Difference between revisions of "Team:EPFL/Results"

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                     <p style="font-size:17px"; align="justify">Finally, we tested the ability of our OnePot PURE system to express super folding GFP.
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                     <p style="font-size:17px"; align="justify">Expression of sf GFP on OnePot and PURExpress for different concentrations of the DNA template, measured in the plate reader using excitation wavelength of 535nm .</br> </br>
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We initiated 10μl reactions using our own Protein Solution, Energy Solution and Ribosome Solution, while altering the concentration of the DNA template. The goal of this experiment was to determine the optimal concentration of DNA in each reaction. In addition, we included similar reactions of PURExpress from NEB to compare our system to the commercially available one.
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In the following graphs we show the Fluorecein concentration of the samples, measured at an excitation wavelength of 535 nm, using 2.5, 5 and 10nM of DNA template.</br> </br>
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                  <div class="post-content"><p style="font-size:17px;"align="justify"> As we can see, OnePot PURE has an even higher expression of sfGFP than PURExpress*. The initial hypothesis, that 5nM of DNA is the optimal concentration, is also confirmed. We still get slightly higher fluorescence at 10nM but the difference is insignificant when taking into account that the concentration of DNA in our sample doubled. </br> </br>
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*Because of the extreme difference between the output of OnePot and PURExpress, we repeated the experiments to rule out the effect of a human error using a different batch of PURExpress, but we got the exact same results.</br> </br>
 
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Revision as of 22:24, 20 October 2019





Results

DNA Extraction


TO PUT: PCR for EC: gBlock, kit extraction, MN extraction, control
Nanodrop graphs: gBlock, kit extraction, MN extraction, control
Comparison of leaves after MN and standard extraction (MN: leaf intact, standard: destroyed)

DNA Extraction:

To test our method of extraction, we decided to try it on a non-infected grapevine leaf. To detect the extraction product, we performed a PCR We compared it to a traditional kit-based extraction, and to our synthetic EC sequence. The kit we used is DNeasy Plant Pro Kit by Qiagen.


DNA Extraction:
Here we performed Nanodrop UV absorption spectra : Red Line corresponds to gBlock;
Black Line corresponds to MN extraction.

DNA Amplification


Multiplexing :
as our final test would contain all 3 primer pairs, we tested if the amplification was functional with various combinations of primer pairs. The results show that amplification is successful for each test, though the endogenous sequence seem to amplify more than the phytoplasma sequences.




Amplification in grapevine extract : We wanted to know if the RPA would be hindered by the presence of plant coumpounds extracted along with the DNA (in particular, phenols and polysaccharides are known to act as PCR inhibitors8). Using our microneedle method, we extracted the DNA of an uninfected grapevine leaf. We then carried out two experiments :

  • We tested that our RPA worked for endogenous control in plant extract
  • We performed a limit of detection by spiking different concentrations of our synthetic FD DNA into the microneedle extract (MNE)


The endogenous control amplification was successful in MNE.
The limit of detection seems to show bands for FD as low as 10 copies/μl (50 copies total). We can see a "ladder pattern" for concentrations equal to or below 1000 copies/μl. This pattern occurs when the concentration of template is too low and unspecific primer-driven amplification happens (See the DNA amplification page for more details).

All in all, RPA has proved to function in grapevine extract.

Toehold switches


Toehold design:
Referred to Green et al. 2014 paper and optimized based on BioBitsTM toehold, we designed the following toeholds. Each group has 4 candidates who ranked as top 4 in their design score.


Toehold assembly :
Here we take BN 2.1 (Bois Noir 2nd Version, N°1) toehold as an example, our desired length is 961 bps which is approved by our Electrophoresis gel:


Toehold functionality:

In our project, we've used two kind of triggers. For the ssDNA trigger, there is no need of T7 polymerase transcription, therefore eliminate some uncertainties. But in the real case, we will use dsDNA as trigger, thus it is essential to compare their expression rates:

The error bar of the expression rate overlaps, no significant difference is detected.

In order to test the limit of detection of our toehold, we've run a test for toehold expression in different concentration of trigger DNA, by theory in the detectable range the difference should be bigger when the concentration of trigger increases:

There is a detectable difference from 100nM, and it grows when the concentration goes up, which suits our theory.

Signal Generation

The DNA sequence coding for catechol-2,3-deoxygenase (CDO), and completed with an ribosome binding site (rbs) and T7 promoter and terminator sites, was successfully assembled from the XylE (gene coding for CDO) template provided in the iGEM 2019 DNA Distribution kit, by using a 2-step PCR protocol. The gene assembly was verified by a Sanger DNA sequencing which showed that the DNA template was 99.8% accurate, for a total sequence length of 1045 bases.

This sequence was then expressed in our OnePot PURE cell-free system and incubated in presence of catechol. A yellow color was observed after 30 minutes of incubation, and it became brighter one hour after the start of the reaction. There were no colors in the t wo controls performed, one without catechol but with CDO template and the other one without CDO template but with catechol. This proved that the color was indeed created by the reaction of CDO with catechol and not by self-oxidation of catechol.

OnePot PURE

Expression of sf GFP on OnePot and PURExpress for different concentrations of the DNA template, measured in the plate reader using excitation wavelength of 535nm .



© iGEM EPFL 2019