Aptamer conformation sensing in nanopore for on-site quantitative detection of cadmium ions at nanomolar...

The detection of heavy metal ions has traditionally relied on laboratory-based spectroscopy techniques, which are often time-consuming, complex, and unsuitable for real-time monitoring. To address this challenge, we introduce an aptamer conformation sensing strategy and evaluate its ability to detect cadmium ions. The sensing strategy qualitatively infers the isolation of cadmium ions (Cd²⁺) by monitoring the docking changes of a single DNA aptamer before and after binding with Cd²⁺ in the nanopore, and quantitatively determines the concentration by extracting the event count of characteristic events.

Molecular dynamics simulations reveal that Cd²⁺ binding induces structural reconfiguration, reducing aptamer penetration depth from 5.20 nm (free DNA) to 1.66 nm (DNA_Cd²⁺). Electrical signatures indicate that unbound aptamers produce sustained current blockades (ΔI/I₀ = 42 %), while Cd²⁺ complexes generate transient signals (ΔI/I₀ = 25 %). Dual-parameter analysis (ΔI/I₀ vs. I_rms) provides precise detection. The sensor achieves a detection limit of 33.8 nM within 10 min and demonstrates >93-fold selectivity over Mn²⁺, Ca²⁺, Cu²⁺, Co²⁺, Ni²⁺, and Fe³⁺. Field validation shows detection accuracy consistent with ICP-MS results.

These findings highlight the potential of nanopore-based aptamer conformation sensing as a powerful platform for real-time, quantitative detection of heavy metal ions in complex environmental matrices.