNA for unwanted secondary structures. This gives valuable insight on whether the sequence is suited to use with Cas13a or whether some modifications are needed. Together with Team Delft's software tool which designs the corresponding crRNA based on the target, we collaborated to develop a powerful tool that suggests crRNA sequences and checks their usability

References

1. Cohen, Limor, and David R. Walt. "Single-Molecule Arrays for Protein and Nucleic Acid Analysis." Annual Review of Analytical Chemistry 0 (2017).
2. Nakano, Michihiko, et al. "Single-molecule PCR using water-in-oil emulsion." Journal of biotechnology 102.2 (2003): 117-124.
3. Taniguchi, Yuichi, et al. "Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells." science 329.5991 (2010): 533-538.
4. Rissin, David M., et al. "Single-molecule enzyme-linked immunosorbent assay detects serum proteins at subfemtomolar concentrations." Nature biotechnology 28.6 (2010): 595-599.
5. Pardee, Keith, et al. "Rapid, low-cost detection of Zika virus using programmable biomolecular components." Cell 165.5 (2016): 1255-1266.
6. Slomovic, Shimyn, Keith Pardee, and James J. Collins. "Synthetic biology devices for in vitro and in vivo diagnostics." Proceedings of the National Academy of Sciences 112.47 (2015): 14429-14435.
7. Tang, Ruihua, et al. "A fully disposable and integrated paper-based device for nucleic acid extraction, amplification and detection." Lab on a Chip 17.7 (2017): 1270-1279.
8. Vashist, Sandeep Kumar, et al. "Emerging technologies for next-generation point-of-care testing." Trends in biotechnology 33.11 (2015): 692-705.
9. Gubala, Vladimir, et al. "Point of care diagnostics: status and future." Analytical chemistry 84.2 (2011): 487-515.
10. Abudayyeh, Omar O., et al. "C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector." Science 353.6299 (2016): aaf5573.
11. Gootenberg, Jonathan S., et al. "Nucleic acid detection with CRISPR-Cas13a/C2c2." Science (2017): eaam9321.
12. https://www.idtdna.com/pages/docs/technical-reports/in_vitro_nuclease_detectionD325FDB69855.pdf (retrieved: 13.10.17)
13. Anraku, Yasuhiro, Ryuta Mizutani, and Yoshinori Satow. "Protein splicing: its discovery and structural insight into novel chemical mechanisms." IUBMB life 57.8 (2005): 563-574.
14. Link, Stephan, and Mostafa A. El-Sayed. "Size and temperature dependence of the plasmon absorption of colloidal gold nanoparticles." The Journal of Physical Chemistry B 103.21 (1999): 4212-4217.