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.