Muhammad Fakhrullah Mohamad AzmiWan Mardhiyana Wan AyubMuhammad Fadzlisyam RedzuanIrfan Danial IsmadiMohd Ifwat Mohd GhazaliMuhamad Arif Mohamad JamaliLiyana AzmiNur Zaireena ZainalNazefah Abdul HamidShahino Mah Abdullah2025-08-052025-08-052025Muhammad Fakhrullah Mohamad Azmi, Wan Mardhiyana Wan Ayub, Muhammad Fadzlisyam Redzuan, Irfan Danial Ismadi, Mohd Ifwat Mohd Ghazali, Muhamad Arif Mohamad Jamali, Liyana Azmi, Nur Zaireena Zainal, Nazefah Abdul Hamid, Shahino Mah Abdullah. (2025). Study of biophysical mechanisms of aptamer-based biosensor for detection of Escherichia coli O157:H7. International Conference and Innovation on Education, Science & Technology (ICIEST 2025), 76–84.978-629-95846-0-5https://flip.usim.edu.my/permatainsan/iciest2025/Proceeding-ICIEST-2025.pdfhttps://oarep.usim.edu.my/handle/123456789/27358International Conference And Innovation On Education, Science & Technology (ICIEST 2025) “Fostering Innovation And Creativity Through Education, Science & Technology” 21st June 2025 Editor : Hatika Kaco, Diani Mardiana Mat Zin, Fadzidah Mohd Idris, Siti Munirah Mohd Nurhidaya Mohamad Jan, Nor Atirah Izzah Zulkefli, Nadiah Suboh Organised by : Education & Advanced Sustainability (EdAS) unit, Kolej PERMATA Insan, Universiti Sains Islam MalaysiaThe 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 and accurate biosensor detection methods such as aptamerbased biosensors due to their high specificity and sensitivity. Aptamers are nucleic acids that can bind with high affinity and specificity to a range of target molecules. In this study, 1,000 shuffled variants of a known aptamer (PDB ID: 2AU4) were generated and evaluated for stability using RNAfold and RNALfoldz based on minimum free energy (MFE). The five most stable sequences were selected and analyzed for their secondary and tertiary structures using RNAComposer. The target protein, Shiga toxin (Stx, PDB ID: 1C48), was modeled with AlphaFold 3 and validated through Ramachandran plot analysis. Molecular docking using the HDOCK server revealed aptamer-protein binding interactions, offering insights into the structural features that influence binding specificity and stability. In conclusion, this research bridges theory for future applications, thereby establishing a theoretical framework to support the future development of aptamer-based biosensors targeting E. coli O157:H7.en-USEscherichia ColiAptamerProteinMolecular free energyMolecular dockingtext::conference output::conference proceedings::conference paper7684