Difference between revisions of "Team:Bielefeld-CeBiTec/Results/PRIA"

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<figcaption><b>Figure 12:</b> Cy3 labeled DNA is shown in red, sfGFP tagged repressor proteins are displayed in green. Common filter paper was the base for this experiment.</figcaption>
 
<figcaption><b>Figure 12:</b> Cy3 labeled DNA is shown in red, sfGFP tagged repressor proteins are displayed in green. Common filter paper was the base for this experiment.</figcaption>
 
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       <p>The next step for us was to establish the DNA-protein complex on paper. In order to test if the complex formation was successful we required at first a method for the simultaneous visualization of both components. Since the repressor proteins were tagged with sfGFP, they could be detected via fluorescence. Cy3-labeled DNA was also detectable on paper. We visualized both components with an Ettan Dige Scanner normally used for 2D-SDS-Pages. (See figure 12) The exposure time and the applied paper were optimized.  </p>
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       <p>The next step for us was to establish the DNA-protein complex on paper. In order to test if the complex formation was successful we required at first a method for the simultaneous visualization of both components. Since the repressor proteins were tagged with sfGFP, they could be detected via fluorescence. Cy3-labeled DNA was also detectable on paper. We visualized both components with an <a href="https://2015.igem.org/Team:Bielefeld-CeBiTec/Protocols#ettan">Ettan Dige Scanner</a> normally used for 2D-SDS-PAGEs. (See figure 12) The exposure time and the applied paper were optimized.  </p>
 
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Revision as of 11:42, 17 September 2015

iGEM Bielefeld 2015


PRIA Results

A Cell-free Detection System based on two purified Components

Introduction

Paper-based and cell-free systems offer lots of advantages. They are easy to use, universally applicable and safe. As a further development of the cell-free protein synthesis (CFPS) we created an in vitro cell-free system based on the binding of a purified repressor protein to purified DNA. Our aim is to establish an alternative kind of assay that works in vitro on paper. Repressor protein and DNA with the operator site form a complex in this assay. If the analyte is added to the complex, the repressor is supposed to change its conformation and release the DNA. For more information about the background, read this part.
In general, there are two different strategies to achieve this. First, the protein is immobilized and the DNA is added afterwards. Second, the DNA is immobilized first and the protein is added afterwards. Alternatively, the DNA-protein complex is formed in solution and immobilized afterwards.
The immobilized DNA-protein complex would then be distributed to the users, they would add their sample and a signal would be generated by the dissociation of the DNA -protein complex.
The first step is to prove that the complex formation and immobilization in vitro is reversible by addition of the analyte. We started our experiments with the repressor of the lac operon from E. coli (LacI) and its corresponding operator site lacO. We chose this model system, because it is good characterized and the substance the repressor reacts to is IPTG, which is easily available in molecular biology laboratories.

Successful Detection of an Analyte in vitro

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Figure 1: Effect of different salt concentrations on amount of DNA in the first elution step
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Figure 2:Quantification of DNA in different steps of PRIA, n=3

The procedure performed for PRIA was based on his-tagged repressor proteins immobilized on Ni-NTA agarose. Herefore, we constructed a device for the expression of his-tagged LacI. After purificatioon of the protein we immobilized it on Ni-NTA agarose in a reaction tube. Plasmid DNA containing the operator site for specific binding of the repressor was added to the Ni-NTA agarose, unbound plasmid was washed out and the remaining plasmid could be eluted by addition of the analyte to the wash buffer. The amount of DNA eluted upon addition of the analyte depends strongly on the salt concentration in the buffer used for washing and elution. (See figure 1) We analyzed the released DNA in the supernatant with agarose gel electrophoresis. The amount of DNA eluted in the first elution step compared to the total amount of DNA bound to the agarose after the forth washing step, is about 90 % .(See figure 2) Thus, the signal generated upon dissociation of the DNA-protein complex is definitely significant. Another explanation for an increased amount of DNA in the elution steps could have been dissociation of the protein and the bound DNA from the Ni-NTA agarose. The last step of the assay is elution of the protein from the Ni-NTA agarose with an imidazole buffer, to confirm the presence of the protein at the end of the prodcedure. Our analysis of the samples via SDS-Page shows clearly, that there is no significant loss of protein during the assay and most of the protein can be recovered upon elution with imidazole. (See figure 3) On a future test strip the immobilized DNA-protein complex would be provided. So the user just needs to add the potentially contaminated water plus sodium chloride and buffer solution which we would provide in the kit.


