General position of the field

Before the start of DYNAMO, solid-state nanopores were already established as a powerful platform for single-molecule biophysics and biomolecular sensing. In the basic experiment, a nanometre-scale pore separates two electrolyte reservoirs. A voltage drives ions through the pore and also drives charged biomolecules such as DNA or RNA through the sensing region. Each translocation produces a short change in ionic current, from which information about molecular size, conformation and transport dynamics can be extracted.

Remaining limitation

However, the field had not yet solved the problem of reliable high-resolution molecular identification. Straightforward ionic-current readout is very sensitive to molecular velocity, signal-to-noise ratio, pore geometry and event-to-event variability. This is especially problematic for short DNA and RNA molecules, modified bases or single-base differences, because the available information must be collected during a very short residence time in the nanopore. A central challenge was therefore not only how to detect that a molecule had passed through a nanopore, but how to control and interpret the molecular motion well enough to identify chemical or structural features.

Motivation for electro-optical approaches

Electro-optical nanopores, including approaches based on fluorescence, FRET, plasmonic enhancement and SERS, were proposed as routes to add molecular specificity beyond standard ionic-current detection. In principle, optical readout could provide chemical or structural fingerprints while the nanopore localises the molecule and provides electrical detection. Yet this strategy still depends critically on translocation dynamics: the molecule must remain in or near the sensing volume for long enough, with sufficiently reproducible orientation and position, for an interpretable optical or electrical signature to be recorded.

State-of-the-art gap

Thus, at the start of DYNAMO, the field had strong proof-of-principle results for single-molecule nanopore detection, but lacked a complete mechanistic understanding of the transport process under realistic experimental conditions. Key unresolved questions included the roles of hydrodynamic drag, electro-osmotic flow, ion-specific effects, local molecular structure, labels, pore geometry and surface interactions. Addressing these questions was essential for translating nanopore detection into robust molecular readout.

Updated field direction

The field has increasingly moved from simple detection of translocation events towards quantitative, interpretable and multi-modal readout. Modern nanopore experiments do not only ask whether a molecule passes through a pore; they ask how the molecule moves, how local features are mapped onto the signal, and how experimental conditions can be adjusted to improve resolution. This is especially important for applications involving molecular barcodes, labelled DNA carriers, short nucleic acids, protein-nucleic-acid complexes and future electro-optical sensing platforms.

Contribution 1: conceptual framework

The first major contribution of the PhD work was a comprehensive review of double-stranded nucleic-acid translocation through solid-state nanopores, now published in Physics of Life Reviews [1]. The review organised the field around the physical processes that determine translocation, including electrophoretic driving, hydrodynamic drag, electro-osmotic effects, polymer conformation, pore geometry, folding and signal formation. This provided a broad framework for interpreting nanopore experiments and for identifying which transport effects matter for future high-resolution sensing.

Contribution 2: molecular labels and readout

A second contribution was an experimental study of how dense molecular labelling affects DNA translocation. Labels are central to many nanopore readout strategies because they can encode sequence position, protein binding or structural information along a carrier molecule. The work showed that dense labelling can leave the global translocation time largely preserved, and the overall velocity profile is preserved across labels. This result is important for designing labelled nanopore assays: labels can be used for obtaining positional and structural information without needing label-specific corrections. [2]

Contribution 3: transport control and electrohydrodynamics

Ongoing work extends this theme by investigating stronger slowdown mechanisms and investigating electro-osmotic flow in nanopore systems with a custom designed electro-optical setup with unprecedented flow resolution, in collaboration with JR(?). Slowing molecules down is directly relevant to the original DYNAMO challenge, because longer residence times increase the time available for electrical or optical interrogation. Electro-osmotic flow measurements are also important because flow can either assist or oppose electrophoretic motion and can vary with salt type, concentration, pH and pore geometry. Understanding these effects helps explain why the same molecule may behave differently under different nanopore conditions. We also demonstrated the passage of multiple DNA&RNA sequences in parallel through two coupled nanopores, one of the key deliverables, demonstrating scalability of the approach.

Relevance to DYNAMO

Taken together, the PhD work contributes to the DYNAMO objective of improved single-molecule nanopore readout by addressing the transport bottleneck that underlies electro-optical detection. The work does not merely optimise one assay; it clarifies the physical conditions required for reliable readout of nucleic acids and molecular features through nanopores. This provides a basis for future implementations in which optical or plasmonic signals are combined with electrical detection to identify short nucleic acids, sequence-dependent features or molecular modifications.

Selected Output

• [1] Brauburger and Keyser, A biophysicist's guide to translocation of double-stranded nucleic acids through solid-state nanopores, Physics of Life Reviews, 2026.
• [2] Brauburger et al., Label type influence on DNA translocation velocity in solid-state nanopores, submitted revisions, ACS Nano, 2026