Application Of Molecular Simulation In The Sensing Detection Of Two Drug Electrochemical Aptasensors

The electrochemical aptamer-based sensor technology of drug small molecules has important theoretical significance and practical application value in the fields of clinical diagnosis,food safety,and environmental monitoring.Although a certain development of this technology has been achieved,the research is mainly focused on the performance investigation of macroscopic representation due to the limitation of experimental methods.It is necessary for the theoretical research and application development of aptamer-based sensor technology to explore new research methods to reveal the microscopic reaction dynamics process and to deeply understand the sensing structure-effect relationship.In this paper,a new attempt was made to apply the molecular dynamics（MD）simulation method to the study of two electrochemical aptamer-based sensing systems for both theophylline and kanamycin,in order to explore new research approaches to clarify the relevant action mechanisms of aptamer-based sensors.The specific research content includes three parts as follows.1.The MD simulation method was applied to the study of signal response behavior for the theophylline RNA aptamer-based electrochemical sensor.Square wave voltammetry was used to record the current changes produced from the recognition reaction.MD simulation technology was used to simulate the dynamic binding process of the aptamer to its target and the corresponding electrochemical response behavior was elucidated with the confirm ed binding mode.The research results showed that both the-27.6±1.1%and 19.9±1.1%of SE in electrochemical response were obtained in two different H₂O solutions of0.1 and 0.5 M Na Cl,respectively.The interaction between the aptamer and its target showed a binding mode dominated by the bonding base spacing,thereby inducing the aptamer to produce weak“lengthening”and“shortening”changes and showing two opposite electrochemical signal response characteristics of“signal off”and“signal on”.2.The MD simulation method was applied to the study of selective recognition behavior for the kanamycin DNA aptamer-based electrochemical sensor.Square wave voltammetry was used to record the current changes produced from the recognition reaction.MD simulation technology was used to simulate the dynamic binding process of the aptamer to its target or the interference m olecules involved and the corresponding electrochemical response behavior was elucidated with the confirmed binding mode.The research results showed that both the 249.1±10.1%and-4.6±2.0%～8.1±2.5%of SE in electrochemical response were obtained for the target and 4 interference molecules,showing a good selectivity.The MD simulation results effectively supported the recognition response behavior with the corresponding binding free energies of-3404±36 and-551±52～-2.8±0.8 KJ·mol^-1,respectively.3.Using methylene violet and toluidine blue as the dual-current labels,a dual-signal replacement reaction-based kanamycin DNA aptasensor was designed and fabricated.Square wave voltammetry was used to record the dual-current changes produced from the replacement reaction.MD simulation technology was used to separately simulate the dynamic binding process of the aptamer to its target of kanamycin or indicator molecules and the simulation results were verified by the actual detection system,thus laying a theoret ical and experimental foundation for the construction of the sensor.The different binding modes determined by the MD simulation method effectively supported the occurrence of displacement reaction with the corresponding binding free energies of-2698±94,-819±19,-128±10,and-235±47 KJ·mol^-1,respectively.Under optimized conditions,the detection limit of the proposed sensor for the target kanamycin was 26.5 n M with the linear range of 1.0μM～2.0 m M and the response equilibrium time of～45 min.