Molecular dynamics simulation and experiment study on a displacement-based electrochemical dual-signal response of interfacial kanamycin aptamer probe

An electrochemical dual-signal response sensing method was developed by designing and fabricating a kanamycin aptamer-based sensor. The signaling mechanism was deciphered by simulating the kinetics evolution process of related displacement reactions. This study emphasizes bridging the tight correlation between molecular dynamics simulations and experiments. [Display omitted] •An electrochemical dual-signal kanamycin aptasensor was designed and fabricated.•The sensing is based on the displacement reaction of the target to label molecules.•The signaling mechanism was deciphered by simulating the displacement evolution.•The study closely bridges the molecular dynamics simulation and the experiment. A displacement-based electrochemical dual-signal kanamycin (KAN) aptamer sensing method was developed using a theory-driven approach, with methylene violet (MV) and toluidine blue (TB) as dual-signal labels. The binding poses were elucidated using molecular dynamics simulation (MDS) while simulating the kinetic evolution process of the displacement reaction. The binding system’s binding free energy (ΔG) was calculated using the g_mmpbsa algorithm. The MDS results guided the sensor fabrication process, and the sensing analytical performance was subsequently investigated. The study demonstrated the thermodynamic feasibility of the displacement reaction, with ΔG values of −3079 ± 122, −955 ± 78, and −879 ± 46 KJ·mol−1 for the three binding systems, respectively. The simulated kinetic evolution process aligned with the displacement reaction’s behavior characteristics, primarily driven by electrostatic attraction, thereby deciphering the sensor’s signaling mechanism. Under optimized conditions, the sensor exhibited a dual-signal response, a detection limit of 0.17 μM, a linear range of 1.0 μM to 2.0 mM, a response equilibrium time of ∼ 45 min., and a discriminated selectivity clarified by the MDS. The mutual support between MDS and experimental results establishes a communication bridge between simulation and experimentation, guiding the sensor fabrication direction and providing a methodological basis and new research example for aptamer-based sensor designs.