Furthermore, we tested many different conditions to further evaluate the robustness of PRIA. Tap water with the analyte alone could not disrupt the binding between the plasmid and the protein, the major part of plasmid remains bound to the protein. In the agarose gel DNA can be detected in the steps where the protein (and the DNA bound to it) is is eluted and in the fraction with the rest of the Ni-NTA agarose, which also still contains protein-DNA complexes. (See figure 4) Thus, the user would be required to add a certain amount of salt to the sample. In our assay we mainly applied pottasium chloride, but common sodium chloride is suitable for that purpose, as we tested. (See figure 5) Nevertheless, the solution should be slightly buffered with TRIS-HCl or sodium/potassium phosphate.

To further reduce the time for the assay we also tested whether the complex could be formed prior to addition of the complex to the Ni-NTA agarose. The results were similar to the performance with water instead of buffer. In this case the bond between repressor and plasmid could not be disrupted at all. In the agarose gel DNA was visible after the elution of the protein with imidazole that was performed to verify the presence of the protein at the end of the assay. Furthermore, it could still be detected on the Ni-NTA agarose. (See figure 6)

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Figure 3: Test for loss of protein in different steps of PRIA
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Figure 4: PRIA performed with water instead of buffer
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Figure 5: Usage of 500 mM NaCl instead of 500 mM KCl
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Figure 6: PRIA with DNA-protein complex added to Ni-NTA agarose

Our Strategies on Paper

After having created a functional assay with lacO-LacI our next step is to implement this approach immobilized on paper. We pursued two strategies. For the first strategy we immobilized repressor proteins fused with a cellulose binding domain from the iGEM team of the Imperial college in 2014 (BBa_1321340) on paper. After having added Cy3-labeled DNA with the operator site, the complex formation should be reversed through the analytes. Herefore, we cloned CBD to LacI for a proof of concept, BlcR (the repressor protein for our biosensor detecting date rape drugs) and ArsR (the repressor for the biosensor detecting arsenic).
Our second strategy is based on immobilized DNA which has a Cy3- and an amino-label. This time we fused super folder GFP to the same repressors (BBa_K1758202, BBa_K1758203, BBa_K1758204) and wanted to detect the released protein after analyte addition. arsO (BBa_J33201), Pblc (BBa_K1758375) and lacO. How we immobilized protein or DNA on paper is further described in the next sections.


Immobilization of Protein on Paper

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Figure 7: Cell lysate containing repressor proteins LacI and BlcR fused to a cellulose binding domain or sfGFP immobilized on paper after overnight washing

We aimed at the development of a paper-based system and optimized the procedure for immobilized protein. So we focused on the approach which was based on repressors fused to a cellulose binding domain (BBa_1321340). We cloned and expressed fusion proteins for our LacI-lacO model system, the repressor ArsR for the detection of arsenic and for the protein BlcR, the repressor of the blc-operon, which we were working with in order to detect date rape drugs. When we added the proteins onto various types of paper, their presence could be confirmed by staining the paper with Coomassie brilliant blue and destaining with destaining solution used for SDS-PAGEs. The binding was unspecific, since the spots with proteins containing the CBD and the spots containing proteins fused with sfGFP, which is not supposed to bind to paper specifically, still showed the same intensity of blue dye after over night washing. (See figure 7) Besides, most CBDs bind to microcrystalline cellulose or cotton (Lethiö et al.). We were not able to find a hint about the binding of CBDs to common paper. Additionally we came across certain difficulties concerning the purification of these proteins. That is why we focused on the second approach with immobilized DNA.

Successful Immobilization of DNA on Paper

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Figure 8: Original scan from the Typhoon. On the left hand side you see the papers prior to washing, on the right hand side the same papers after 45 min of washing in different solutions.

