Team:Freiburg/Results
Main Results
Our aim was to develop a novel diagnostic tool enabling fast, simultaneous and label-free detection of antibodies in human blood sera. We successfully generated our self-established cell-free expression system based on an E. coli lysate, which revealed an expression efficiency comparable to a commercial kit. To immobilize the expressed proteins, we established a surface that specifically binds our target proteins. Combined in a microfluidic chamber we produced a protein array that can be flushed with a serum sample Label-free detection of antigen-antibody binding can be done in real-time by the interferometric method called iRIf (imaging Reflectometric Interference). Finally we built our own detection device in a simplified and cost-efficient manner and thus, making it available for future iGEM Teams. Using the DiaCHIP, we did not only show the presence of antibodies in distinct solutions but also verified them in complex samples as human blood serum.
Detection of Anti-Tetanus Antibodies in Human Blood Serum
To test the DiaCHIP under real-life conditions, we analysed the blood serum of a person that has been immunized against tetanus for the presence of anti-tetanus antibodies. First we confirmed the binding of antibodies present in the blood to our purified tetanus antigen by ELISA. Then we spotted the antigen and GFP, which both were expressed in E.coli and purified by His-tag affinity purification, on a PDITC surface. The much stronger binding of blood components to the tetanus antigen spots compared to GFP spots indicates specific interactions. By confirming that the bound blood components are human antibodies with anti-human, we successfully demonstrated that we are able to detect antibody binding even in complex samples. ▼ Detailed Description.
Figure 2: Western Blot of His-tagged C. tetani antigen with anti His-tag HRP Conjugate. The soluble fraction of the overexpressed protein was used for this Western Blot. The expected molecular weight is 50 kDa. Anti- His Tag HRP conjugated antibody was used in a 1:1000 dilution in blocking buffer.
The antigen used for detection of anti-tetanus antibodies is derived from the tetanus neurotoxin and commonly used for in vitro testing. For preparation of the DiaCHIP, this antigen had to be overexpressed in E. coli and purified from whole cell lysate. To verify the successful purification of the antigen, Western Blot analysis was performed (figure 2). The usage of an antibody against the N-terminal His-tag revealed a protein with a molecular weight of about 50 kDa. This correlates with the expected molecular weight of the antigen 1).
We performed an ELISA to investigate, whether the blood samples we obtained contain antibodies that bind specific to our purified tetanus antigen. Therefore, we spotted tetanus antigen and bBSA of the same concentration (12.5 µg/mL) and 2 times PBS as negative controls. The tetanus antigen and one PBS well were incubated with 5 mg/mL BSA, blood serum, and HRP-labeled anti-human for 1 h, respectively. The bBSA and the other PBS well were incubated with HRP-labeled Streptavidin (0.5 µg/mL) for 1 h (positive control). After each step the wells were washed with PBS. To visualize the binding, Tetramethylbenzidine was added and the absorption at 650 nm was measured in a plate reader over time (figure 3). The absorption signal for tetanus is even higher than the positive control, which illustrates the successful binding of antibodies from the blood to tetanus antigen.
After the validation of the antigen antibody binding for tetanus by ELISA we wanted to see if we can detect this interaction also with iRIf. Therefore we first expressed our Clostridium tetani antigen and GFP in E.coli. The purified His-tagged proteins then were spotted on a PDITC surface. The slide with the immobilized proteins was flushed with human blood serum, and anti-human antibody. Strong binding was detected for the tetanus antigen spots, while the GFP spots only exhibited minimal binding (see figure 1A-D). This indicates that components contained in the blood serum bind specifically to the tetanus antigen. The subsequent binding of anti-human antibody to the tetanus antigen spots (figure 4) confirms the presents and binding of human antibodies to the spotted tetanus antigens. These results successfully demonstrate that it is possible to detect the binding of antibodies from blood serum to antigens immobilized, on a surface.
With an additional experiment we wanted to see if we can differentiate the vaccination status of patients with our system. Therefore we used blood serum samples, taken before and two weeks after immunization against tetanus. A slide with immobilized tetanus antigen and GFP was prepared (figure 5). It was consecutively flushed with both blood sera. The blood serum taken after vaccination exhibits a much more intense binding to the tetanus spot than the serum taken before binding. Unfortunately we did not had enough anti-human antibody to proof further the presents of bound human antibodies from blood serum.
