In this project we have worked on the synthesis and optimization of the enzyme-conjugated DNA sensor. According to the general idea, the addition of the enzymatic substrate can cause the production or consumption of protons, so that the induced pH-change can be detected by a DNA device.
In order to obtain a better communication between the enzymes and the DNA devices, we investigated the possibility of employing a polymeric DNA-based structure as a scaffold to co-localize the enzyme with the DNA-responsive module. To do that, we have used the well-known DNA nanotubes, a design reported by Winfree, Rothemund and Franco. It is also already demonstrated that the disassembly and re-assembly of such structures can be easily controlled with the addition of several regulator strands.
In this reporting period we have reached several results. We first focused the attention on the characterization of several DNA-based systems, like pH-dependent triplex structures or also aptamer-based nanodevices, that can be controlled through different inputs, like pH, light, enzymes or small molecules.
We then demonstrated the possibility to functionalize the above described tile-based DNA structures with multiple functional groups. For example, we have employed pH-dependent DNA nanoswitch to obtain scaffolds that can be visualized in a pH-dependent way. Then, we have also developed novel strategies that allow to dynamically exchange the decoration on the DNA structures without destroying the scaffold itself.
Moreover, to better control the communication between the functional groups of the different tiles, we also investigated novel strategies to finely control the assembly/disassembly process of such DNA-based structures or also to trigger the re-organization of such DNA structures, for example from homopolymers to random copolymers and block copolymers. Specifically, we demonstrated novel strategies to achieve this re-organization in a spontaneous way by employing enzymatic or chemical dissipative reactions.
Finally, more recently, we are investigating the possibility of employing such tile-based DNA structures as nanomaterials to generate a readout signal in a lateral flow assay (LFA).
During this period I also participated to several international conferences, and among them I received two invitations, one as a finalist for the “European Young Chemist Award”, for which I received the Silver Medal.
