The first step needed for copying the DNA array was to genetically fuse antigen coding sequences to a 10xHis tag that was used for surface immobilization later. The whole expression cassette including promoter and terminator regions was amplified by PCR using an amino-labeled reverse primer. Via this amino group, the DNA was immobilized on an activated PDMS surface. The forward primer used for this PCR was labeled with Cy3. As it is shown in figure 1, spotting the DNA on the activated surface resulted in a distinct pattern visualized by Cy3 fluorescence.
More details about vector design and cloning strategies can be found here.

Cell-free expression

To establish a cell-free expression system, a bacterial lysate was produced and supplemented with several energy sources as well as co-factors and ions. GFP expression in our system was compared to a commercially available kit. In figure 2, the relative fluorescence of the samples is shown over time. After two hours the fluorescence indicates a x fold change of the amount of GFP in the sample compared to the beginning of the reaction. The commercially available kit reaches an x fold increase in relative fluorescence.
Additionally, it was shown that the expressed GFP is not only functional in terms of fluorescence but it also exhibits the same binding affinity to a commercial anti-GFP antibody as conventionally purified GFP (figure 3). Thus, our cell-free expression system can be used to mediate the copying process from a DNA template to a protein microarray.
The process of establishment and optimization of our cell-free expression system can be retraced here.

Figure 2: Comparison with self-made cell-free expression system and a commercially available kit. The relative fluorescence of cell-free expressed GFP is monitored over 2 hours in comparison with a commercial kit. For each system a no-DNA control was added enabling to calculate the fold change.

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Figure 3: Western Blot of conventionally and cell-free expressed GFP.

Specific surface

Using a cell-free expression system requires the establishment of a specific surface that prevents the binding of non-target proteins. A stable protocol for the production of Ni-NTA surfaces was developed. The 10xHis Tag complexes nickel ions on the surface resulting in a sufficiently strong binding of the protein. In figure 4, an unspecific PDITC surface and a Ni-NTA surface are compared. Flushing the slides with the same antibody solution resulted in a weaker signal for PDITC, which is explained by the binding of many non-target proteins blocking the surface for the His-tagged protein.
Additionally, we have shown that cell-free expressed and therefore non-purified protein can be efficiently immobilized on the surface in a sufficient amount to detect antibody binding by iRIf (figure 5). Figure 6 shows that several different antigen spots can be distinguished by flushing the slide with antibodies that are specifically binding to just one of them. Only the spot where the antigen corresponding to the used antibody is immobilized exhibits a signal.
The establishment of such a specific and reliable surface chemistry was a really challenging task. Here, you find all the improvements we achieved in this field.

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Figure 4: Quotion picture of an iRIf meassurement of non-purified, His-tagged GFP(?) on PDITC compared to Ni-NTA. Whole cell lysate was spotted either on an unspecific PDITC surface (A) or on a specific Ni-NTA surface (B) and flushed with anti-GFP(?). The quotion picture shows the change in thickness at distinct spots related to the rest of the surface.

Figure 5: Binding curve of anti-GFP to cell-free expressed GFP on a Ni-NTA surface. Cell-free expressed GFP was spotted on a specific Ni-NTA surface and flushed with anti-GFP. The binding curve indicated a binding event a certain spot.