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: 3]. Solid-state nanopores were widely investigated because of their stability, tunable geometry, and compatibility with electrical detection techniques[cite: 3]. At the same time, DNA origami emerged as a powerful platform for constructing programmable nanoscale architectures with controllable geometries and functionalities[cite: 3]. Early studies demonstrated that DNA-origami nanopores could be integrated with solid-state membranes to create hybrid systems with improved selectivity and controllable molecular transport[cite: 3]. 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[cite: 3]. Subsequent work extended the concept to graphene membranes and to programmable DNA nanoswitches read out by ionic current[cite: 3]. 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[cite: 3].

Electroosmotic flow in nanopores and nanocapillaries. Electroosmotic flow (EOF) had also already been identified as an important mechanism governing transport inside nanopores and nanocapillaries[cite: 3]. Previous studies showed that EOF could influence translocation dynamics, trapping efficiency, and ionic transport near charged surfaces[cite: 3]. 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[cite: 3], and similar trapping concepts were extended to whole proteins inside engineered biological pores[cite: 3]. 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[cite: 3]. 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: 3]. 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[cite: 3].

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[cite: 3]. 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[cite: 3]. 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: 3]. Theoretical and coarse-grained simulation work had outlined a picture of hybridization proceeding through non-specific contact, stochastic nucleation, and zipping[cite: 3], but direct experimental access to these elementary steps for short, surface-tethered strands embedded in nanofluidic environments was still largely missing[cite: 3].

References

1. Dekker, C. Solid-state nanopores. Nat. Nanotechnol. 2, 209–215 (2007).[cite: 3]
2. Hernández-Ainsa, S. & Keyser, U. F. DNA-origami nanopores: developments, challenges and perspectives. Nanoscale 6, 14121–14132 (2014).[cite: 3]
3. Rothemund, P. W. K. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006).[cite: 3]
4. Dietz, H., Douglas, S. M. & Shih, W. M. Folding DNA into twisted and curved nanoscale shapes. Science 325, 725–730 (2009).[cite: 3]
5. Bell, N. A. W. et al. DNA origami nanopores. Nano Lett. 12, 512–517 (2012).[cite: 3]
6. Barati Farimani, A. et al. DNA origami–graphene hybrid nanopore for DNA detection. ACS Appl. Mater. Interfaces 9, 92–100 (2017).[cite: 3]
7. Bell, N. A. W. & Keyser, U. F. Specific protein detection using designed DNA carriers and nanopores. J. Am. Chem. Soc. 137, 2035–2041 (2015).[cite: 3]
8. Firnkes, M. et al. Electrically facilitated translocations of proteins through silicon nitride nanopores: conjoint and competitive action of diffusion, electrophoresis, and electroosmosis. Nano Lett. 10, 2162–2167 (2010).[cite: 3]
9. Laohakunakorn, N. et al. Electroosmotic flow reversal outside glass nanopores. Nano Lett. 15, 695–702 (2015).[cite: 3]
10. Asandei, A. et al. Electroosmotic trap against the electrophoretic force near a protein nanopore reveals peptide dynamics during capture and translocation. ACS Appl. Mater. Interfaces 8, 13166–13179 (2016).[cite: 3]
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: 3]
12. Mc Hugh, J., Andresen, K. & Keyser, U. F. Cation-dependent electroosmotic flow in glass nanopores. Appl. Phys. Lett. 115, 113702 (2019).[cite: 3]
13. Mc Hugh, J., Thorneywork, A. L., Andresen, K. & Keyser, U. F. 3D flow field measurements outside nanopores. Rev. Sci. Instrum. 93, 053703 (2022).[cite: 3]
14. Ijäs, H. et al. Reconfigurable DNA origami nanocapsule for pH-controlled encapsulation and display of cargo. ACS Nano 13, 5959–5967 (2019).[cite: 3]
15. Kosuri, P., Altheimer, B. D., Dai, M., Yin, P. & Zhuang, X. Rotation tracking of genome-processing enzymes using DNA origami rotors. Nature 572, 136–140 (2019).[cite: 3]
16. Marras, A. E., Zhou, L., Su, H.-J. & Castro, C. E. Programmable motion of DNA origami mechanisms. Proc. Natl. Acad. Sci. USA 112, 713–718 (2015).[cite: 3]
17. Ouldridge, T. E. et al. DNA hybridization kinetics: zippering, internal displacement and sequence dependence. Nucleic Acids Res. 41, 8886–8895 (2013).[cite: 3]
18. SantaLucia, J. & Hicks, D. The thermodynamics of DNA structural motifs. Annu. Rev. Biophys. Biomol. Struct. 33, 415–440 (2004).[cite: 3]
19. Bhattacharya, S. et al. Changes in salt concentration modify the translocation of neutral molecules through a ΔCymA nanopore in a non-monotonic manner. ACS Nano 16, 9355–9366 (2022).[cite: 3]
20. Brown, W. et al. Higher ion selectivity with lower energy usage promoted by electro-osmotic flow in the transport through conical nanopores. J. Phys. Chem. C 125, 3269–3276 (2021).[cite: 3]
21. Teahan, J. et al. Scanning ion conductance microscopy: surface charge effects on electroosmotic flow delivery from a nanopipette. Anal. Chem. 93, 12281–12288 (2021).[cite: 3]
22. Verpillat, F., Joud, F., Desbiolles, P. & Gross, M. Dark-field digital holographic microscopy for 3D-tracking of gold nanoparticles. Opt. Express 19, 26044–26055 (2011).[cite: 3]
23. Hertel, S. et al. The stability and number of nucleating interactions determine DNA hybridization rates in the absence of secondary structure. Nucleic Acids Res. 50, 7829–7841 (2022).[cite: 3]
24. Jungmann, R. et al. Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT. Nat. Methods 11, 313–318 (2014).[cite: 3]
25. Yu, L. et al. Compliant DNA origami nanoactuators as size-selective nanopores. Adv. Mater. 36, 2405104 (2024).[cite: 3]