Engineering Nanopores for Biomolecular Sensing, Transport and Trapping

Doktorsavhandling, 2026

The ability to study and control biomolecules at the single-molecule level offers new possibilities to improve our understanding of life. Many single-molecule methods, however, require the molecules to be immobilised or exposed to external forces, which may alter their natural behaviour. This thesis presents new types of nanostructures and surface functionalisations with polymer brushes, tailored for sensing, transport and trapping of biomolecules, with the aim of non-intrusive, long-term trapping of proteins in a nanoscale cavity.

Nanopore sensors detect single molecules through transient modulations of the ionic current as they pass through a nanopore. New algorithms for baseline correction and event detection are introduced, which enable accurate event frequency analysis at high voltages and thereby label-free, calibration-free quantification of analytes. Long measurements at high voltages also require stable pores, which motivated the fabrication of nanopores by electron beam lithography and reactive ion etching, a wafer-scale process that can produce both single pores and arrays. With these pores, the strong electric field in nanopores was shown to disrupt even strong biomolecular interactions, implying that binding affinities determined with nanopore sensors may differ from those in the absence of a field.

To keep proteins trapped, they must be prevented from escaping by diffusion, for instance by a barrier of polymer brushes. Nanopores were therefore functionalised with brushes of poly(ethylene glycol) or poly(N-(2-hydroxyethyl)acrylamide), and the voltage bias used in nanopore sensing was used to drive biomolecules through the brush barrier. Both DNA and proteins of different size and charge passed through these nanopores only above a threshold voltage, with no leakage at lower voltages. This demonstrates voltage-controlled transport of biomolecules with single-molecule readout.

Finally, a pore-cavity-pore device with material-selective surface functionalisation is presented, together with preliminary trapping results. Loading such a cavity through a polymer brush functionalised nanopore would make it possible to count the molecules as they enter, giving ultimate control over the trapping. Together, these results lay the foundation for loading, counting and non-intrusively retaining individual proteins in nanoscale cavities.