Cucurbituril-aerolysin nanopore interactions for molecular recognition

Cucurbit[n]urils (CBn, n = 5-8) are macrocyclic hosts that form stable inclusion complexes with a variety of guest molecules, including amino acids and peptides. In this study, we investigate the interactions of CBn homologues with the aerolysin (AeL) protein nanopore using single-molecule ionic current recordings and molecular docking simulations, with the goal of developing a selective sensing platform for complex biofluids. Under an applied voltage, CBn molecules enter the AeL nanopore exclusively through its extracellular cap domain, inducing characteristic ionic current blockades. These events are influenced by voltage, electrolyte type (KCl, NaCl, CsCl), and ionic strength. Both the frequency and dwell time of blockade events increase with voltage, with CB6 generating particularly long blockades-lasting several seconds-enabling real-time monitoring of host-guest interactions at the single-molecule level. Molecular docking simulations support these observations, revealing that CB5, CB7, and CB8 preferentially bind to the extracellular region of AeL, while CB6 shows strongest affinity for the intracellular region. Among all homologues, CB5 forms the most stable complex with AeL. Hydrophobic interactions dominate binding across all complexes. Importantly, none of the CBn species translocate through the pore, consistent with experimental data. These findings highlight the utility of AeL nanopores for probing CBn interactions with high temporal resolution and selectivity. This approach may support future developments in nanopore-based sequencing and diagnostic technologies.