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Three-dimensional ordered macroporous MOF-based smart gating membrane with size screening effect and aptamer specificity for highly efficient thrombin isolation. J Memb Sci 2023. [DOI: 10.1016/j.memsci.2022.121132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Zhu M, Xu F, Miao S, Xie C, Li H, Li S, Xia F. Incorporation of a Multi-Valent Aptamer into Electrochemical Biosensors to Achieve an Improved Performance for Thrombin Analysis in Blood Serum. Chempluschem 2022; 87:e202200325. [PMID: 36410784 DOI: 10.1002/cplu.202200325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/10/2022] [Indexed: 11/23/2022]
Abstract
The electrochemical aptamer-based (E-AB) biosensor usually has a long reaction time when detecting thrombin. This work reports the design of an E-AB biosensor with dual recognition sites to quickly detect thrombin. Specifically, two specific recognition sites of thrombin were used to design three aptamer sequences (TBA-15, TBA-29 and TBA-U), followed by fabrication of corresponding sensors. First, we tested these three types of biosensors in tris buffer solution, and found that the response time of the TBA-U sensor to the same concentration of thrombin was about 2 hours, which is shorter than TBA-15 and TBA-29 sensors. Then, we also did the same test in 50 % diluted serum with 500 nM thrombin. The response time of the TBA-U sensor was about 2 hours, which is still faster than the 3 hours of TBA-15 sensor and the 5.5 hours for TBA-29 sensor. In addition, in terms of dynamic range and specificity, TBA-U has good performance.
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Affiliation(s)
- Man Zhu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Fan Xu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Siyuan Miao
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Chongyu Xie
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Hui Li
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Shaoguang Li
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
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Khoshbin Z, Housaindokht MR, Izadyar M, Bozorgmehr MR, Verdian A. Temperature and molecular crowding effects on the sensitivity of T30695 aptamer toward Pb2+ion: a joint molecular dynamics simulation and experimental study. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1751842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Zahra Khoshbin
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Mohammad Izadyar
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Asma Verdian
- Department of Food Safety and Quality Control, Research Institute of Food Science and Technology (RIFST), Mashhad, Iran
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Fu X, Peng F, Lee J, Yang Q, Zhang F, Xiong M, Kong G, Meng HM, Ke G, Zhang XB. Aptamer-Functionalized DNA Nanostructures for Biological Applications. Top Curr Chem (Cham) 2020; 378:21. [PMID: 32030541 DOI: 10.1007/s41061-020-0283-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/17/2020] [Indexed: 12/31/2022]
Abstract
DNA nanostructures hold great promise for various applications due to their remarkable properties, including programmable assembly, nanometric positional precision, and dynamic structural control. The past few decades have seen the development of various kinds of DNA nanostructures that can be employed as useful tools in fields such as chemistry, materials, biology, and medicine. Aptamers are short single-stranded nucleic acids that bind to specific targets with excellent selectivity and high affinity and play critical roles in molecular recognition. Recently, many attempts have been made to integrate aptamers with DNA nanostructures for a range of biological applications. This review starts with an introduction to the features of aptamer-functionalized DNA nanostructures. The discussion then focuses on recent progress (particularly during the last five years) in the applications of these nanostructures in areas such as biosensing, bioimaging, cancer therapy, and biophysics. Finally, challenges involved in the practical application of aptamer-functionalized DNA nanostructures are discussed, and perspectives on future directions for research into and applications of aptamer-functionalized DNA nanostructures are provided.