Based on a method proposed by Araújo et al., DNA was immobilized on filter paper previously activated with p-phenylene-diisothiocyanate (PDITC). To accomplish this, amino-labeled DNA is required. We made some adaptations to the original protocol in order to immobilize dsDNA instead of ssDNA. We omitted a 30 min washing step with 4x SSC buffer, since this serves for the denaturing of DNA. Furthermore, we hybridized the amino-labeled operator strand with the complementary strand that was Cy3 labeled to be able to quantify the DNA immobilized on the paper. This was performed via a simple annealing of these two oligonucleotides. So by detecting the Cy3 label via the Typhoon fluorescence scanner, we could be sure, that the immobilized DNA was the correct dsDNA.

We dissolved PDITC, the substance for activation of paper for DNA immobilization, in pure ethanol and DMSO. We compared which solvent is better for the activation. Herefore, we washed the immobilized DNA on paper, which was activated differently, and compared the remaining intensities of the Cy3 label on paper after washing. The immobilization works even better if ethanol is used as a solvent for the PDITC. The loss of signal can be mainly attributed to the washing out of DNA, since a control showed that the decrease of fluorescence of the Cy3 dye due to repeated scanning is minimal. We applied three different liquids for washing:

  1. an antibody stripping buffer that is normally used to disrupt all protein-protein interactions in a western blot. This resulted in strong blurring of the DNA spots.
  2. water
  3. the binding buffer that was normally used in PRIA

Compared to the remaining fluorescence signal on the activated papers the signal on the unactivated paper decreases strongly. (See figures 9 and 10) This indicated, that the immobilization of DNA on activated paper was successful. The fluorescence signals were quantified with imageJ.


Washing with binding buffer Sorry, cannot load this file at the moment
Figure 9: Development of the fluorescence signal of Cy3 labeled DNA that was immobilized on paper activated with PDITC dissolved in DMSO or ethanol respectively. Unactivated paper served as negative control. The paper was washed for 45 min with the binding buffer used in PRIA for stabilizing the protein DNA complex and scanned with the Typhoon fluorescence scanner various times during this process. The fluorescence was quantified with ImageJ and the peak areas were normalized to the values before the first wash.
Washing with water Sorry, cannot load this file at the moment
Figure 10: Development of the fluorescence signal of Cy3 labeled DNA that was immobilized on paper activated with PDITC dissolved in DMSO or ethanol respectively. Unactivated paper served as negative control. The paper was washed for 45 min with water and scanned with the Typhoon various times during this process. The fluorescence was quantified with ImageJ and the peak areas were normalized to the values before the first wash.

Successful Expression and Purification of functional sfGFP-tagged Repressor Proteins

For the approach to a paper-based test strip with immobilized DNA, super folding Green Fluorescent Protein (sfGFP)-tagged repressor proteins are required for the generation of a signal upon release. We tagged the repressors for the detection of arsenic, date rape drugs, as well as our model protein LacI with sfGFP C-terminally. Their specific binding to the operator DNA could be proven by electrophoretic mobility shift assay (EMSA). Upon increasing amounts of protein binding to the DNA the electrophoretic mobility of the DNA fragments decreases. This results in a shift between protein-DNA complexes and free DNA. It is visible that the labeled operator sites without protein added to them run faster in the gel compared to the operator sites occupied by specifically binding proteins. (See figure 11) So all fusion proteins retained their DNA-binding function. The two different shifts in the LacI-sfGFP EMSA result from the formation of tetramers that is typical for LacI. In some cases dithiothreitol was added to the reaction. It simulates reducing conditions, that are normally present in the cell. This can influence the performance of the repressors. In the case of BlcR it had no effect, but it enhances the binding of sfGFP-LacI to its corresponding binding site.

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Figure 11: EMSA shift caused by addition of different amounts of indicated protein to 0.05 pmol (0.5 pmol for ArsR-sfGFP) Cy3-labeled operator site. +/- refers to the presence of dithiothreitol in the reaction.

