Biophysical Mechanisms of Aptamer and Shiga Toxin Interaction for Aptamer-Based Biosensor Detection: In-Silico Analysis

The increasing prevalence of pathogenic Escherichia coli (E. coli) in water and food sources poses a significant threat to public health, necessitating the development of rapid, accurate, and reliable biosensor detection methods. Among the promising approaches, aptamer-based biosensors have attracted considerable attention due to their high specificity, sensitivity, ease of synthesis, and stability under various conditions. DNA molecules like aptamer can bind with high affinity and selectivity to a wide range of target molecules, including proteins, and small molecules. This research aims to investigate the underlying biophysical mechanisms governing aptamer-target interactions by utilizing in-silico simulation techniques, including molecular free energy calculations and molecular docking. Specifically, the study focuses on elucidating the interaction between selected aptamers and key E. coli virulence factors such as Shiga Toxin (Stx) protein. The methodology involves detailed characterization of aptamer-E. coli binding dynamics, identification of critical structural for enhanced binding affinity and comprehensive docking analysis to model and predict the strength of binding interaction. In conclusion, this research bridges theoretical biophysics with practical biosensor development, providing a robust in-silico framework for the rational design of next-generation biosensing technologies. Moreover, the insights gained from this work hold significant commercialization potential, enabling the creation of cost-effective, portable, and highly sensitive biosensors for real-world applications in food safety and water quality assessment, and early-stage clinical diagnostics.