What is your role in DeDNAed?

In addition to coordinating the project, TUC leads work packages on “Integration of DNA origami hybrids” and “Transfer to flexible substrates and biosafety”. There our task is to integrate the DNA origami hybrid, so to say the biosensor platform on the substrate – this is done in WP5 in a solid way and in WP7 on a flexible substrate. We are a bridge between the nanocomponents, such as particles and the DNA origami and the more micro- and macroscopic world of the SERS measurement, the microfluidic cell and the substrate.

What are you working on at the moment?

Right now we are spending the most time on the immobilization of the DNA origami hybrid, testing variations of buffer conditions and surface modifications, as well as incubation times. In short, we are trying to optimize the whole process.

In the clean rooms we are structuring or etching the glass substrates for the flow cell and SERS measurement.

What have you achieved so far?

One milestone reached is that we can now immobilize the DNA origami itself, without functionalization. This can be done with different thin film systems now. We already achieved a variation of very these precise nanosized binding spots on the substrate to immobilize the DNA origami. Now we are going to transfer these experiments to the hybrid.

Have you changed course at all?

At the beginning we started with silicon wafers because that is the standard for microtechnology. But after some time, we had discussions with our partner at University of Le Mans and we decided to change the substrate to glass. The reason was that the silicon wafers have a strong SERS signal. For microtechnology processing this is a pretty critical change because we need silicon oxide for DNA origami and silicon oxide is easier to synthesise on the silicon wafer. However, we now use glass, which is basically already silicon oxide, but in comparison to our silicon oxide produced by thermal oxidation it is not sufficiently homogeneous in its structure and can contain impurities such as metals. Therefore, we do not use it for DNA origami deposition, but integrate an additional process step to create a reproducibly homogeneous SiO2 layer on the surface.. The switch to glass also leads to various other changes and challenges in the process, such as the characterization methods.

When we started the project initially, we hoped to use CF polymer as a bound-resistance layer in our thin-film system. But it was not possible in such a straightforward way, so we switched to parylene, which is promising material with superb chemical properties. But it turned out that the surface of Parylene was not as resistant to some processing as CF-polymer. However, now we are finally switching to CF polymer again due to its excellent properties as a bond-resistant layer and try Parylene and CF polymer in parallel.

We have also started the immobilization process with a surface functionalization poly-L-lysine and pluronics, which is already published. Now we want to change it up a bit further because the surface chemistry and kinetics of the hybrid are completely different from those of the DNA origami alone, so we have to add some modifications.

What do you expect from the final stage of the project?

We hope we can measure something [laughs]!

I hope that we can realize the demonstrator. This means that we can immobilize the DNA origami hybrids on the substrate surface and integrate them into the flow cell and start characterizing the SERS biosensor and determine that it is so sensitive that it is worth improving it further in a follow-up project.

Will DeDNAed have an impact in your field?

Yes, in two ways: first, for microtechnology it will be interesting because we do nanostructuring and etching on two layers on a transparent and isolating substrate, which is no standard substrate in nanotechnology using an electron beam lithography (eBeam). This is not that easy to do and will be worth publishing. (We have already shown it in a poster presentation.) This is something that will be interesting to add to existing nanostructuring processes, using the eBeam.

On the other hand, we have the immobilization of a DNA origami hybrid, which is not common. Normally DNA origami is only selectively immobilized without functional elements on its surface. However, the most novel part is the immobilization on a flexible substrate. Once we have it all figured out this will have a big impact on the DNA origami community.

And of course, the sensor itself will have a big impact on the biosensor and point of need market if we can demonstrate the high sensitivity we expect.