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| − | <p>
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| − | We wanted to start our project by showing that Cas13a's collateral activity could be used to detect the presence of specific RNA. For this, we used the RNAse alert system, as done in a recent publication<sup><a class="myLink" href="#ref_11">11</a></sup>, to detect RNA digestion. In this assay, the presence of RNAse-like activity is detected by an increase in green fluorescence. Our experiments yielded a convincing proof-of-principle which we went on to model. Moreover, CascAID can be used to detect a wide spectrum of pathogens, as our experiments with gram-positive and viral targets suggested. As we wanted to make CascAID available for everyone, we focused on building an inexpensive fluorescence detector to measure the presence of the target. Our detector “Lightbringer” was designed to be able to detect the fluorescence produced by the fluorescein in the Rnase alert system<sup><a class="myLink" href="#ref_12">12</a></sup>, but we theorize that changing the filters allows detection of other fluorophores. In addition, we experimented with freeze-drying on paper to make CascAID durable and easily portable.
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| − | </p>
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| − | <img src="https://static.igem.org/mediawiki/2017/7/7f/T--Munich--Description_Cas13a_Readout_Comparision.svg">
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| − | <p>Cas13a can be used to detect specific RNA sequences</p>
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| − | </td>
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| − | <a href="http://www.uni-muenchen.de/studium/lehre_at_lmu/index.html"><img src="https://static.igem.org/mediawiki/2017/9/9a/T--Munich--Logo_LehreLMU.gif" width="200"></a>
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| − | <p>Picture of the Thermocycler</p>
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| − | </td>
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| − | <p>
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| − | 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.
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| − | </p>
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| − | </td>
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| − | <h3>Colorimetric read-outs</h3>
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| − | <p>
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| − | To couple CascAID with an easy read-out method we explored three colorimetric read-outs:
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| − | </p>
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| − | </td>
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| − | <p>
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| − | <b>AeBlue</b>: The RNA strand in a specially designed RNA/DNA dimer is cut by Cas13a's collateral
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| − | activity. After digestion, the interaction between the two strands is too weak to hold the dimer and it
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| − | decays. We can then use the DNA-strand as template to translate the chromoprotein <a href="http://parts.igem.org/Part:BBa_K864401">aeBlue</a>.
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| − | </p>
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| − | </td>
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| − | <td colspan=4 align=center valign=center>
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| − | <img src="https://static.igem.org/mediawiki/2017/9/90/T--Munich--Description_aeBlue.svg">
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| − | <p>Diagram of aeBlue</p>
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| − | </td>
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| − | </tr>
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| − | <p>
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| − | <b>Intein-Extein</b>: By binding TEV-protease with a RNA-linker we can use Cas13a's collateral activity
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| − | to regulate the protease's diffusion and use it to cleave a TEV tag separating the intein regions of a
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| − | modified chromophore. After the first cleavage, the intein segment excises itself<sup><a class="myLink" href="#13">13</a></sup>, bringing together the
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| − | halves of the chromophore. Only then is the chromophore functional and produces the colorimetric
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| − | read-out.
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| − | </p>
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| − | </td>
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| − | <a href="http://www.uni-muenchen.de/studium/lehre_at_lmu/index.html"><img src="https://static.igem.org/mediawiki/2017/9/9a/T--Munich--Logo_LehreLMU.gif" width="200"></a>
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| − | <p>Diagram of Intein-Extein</p>
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| − | </td>
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| − | </tr>
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| − | <tr class="lastRow"><td colspan=2 align=center valign=center>
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| − | <p>
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| − | <b>Gold nanoparticles</b>: Gold nanoparticles coated with short DNA sequences are held closely
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| − | together by a complementary linker RNA, which makes the solution intense blue<sup><a class="myLink" href="#14">14</a></sup>. Activated Cas13a cuts
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| − | the linker RNA, causing the nanoparticles to diffuse away from each other. This increase in distance
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| − | causes a color change to intense red.
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| − | </p>
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| − | </td>
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| − | <td colspan=4 align=center valign=center>
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| − | <img src="https://static.igem.org/mediawiki/2017/b/b3/T--Munich--Description_Goldnanoparticles.svg">
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| − | <p>Gold nanoparticles</p>
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| − | </td>
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| − | </tr>
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| − | <h3>Software</h3>
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| − | <p>
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| − | To help facilitate the design of crRNA, the sequences that give CascAID its specificity, we developed a
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| − | software tool that checks crRNA for unwanted secondary structures. This gives valuable insight on
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| − | whether the sequence is suited to use with Cas13a or whether some modifications are needed.
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| − | Together with Team Delft's software tool which designs the corresponding crRNA based on the target,
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| − | we collaborated to develop a powerful tool that suggests crRNA sequences and checks their usability
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| − | </p>
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| − | </td>
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| − | </tr>
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| − | <h3>References</h3>
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| − | <p>
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| − | <ol style="text-align: left">
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| − | <li id="ref_1">Cohen, Limor, and David R. Walt. "Single-Molecule Arrays for Protein and Nucleic Acid Analysis." Annual Review of Analytical Chemistry 0 (2017).</li>
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| − | <li id="ref_2">Nakano, Michihiko, et al. "Single-molecule PCR using water-in-oil emulsion." Journal of biotechnology 102.2 (2003): 117-124.</li>
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| − | <li id="ref_3">Taniguchi, Yuichi, et al. "Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells." science 329.5991 (2010): 533-538.</li>
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| − | <li id="ref_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.</li>
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| − | <li id="ref_5">Pardee, Keith, et al. "Rapid, low-cost detection of Zika virus using programmable biomolecular components." Cell 165.5 (2016): 1255-1266.</li>
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| − | <li id="ref_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.</li>
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| − | <li id="ref_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.</li>
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| − | <li id="ref_8">Vashist, Sandeep Kumar, et al. "Emerging technologies for next-generation point-of-care testing." Trends in biotechnology 33.11 (2015): 692-705.</li>
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| − | <li id="ref_9">Gubala, Vladimir, et al. "Point of care diagnostics: status and future." Analytical chemistry 84.2 (2011): 487-515.</li>
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| − | <li id="ref_10">Abudayyeh, Omar O., et al. "C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector." Science 353.6299 (2016): aaf5573.</li>
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| − | <li id="ref_11">Gootenberg, Jonathan S., et al. "Nucleic acid detection with CRISPR-Cas13a/C2c2." Science (2017): eaam9321.</li>
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| − | <li id="ref_12">https://www.idtdna.com/pages/docs/technical-reports/in_vitro_nuclease_detectionD325FDB69855.pdf (retrieved: 13.10.17)</li>
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| − | <li id="ref_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.</li>
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| − | <li id="ref_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.</li>
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| − | </ol>
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| − | </p>
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