Fluorescent biosensor based on aptamer-cDNA hybridization for Cd2+ detection and molecular mechanism investigation

Cadmium ion (Cd 2+ ) pollution poses severe environmental and health risks due to its high toxicity, bioaccumulation potential, and persistence. Although traditional detection methods require bulky instruments and complex procedures, limiting the suitability for rapid on-site analysis. The paper introduces aptamer-based fluorescent probes and double-stranded fluorescent probe based on an aptamer and its complementary DNA (cDNA). The former is composed of aptamers and SYBR Green dyes. The detection range of Cd 2+ is 0–8 μM, and limit of detection (LOD) is 15 nM. The probe consists of a double-stranded structure formed by a 5′-FAM-labeled Cd 2+ aptamer and a 3′-BHQ1-modified cDNA. By combining this probe with a hydrogel matrix, a smartphone-based sensing platform is constructed, which enables highly sensitive and convenient detection of Cd 2+ . It indicated that the detection range of the probe for Cd 2+ is 0–50 μM, with the LOD of 27.6 nM. Molecular dynamics simulations (MD) disclosed the binding mechanism of the aptamer and Cd 2+ : the specific recognition by nucleobases such as G9, C12, and T17 in the Coulomb force-driven double-twisted folding conformation plays a crucial role. Further integrating the probe into the hydrogel matrix constructed the dsDNA@hydrogel platform successfully achieved real-time visual detection of Cd 2+ in environmental samples. It not only offers a highly sensitive and cost-effective new approach for heavy metal detection, but promotes the advancement of portable environmental monitoring technologies through the innovation of the aptamer-hydrogel system.