Successful simultaneous Visualization of Protein and DNA on Paper

Sorry, cannot show you these brilliant spots at the moment
Figure 12: Cy3 labeled DNA is shown in red, sfGFP tagged repressor proteins are displayed in green. Common filter paper was the base for this experiment.

The next step for us was to establish the DNA-protein complex on paper. In order to test if the complex formation was successful we required at first a method for the simultaneous visualization of both components. Since the repressor proteins were tagged with sfGFP, they could be detected via fluorescence. Cy3-labeled DNA was also detectable on paper. We visualized both components with an Ettan Dige Scanner normally used for 2D-SDS-PAGEs. (See figure 12) The exposure time and the applied paper were optimized.

Fluorescence Measurements in Plate Reader

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Figure 13: Change in fluorescence upon addition of arsenic in a 96-well plate coated with cellulose and with immobilized DNA. Different conditions were tested.

As an first approach to check whether the formation and dissociation of the complex was measureable and quantifiable, we decided to adapt an method for the examination of in vitro complex formation and dissociation described earlier: Siddiki et al. immobilized biotinylated DNA in a 96-well plate and added cell lysates to each well. The cell lysates contained GFP-tagged repressor proteins. After washing the wells once they would add their sample to the wells, wait for 15-30 minutes and measure the fluorescence in the supernatant. They report a concentration-dependent increase of the fluorescence in response to cadmium and arsenic. This increase in fluorescence was due to the dissociation of the GFP-tagged repressor proteins from the immobilized operator sites: the tagged proteins were eluted from the wells and became part of the supernatant. (Siddiki et al.)
We tried to reproduce these finding with a 96 well plate coated with Avicell microcrystalline cellulose. The measurement in the Tecan plate reader suggests that DNA was immobilized because the Cy3 signal is significantly above the background signal generated by the cellulose. Nevertheless, the measurement of the supernatant fluorescence showed no clear tendency, neither did the fluorescence that remained in the wells. We tested different conditions in order to optimize the protocol: the buffers used in our optimized PRIA protocol and the buffers described by Siddiki et al., to avoid unspecific binding of the protein to the cellulose we tested the effect of blocking the wells with milk powder solution prior to addition of the cell lysate for both buffer combinations. None of the observed changes were significant. (See figure 13) Probably this was due to the Avicell cellulose, which was not easy to handle, since great parts of it was lost during the different washing or transfer steps.

Conclusion

In summary PRIA has the potential to become a robust real world application. We delivered a convincing proof of concept for the detection of an analyte based solely upon in vitro interaction of protein and DNA. Nevertheless, buffers need to be optimized and adjusted to the certain proteins. The assay is functional on Ni-NTA agarose and only takes 15 min for the generation of a signal. Applying the method to paper will be a challenge, since the unspecific absorption of the protein by the paper has to be avoided in order to be able to establish a stable protein-DNA complex. Our results concerning the immobilization of DNA are encouraging, the DNA is bound with high stability onto common filter paper and can be washed for at least 45 min without significant loss. In future applications, PRIA can be adapted to detect several substances, for example heavy metals

References

Araújo, Ana Caterina; Song, Yajing; Lundeberg, Joakim; Stahl, Patrik L.; Brumer, Harry (2012): Activated Paper Surfaces for the Rapid Hybridization of DNA through Capillary Transport. In Anal. Chem. 2012, 84, pp. 3311-3317. DOI: 10.1021/ac300025v

Lehtiö, Janne; Wernerús, Henrik; Samuelson, Patrik; Teeri, Tuula T.; Stahl, Stefan (2001): Directed immobillization of recombinant staphylococci on cotton fibers by functional display of a fungal cellulose-binding domain. In FEMS Microbiol Lett. 2001, 195(2), pp. 197-204. DOI: 10.1111/j.1574-6968.2001.tb10521.x 197-204

Siddiki, Mohammad Shohel Rana; Kawakami, Yasunari; Ueda, Shunsaku; Maeda, Isamu (2011): Solid Phase Biosensors for Arsenic or Cadmium Composed of A trans Factor and cis Element Complex.In Sensors 2011, 11, pp. 10063-10073. 10.3390/s111110063