While the outcome of this first experiment looked promising for our future application to determine the vaccination status of patients, further experimentation did not confirm these initial results. We were still able to detect binding of both blood sera to the tetanus antigen, but no difference in binding intensity was visible. To test the assumption that the used blood was not fresh enough and therefore lost some of its binding capabilities a fresh blood sample five weeks after vaccination was taken for the experiment (See figure 6B and C). To determine whether the identification of the vaccination status is possible with our system further experimentation needs to be done.
Besides tetanus, other antigens of immunological relevance were taken into account. See all the results we obtained in terms of diagnostics.
Detection of Anti-GFP Antibodies using Cell-Free Expressed GFP on Ni-NTA
Our self-made cell-free expression mix, the DiaMIX, in combination
with specific glass surfaces allows the expression and immobilization of
target proteins in a distinct manner. The DiaMIX, after expressing His-
tagged GFP, was spotted onto a Ni-NTA coated glass slide side-by-side with
conventionally purified His-GFP. Even after several washing steps it could
be shown that the proteins maintain stable on the surface. This is shown via
an iRIf measurement: Antibodies against GFP are flushed over the slide to
detect GFP that is bound to the slide. The specific binding of anti-GFP
antibodies to the control spot (purified GFP) and the cellfree expressed GFP
confirms the success of cellfree GFP expression and its immobilization on
the surface.
▼ Detailed
Description.
We could successfully show that the cell-free expression of His-GFP results in functional GFP proteins that are bound by anti-GFP antibody during an iRIf measurement. The DNA coding for GFP fused to a 10x His-tag was added to the DiaMIX and expression was performed for 2 h. The DiaMIX containing cell-free expressed His-GFP was then spotted on an iRIf slide with a Ni-NTA surface by hand (figure 1). The spots were incubated on the slide overnight.
This specific surface allows binding of the expressed His-GFP via the His-tag while all the other proteins present in the DiaMIX are not bound to the surface. This step was followed by the blocking and washing protocol to prevent further unspecific binding.
The iRIf slide was then flushed with an anti-GFP antibody solution, to analyze the binding to the cell-free expressed His-GFP. As a positive control we spotted a purified His-GFP onto the surface as well as DiaMIX that did not contain any DNA as negative control figure 2).
Find out more about the preparation of the DiaCHIP by producing a protein microarray from a DNA template
using cell-free expression.
The measurement shows a high signal for the cell-free expressed His-GFP and the positive control as can also be seen in the respective binding curve shown in figure 3.
Building Our Low-Cost DiaCHIP Measuring Device
Commercial systems using the iRIf technology (imaging Reflectomretric Interference) are mostly bulky and expensive machines even though the components they are based on are rather simple. So we decided on building our own device consisting of not much more than two lenses, an LED and a camera. With this system we were able to reliably detect the binding of anti-GFP to GFP, thus confirming a detection sensitivity in the range of protein-protein interactions. To enable future iGEM Teams to profit from this device as we did, we provide all plans and parts necessary to rebuild it on this website for everyone to download and use. ▼ Detailed Description.
To test our device we aimed at reproducing measurements that we were previously able to perform in our commercial device. For this reason we focused on using two antibodies: anti-GFP and polyclonal anti-rabbit. GFP and rabbit derived anti-HCV (Hepatitis C Virus) antibody were used as antigens in this experiment. Note that the anti-HCV antibody only served as binding partners for the anti-rabbit antibodies, since no HCV proteins were used in this experiment. The antigens were spotted onto an iRIf slide with an APTES/PDITC surface. The spots on the slide were produced by pipetting 3.5 µl [1 mg/ml] rabbit-anti-HCV protein and 3.5 µl [1 mg/ml] GFP onto the slide and incubated overnight. After incubation the slide was blocked for 30 min in BSA solution. A Canon 50D camera was used to record the measurement and was set to take one picture every 5 seconds. The exposure time was set in order for the pixels in the image to be approx. 80% of maximum light saturation before the solution was flushed onto the chip. The antibody solutions were pipetted into the flow-chamber without the use of any microfluidic device. Instead, a syringe was loaded with 660 µl [5 µg/ml] anti-GFP antibody solution (diluted in PBS) and connected to the input pipe of our device. The content of the syringe was then slowly released via this pipe into the chamber of the device by gently dispensing the solution from the syringe. When the whole volume was run over the chip, the process was repeated with 660 µl [5 µg/ml] anti-rabbit antibody solution in the same way. The injection of both solutions was performed during approximately 45 minutes.
The quotient pictures show all intensity shifts that occurred during the measurement. Two left spots: GFP spots at which an intensity shift occurred during anti-GFP flush. Right spot: anti-HCV antibody (derived from rabbit), at which an intensity shift occurred during the flush with anti-Rabbit.
