Exploration of the Interaction of Cadmium and Aptamer by Molecular Simulation and Development of Sensitive Capillary Zone Electrophoresis-Based Aptasensor.

The presence of cadmium ions (Cd2+) in environmental samples demands a fast, sensitive, and selective analytical method that can measure toxic levels. Biosensors based on aptamers (aptasensors) have been developed, but some of them suffer from poor sensitivity and specificity due to the immobilization of aptamers. Here, we employed circular dichroism, molecular docking, and molecular dynamics simulation to reveal that the aptamer gradually undergoes significant conformational changes upon Cd2+ binding. This fact highlights the advantages of biosensors based on free aptamers. So, keeping these results, an analytical method was established for the detection of Cd2+ by utilizing capillary zone electrophoresis (CZE), which is adapted for the free aptamer. So, CZE equipped with aptamer as a detection probe can detect Cd2+ within 4 min in the range from 5 to 250 nM with R2 = 0.994, limit of detection 5 nM (signal-to-noise ratio = 3), and recovery from 92.6 ± 1.6 to 107.4 ± 1.0% in river water samples. Furthermore, the detected concentration in water samples is below the harmful levels (267 nM) recommended by World Health Organization standards in drinking water. This method displays a high sensitivity and specificity for Cd2+. It is found to be superior to existing methods, which use immobilized aptamers, and can be readily expanded to design aptasensors for other targets.

Molecular simulation-guided aptasensor design of robust and sensitive lateral flow strip for cadmium ion detection.

Lateral flow fluorescence strip (LFFS) aptasensor have been widely used for on-site target detection. However, they are limited by low sensitivity and strong background signals owing to the inappropriate design of molecule probes. Herein, we employed molecular simulations to improve the sensitivity of LFFS by the optimization of the DNA probe length and sequence, which is a critical parameter for the competitive approach of the aptasensor. Simulation results revealed that a probe with 30 nt can maximize the hybridization yield of aptamer to reduce the background signal. More importantly, the simulation results highlighted the Cd2+ concentration-dependent conformational changes in the aptamer. It is essential to block its hybridization with a probe, and consequently, yield sensitive and target concentration-dependent fluorescence signal. Considering these results, we developed a sensitive aptamer-based fluorescent lateral flow strip for rapid Cd2+ detection. The fluorescence intensity of this strip exhibited an excellent linear relationship with the Cd2+ concentration ranging from 63 nM to 1000 nM (R2 = 0.9724). The limit of detection was determined to be 30 nM (S/N = 3). This method was also applied for the detection of Cd2+ in river water samples in the range from 92.9 ± 1.0% to 108.6 ± 1.4%. Moreover, the detected concentration in water samples is below the harmful levels (267 nM) recommended by WHO standards in drinking water. The use of molecular simulations is a significant addition to cost and resource-effective aptasensor development protocol, and it can be readily expanded to design aptasensors for other targets.