Molecular simulation-guided design of aptamer-photonic crystal hydrogel biosensor overcoming cross-reactivity for specific, visual detection of cadmium in water

Cadmium (Cd²⁺) aptasensors often suffer from cross-reactivity and pH-dependent drift. We report a molecular-simulation-guided aptamer–photonic crystal (APC) hydrogel that transduces target binding into a lattice contraction read optically. Molecular dynamics indicated pH 7.4 minimizes conformational fluctuations (RMSD <0.5 Å; radius of gyration ≈2.1 Å), informing buffer selection and a polyacrylamide-co-acrylic acid matrix with low nonspecific metal binding. The sensor is linear from 250 pM to 1 μM (LOD 125 pM), with spacing contracting from 3652 ± 18 nm to 895 ± 21 nm at 1 μM and a blue→green shift. Interference tests with Pb²⁺, Cu²⁺, Zn²⁺, Mg²⁺, Ca²⁺, Na⁺, and K⁺ at competitor:Cd = 1:1–100:1 showed modest suppression (≤14 % for Mg²⁺/Ca²⁺/Na⁺/K⁺; ≤22 % Zn²⁺; ≤28 % Cu²⁺; Pb²⁺ ≤ 35 %); an all-ion matrix at 100:1 yielded 21.9 % suppression and + 7.8 % bias at 10 nM that fell to ≤3.9 % at ≥100 nM. Blind split validation on natural waters (0.1–800 nM) versus ICP-MS gave y(APC) = 0.98× + 0.8 nM (R² = 0.991) and 4.1 % absolute percent error near the LOD. Fabrication was reproducible (intra-batch CV 3.8–6.9 %; inter-batch 6.1–8.7 %) and robust through ≥10 regenerations (signal retained 91.1 % with EDTA; 88.3 % with pH-switch). On-hydrogel FRET/anisotropy/circular dichroism and isothermal titration calorimetry—together with reverse, scrambled, and buffer controls—verified a biphasic interaction (K_D1 ≈ 18 nM; K_D2 ≈ 0.9 μM) that drives contraction rather than Donnan effects. Operation was stable across pH 6.0–8.5, 5–40 °C, and 1–50 mM ionic strength; response half-times were 45–120 s (t₉₀ 96–260 s). This APC hydrogel delivers accurate, selective, and regenerable Cd²⁺ quantification suitable for complex environmental waters.