Aim of this project is to set up a screening process for the selection of aptamers that can act as antimicrobials. We will collaborate with the teams’ specialists in nanopores sensing (Keyser) and in the antimicrobial activity of DNA nanostructures (Mela). We will test the affinity of both RNA and DNA aptamer binding to pharmacologically relevant target proteins (Mela) in a single nanopore experiment. We will focus on selection of nucleic acid structures that can form non-covalent hybrids with proteins that are crucial for bacterial function. The relative ease in varying the aptamer sequences enabled by the design of both RNA and DNA hybrid nanostructures for nanopore sensing will rapidly yield quantitative data. The binding studies will guide a deeper understanding of the design rules for selective aptamer binding. The project will provide data for the collaborators in the BioHYBRITE project who will input and suggest possible improvements of the aptamer designs and analysis of the nanopore translocation data. In the second part of the project, the selected aptamers will be chemically modified to enable covalent binding to improve the dissociation constant compared to conventional antibody designs. The project will concentrate on antibacterial aptamers (Mela) and include the characterization of off-target effects and toxicity of the designed RNA and DNA aptamers for human cells.