Solid-state and DNA-origami hybrid nanopores

Before the start of the DYNAMO project, nanopore technologies and DNA nanotechnology had already demonstrated strong potential for single-molecule sensing and sequencing applications[cite: 14]. Solid-state nanopores were widely investigated because of their stability, tunable geometry, and compatibility with electrical detection techniques [1,2][cite: 14]. At the same time, DNA origami emerged as a powerful platform for constructing programmable nanoscale architectures with controllable geometries and functionalities [3,4][cite: 14]. Early studies demonstrated that DNA-origami nanopores could be integrated with solid-state membranes to create hybrid systems with improved sensitivity and controllable molecular transport [5,6][cite: 14]. Bell et al. (2012) first showed that DNA-origami structures could be docked into and ejected from solid-state nanopores under applied voltage, enabling the resistive-pulse detection of λ-DNA through hybrid pores [5][cite: 14]. Subsequent work extended the concept to graphene membranes and to programmable DNA nanoswitches read out by ionic current [6,7][cite: 14]. However, recurring limitations were reported, including residual leakage currents through the DNA scaffold, elevated and variable ionic noise compared with bare solid-state pores, and only partial control over the orientation and stability of the inserted origami [2][cite: 14].

Electroosmotic flow in nanopores and nanocapillaries

Electroosmotic flow (EOF) had also already been identified as an important mechanism governing transport inside nanopores and nanocapillaries [8,9][cite: 14]. Previous studies showed that EOF could influence translocation dynamics, trapping efficiency, and ionic transport near charged surfaces [9,10][cite: 14]. Asandei et al. (2016) demonstrated that EOF could be used as an electroosmotic trap against the electrophoretic force to capture peptides at a protein nanopore [10][cite: 14], and similar trapping concepts were extended to whole proteins inside engineered biological pores [11][cite: 14]. In glass nanocapillaries, Laohakunakorn and Keyser established that EOF profiles depend strongly on pore geometry and ionic strength, with flow reversal observed outside conical pores when the salt concentration is lowered [9,12][cite: 14]. However, most experimental investigations were performed under relatively limited conditions, often focusing on a single salt type (typically KCl), narrow concentration ranges, or comparatively large capillary geometries with limited spatial resolution of the flow field[cite: 14]. As a result, the detailed dependence of EOF on ion identity, concentration, and nanoscale confinement remained insufficiently understood, and three-dimensional mapping of the flow field outside a nanopore had only just been demonstrated as a proof of concept [13][cite: 14].

Thermally responsive DNA nanostructures and hybridization physics

Thermally responsive DNA nanostructures and reversible DNA melting had already demonstrated the possibility of controllable structural switching at the nanoscale [14,15][cite: 14]. DNA origami nanocapsules and lattices reconfigurable by pH, temperature, or strand displacement had been reported, often relying on toehold-mediated strand exchange or triplex-forming pH latches [14,15,16][cite: 14]. Nevertheless, most earlier studies primarily focused on proof-of-concept demonstrations of structural reconfiguration, while the underlying physics of DNA hybridization remained only partially understood, especially under confined nanopore conditions and at the single-molecule level[cite: 14]. Theoretical and coarse-grained simulation work had outlined a picture of hybridization proceeding through non-specific contact, stochastic nucleation, and zipping [17,18][cite: 14], but direct experimental access to these elementary steps for short, surface-tethered strands embedded in nanofluidic environments was still largely missing[cite: 14].

References

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• [11] Schmid, S. et al. Nanopore electro-osmotic trap for the label-free study of single proteins and their conformations. Nat. Nanotechnol. 16, 1244–1250 (2021)[cite: 14].
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