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Cucurbituril-aerolysin nanopore interactions for molecular recognition.
Hadjer Ouldali1, Camille Dejoux1,2, Manuela Pastoriza-Gallego1
1CNRS, Université Paris-Saclay, Université Evry, CY Cergy Paris Université, LAMBE, 95000, Cergy, France.
The European Physical Journal. E, Soft Matter
|November 7, 2025
Summary
Cucurbit[n]urils (CBn) interacting with aerolysin (AeL) protein nanopores were studied. This research advances selective sensing platforms for biofluids using nanopore technology.
Area of Science:
- Supramolecular Chemistry
- Nanotechnology
- Biophysics
Background:
- Cucurbit[n]urils (CBn) are macrocyclic hosts forming stable inclusion complexes.
- Aerolysin (AeL) protein nanopores offer a platform for single-molecule analysis.
Purpose of the Study:
- Investigate Cucurbit[n]uril (CBn) interactions with aerolysin (AeL) protein nanopores.
- Develop a selective sensing platform for complex biofluids using CBn-AeL interactions.
Main Methods:
- Single-molecule ionic current recordings.
- Molecular docking simulations.
- Utilized varying voltages and electrolyte conditions (KCl, NaCl, CsCl).
Main Results:
- CBn molecules enter the AeL nanopore via the extracellular cap, causing ionic current blockades.
- CB6 generated long blockades (seconds), enabling real-time monitoring.
- Molecular docking revealed preferential binding sites for different CBn homologues, with CB5 forming the most stable complex.
Conclusions:
- AeL nanopores effectively probe CBn interactions with high temporal resolution and selectivity.
- Hydrophobic interactions are key to CBn-AeL complex stability.
- This approach holds potential for nanopore-based sequencing and diagnostics.
