What is your role in DeDNAed?

We are responsible for making two parts of the sensor platform. On the one hand we create the plasmonic particles for the enhancement of the optical readout signal, which is crucial for the Raman spectroscopy. Basically, by creating this hotspot between two plasmonic particles we can increase the signal by quite a big factor compared to standard Raman spectroscopy.

What I’m doing is synthesizing these particles, which are rather big gold spheres. We have an interesting technique for ensuring good quality (round shape and high monodispersity), well surpassing commercially available options. Then I need to functionalize these gold spheres with single-stranded DNA so we can attach them to the DNA origami platform in the end.

Our other role is making one of the sensing elements. We have this interchangeable sensing element linker on the DNA origami and one of the elements that we want to try there is also single-strand DNA-based – a DNA aptamer for the detection, in this case of food toxins. We have developed two aptamers now, one of which is for the detection of Aflatoxin B₁, which is a toxin that can be found e.g. in things like peanuts, for which it is important to detect it with high sensitivity. The other toxin we were working on is Ochratoxin A, which can appear e.g. in wine and other grape products. These aptamer have further been functionalized with metallic nano-clusters (atomic clusters) as an additional readout for verification of the correct attachment of the aptamer to the DNA origami platform. The advantage of all these is that they are biocompatible and non-toxic.

What are you working on at the moment?

I am always making particles for the other teams: especially now in the end phase they are trying loads of different options for the final assembly. And then I am also still verifying the aptamers so we have a better handle on their sensitivity and to have a cross-reference for our sensor for future publications. We do this also because we saw some differences to the literature, so I am doing some additional checks with these aptamers in a reduced system only using nanoparticles and aptamers. I am doing this in close collaboration with Saloni Agarwal from University of Potsdam using switchSENSE technology and Aicha Azziz from IMMM using SERS spectroscopy.

What have you achieved so far?

First, the nanoparticles work quite well: they attach nicely to the DNA origami.

As for the aptamers, we had a nice milestone of making a 3-segmented DNA strand with the attachment for the DNA origami, the aptamer part and the part for functionalizing it with the atomic clusters. We have been able to verify this for both aptamers, so we could already show that this works as a system. Now we are just doing some final tests to get more data.

Have you changed course at all?

We added one aptamer because the first one for Aflatoxin B₁ had a lower sensitivity than what we had expected from the literature. We had cross-checks done by UP and IMMM, but they confirmed the low sensitivity. We then decided to try another aptamer, which is more reliable but is showing similar problems, which is the reason for the additional testing that is still ongoing. So altogether, we have more tools in our box now.

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

We will need to coordinate very well in the last phase, but it looks promising that we will soon have a working sensor platform.

Will DeDNAed have an impact in your field?

I think this concept of DNA as a nano-breadboard is very promising for other applications and sensor designs. It could be used as a template for other non-SERS-based approaches also using other optical techniques or chemical readouts.