Label-free optical biosensor for target detection based on simulation-assisted catalyzed hairpin assembly |
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| Affiliation: | 1. School of Computer Science, Shaanxi Normal University, Xi’an, 710119, China;2. College of Life Sciences, Shaanxi Normal University, Xi’an, 710119, China;3. National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China;1. Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 043 53 Košice, Slovak Republic;2. Bogoliubov Laboratory of Theoretical Physics, Joint Institute for Nuclear Research, 141980 Dubna, Moscow Region, Russia;3. Institute of Physics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 11 Bratislava, Slovak Republic;1. Instituto Politécnico Nacional, Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada (CICATA-Legaria), Calzada Legaria 694 Col. Irrigación, Del. Miguel Hidalgo, Mexico D.F. 11500, Mexico;2. Department of Physics and Engineering and Optical Science Center for Applied Research, Delaware State University, 1200 North Dupont Highway, Dover, DE 19901, USA;1. Institute of Computational Science and Technology, Guangzhou University, Guangzhou, 510006, China;2. Department of Computer and Information Science, Fordham University, New York, NY, 10458, USA;3. Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China;1. School of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, PR China;2. College of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, PR China;3. Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211816, PR China;4. School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, PR China;1. State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, 350002, China;2. Department of Otorhinolaryngology, Fujian Institute of Otorhinolaryngology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian Province, China;3. Breast Cancer Institute, Department of Breast Surgery, The Affiliated Union Hospital of Fujian Medical University, Fuzhou, 350001, China;4. The School of Pharmacy, Fujian Medical University, Fuzhou, Fujian, 350004, China;5. University of Chinese Academy of Sciences, Beijing, 100049, China |
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| Abstract: | The development of efficient and convenient strategy without involving enzyme or complex nanomaterial for the micro molecules detection has profound meaning in the diagnosis of diseases. Herein, taking the advantages of the strong affinity of aptamer and catalyzed hairpin assembly, we develop a new non-label optical amplified strategy for thrombin detection in this work. To support both biological inquiry and technological innovation, thermodynamic models are introduced to predict the minimum energy secondary structure of interacting nucleic acid strands and calculate the partition function and equilibrium concentration for complexes in our system. Then, the thermodynamics properties of interacting DNA strands and the reactions of toehold strand displacement-driven assembly have been simulated, validating the feasibility of the theory and optimizing the follow-up lab tests. Following that, our strategy for thrombin detection is proved to be feasible and effective in biological experiment. Taken together, such a biosensor has a good potential in bioactive molecules detection and disease diagnosis for future biological research. |
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| Keywords: | Computation and simulation Catalyzed hairpin assembly Fluorescence biosensor DNA strand displacement G-quadruplex |
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