The binding pattern of the docked two-segment-aptamer to penicillin G and its impedance sensing performance

Abstract

A penicillin G (PEN-G) aptamer-docking-based impedance sensor was purposely designed and fabricated. The molecular dynamics simulation (MDS) method was used to decipher the binding pattern of the aptamer to PEN-G. Three electrochemistry techniques were involved in optimizing the key sensing parameters, characterizing the sensing process effectiveness, and systematically investigating the basic analytical performances. A comparative analysis of the binding pattern clarified the theoretical reason for the high impedance response produced by the optimized docked aptamer sequence. The research results indicated that the cis-D-5 T-PEN probe performed best among the four docked aptamers with the maximum impedance response when binding to the target. Compared with the parent single-sequence aptamer, the docked aptamers contain more active binding sites, which is conducive to generating larger impedance values to improve the method’s sensitivity. The sensor derived from the cis-D-5 T-PEN probe showed excellent analytical performance for detecting PEN-G residues in tap water. The detection limit and the linear range were confirmed to be ∼0.3 pM and 0.001–100.0 nM, respectively. The method’s average spiked recoveries were 79.8–92.1 %, with a relative standard deviation (RSD) of less than 20 %. The entire testing process could be completed within 1 h. The proposed sensor exhibits the advantages of simple operation, high sensitivity, and fast detection speed. Theoretical simulation effectively supports the experimental results, providing a new example and reference for introducing the MDS method into studying aptamer sensing systems.