Video 1 shows the results of the measurement. Both, binding of anti- GFP and anti-rabbit to the corresponding antigen spots, could be observed. Due to the fact that the experiment was performed on our DiaCHIP device which was built with a transparent casing, fluctuations in surrounding light had a strong, detrimental influence on the measurement quality. To minimize the influence of the unstable surrounding light, the resulting pictures had to be averaged over 10 pictures each. This in turn led to a more stable light situation, however the signal strength dropped as a consequence. Figure 3 shows a quotient picture of the measurement where the light situation was temporarily appropriate. The problem of surrounding light scattering into the device can of course be overcome using a non-transparent casing. An evaluation of how well our device performs in comparison with the professional device was not performed, mainly due to time constraints. However our results hint that we get comparable results for strong binding such as GFP/anti-GFP, as can be seen in figure 4.
▲ Close BoxEstablishing a Highly Specific Ni-NTA Surface
Figure 1: Cell-free expressed GFP-His spotted on a Ni-NTA slide. Cell-free expression was performed for 2 hours at 37°C. The positive control was purified GFP-His, the negative control was a sample of cell-free expression mix not containing DNA.
Since there are a variety of proteins present in the cell-free mix a specific surface on the future protein array is essential. That is why we established our Ni-NTA surface for the immobilization of the antigens on the chip. All expression constructs contain a His-tag fused to the coding sequence, resulting in antigens that can bind specifically to our Ni-NTA surface. Compared to an unspecific surface (PDITC) we could show that this Ni-NTA surface allows efficient binding of the target protein and prevents unspecific binding of other proteins that are present in the cell-free mix (figure 1). ▼ Detailed description.
For cell-free protein expression lots of different proteins, like RNA-polymerases, ribosomes and other E. coli proteins are essential. During the process of cell-free expression all these proteins are, besides the target protein, also present in the microfluidic chamber. To have a sufficient amount of target protein immobilized on the chip we established a specific surface chemistry on the glass slide. After testing several tag systems we established a Ni-NTA surface. Using a Ni-NTA covered glass slide (figure 1) we could increase the amount of bound cell-free expressed His-GFP compared to an unspecific surface (figure 2). In both experiments 1.5 µg of self purified GFP-His was used as positive control. The cell-free expression mix without DNA is supposed to result in no target protein and served as negative control. The cell-free reactions were performed for 2 hours at 37°C in a seperate tube prior to pipetting the samples by hand onto the surfaces and incubated on the slide overnight. Before measurment in the iRIf device, the optical detection method we use, the slides were blocked with BSA and then flushed with anti-GFP antibodies. An increase in light intensity where the spotted protein was located represents a binding event. Due to less unspecific binding of proteins to the surface, the interaction of anti-GFP antibodies with cell-free expressed His-GFP is higher on the Ni-NTA surface.
▲ Close BoxProducing Our Cell-free Expression Mix
A key feature of our DiaCHIP is the on-demand antigen production via cell-free expression. Thereby, a fixed DNA template is copied into our desired antigen, which in turn can bind to our specific surface. Our expression mix called DiaMIX was established from scratch. It is based on an E. coli lysate. In a direct comparison with a commercial product our mix showed comparable expression rates, indicating its performance capability (figure 1). ▼ Detailed Description.
Our DiaMIX is a complex system consisting of several individually
adjusted components that allow us to make use of the cells own production
system, without the tedious drawbacks of normal cell-based protein
expression.
As a main component of the DiaMIX the E. coli lysate contains the
necessary transcription and translation apperatus. The lysate is
complemented by additives needed for energy regeneration, buffering, and
generation of the protein. An overview of cell-free expression systems and
its components can be found on our project
pages.
As ultimate evaluation, we compared the DiaMIX to a commercial kit
as seen in figure 1.
Both expression systems successfully expressed the applied
vector.
Furthermore, the cell-free expression of GFP with our cell-free mix
could be verified in an iRIf measurement.
To obtain these final results, a lot of optimization and testing had
to be done. Want to know more about how we established the DiaMIX? You can
find detailed information about the most important experiments on the cell-free
expression results page.
Explore the DiaCHIP
For establishing our device, we optimized all steps from the
immobilization of DNA on the silicone of the flow-chamber to the specific
binding of the target proteins on the glass slide. This way, we generated
protein arrays we can use to detect different antibodies in human and rabbit
serum with the iRIf detection method.
Click on the images below to
explore our experiments from expression to detection!
Assembling the DiaCHIP
Diagnosis of Antigens
Click on one of the images to get a further insight on how we build our DiaCHIP