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Affiliation(s)
- Xiaoyi Fu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Fangqi Peng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Jungyeon Lee
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, NJ, 07102, USA
| | - Qi Yang
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, NJ, 07102, USA
| | - Fei Zhang
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, NJ, 07102, USA
| | - Mengyi Xiong
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Gezhi Kong
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Hong-Min Meng
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Guoliang Ke
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
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Santini BL, Zúñiga-Bustos M, Vidal-Limon A, Alderete JB, Águila SA, Jiménez VA. In Silico Design of Novel Mutant Anti-MUC1 Aptamers for Targeted Cancer Therapy. J Chem Inf Model 2019; 60:786-793. [PMID: 31657548 DOI: 10.1021/acs.jcim.9b00756] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The transmembrane glycoprotein mucin 1 (MUC1) is an attractive tumor marker for cancer therapy and diagnosis. The nine amino acid extracellular epitope APDTRPAPG of this protein is selectively recognized by the S2.2 single-stranded DNA anti-MUC1 aptamer, which has emerged as a promising template for designing novel targeting agents for MUC1-directed therapy. In this work, 100 ns molecular dynamics (MD) simulations, MM/GBSA binding free energy calculations, and conformational analysis were employed to propose a novel prospective anti-MUC1 aptamer with increased affinity toward the MUC1 epitope resulting from the double mutation of the T11 and T12 residues with PSU and U nucleosides, respectively. The double mutant aptamer exhibits a tight interaction with the MUC1 epitope and adopts a groove conformation that structurally favors the intermolecular contact with the epitope through the intermediate T11-A18 region leaving the 3' and 5' ends free for further chemical conjugation with a nanocarrier or pharmaceutical. These results are valuable to gain understanding about the molecular features governing aptamer-epitope interactions and constitute a first key step for the design of novel aptamer-based nanocarriers for MUC1-targeted cancer therapy.
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Affiliation(s)
- Brianda L Santini
- Centro de Nanociencias y Nanotecnología , Universidad Nacional Autónoma de México , Km. 107 Carretera Tijuana-Ensenada , Ensenada , Baja California , Mexico , C.P. 22860
| | - Matías Zúñiga-Bustos
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas , Universidad Andres Bello , Sede Concepción, Autopista Concepción-Talcahuano 7100 , Talcahuano 4260000 , Chile
| | - Abraham Vidal-Limon
- Centro de Nanociencias y Nanotecnología , Universidad Nacional Autónoma de México , Km. 107 Carretera Tijuana-Ensenada , Ensenada , Baja California , Mexico , C.P. 22860
| | - Joel B Alderete
- Instituto de Química de Recursos Naturales , Universidad de Talca , Casilla 747 , Talca 3460000 , Chile
| | - Sergio A Águila
- Centro de Nanociencias y Nanotecnología , Universidad Nacional Autónoma de México , Km. 107 Carretera Tijuana-Ensenada , Ensenada , Baja California , Mexico , C.P. 22860
| | - Verónica A Jiménez
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas , Universidad Andres Bello , Sede Concepción, Autopista Concepción-Talcahuano 7100 , Talcahuano 4260000 , Chile
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Lee AJ, Wälti C. DNA nanostructures: A versatile lab-bench for interrogating biological reactions. Comput Struct Biotechnol J 2019; 17:832-842. [PMID: 31316727 PMCID: PMC6611922 DOI: 10.1016/j.csbj.2019.06.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/05/2019] [Accepted: 06/11/2019] [Indexed: 01/10/2023] Open
Abstract
At its inception DNA nanotechnology was conceived as a tool for spatially arranging biological molecules in a programmable and deterministic way to improve their interrogation. To date, DNA nanotechnology has provided a versatile toolset of nanostructures and functional devices to augment traditional single molecule investigation approaches - including atomic force microscopy - by isolating, arranging and contextualising biological systems at the single molecule level. This review explores the state-of-the-art of DNA-based nanoscale tools employed to enhance and tune the interrogation of biological reactions, the study of spatially distributed pathways, the visualisation of enzyme interactions, the application and detection of forces to biological systems, and biosensing platforms.
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Affiliation(s)
- Andrew J. Lee
- Bioelectronics, The Pollard Institute, School of Electronic & Electrical Engineering, University of Leeds, LS2 9JT, United Kingdom
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Lin TX, Lai PX, Mao JY, Chu HW, Unnikrishnan B, Anand A, Huang CC. Supramolecular Aptamers on Graphene Oxide for Efficient Inhibition of Thrombin Activity. Front Chem 2019; 7:280. [PMID: 31157200 PMCID: PMC6532589 DOI: 10.3389/fchem.2019.00280] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 04/05/2019] [Indexed: 01/08/2023] Open
Abstract
Graphene oxide (GO), a two-dimensional material with a high aspect ratio and polar functional groups, can physically adsorb single-strand DNA through different types of interactions, such as hydrogen bonding and π-π stacking, making it an attractive nanocarrier for nucleic acids. In this work, we demonstrate a strategy to target exosites I and II of thrombin simultaneously by using programmed hybrid-aptamers for enhanced anticoagulation efficiency and stability. The targeting ligand is denoted as Supra-TBA15/29 (supramolecular TBA15/29), containing TBA15 (a 15-base nucleotide, targeting exosite I of thrombin) and TBA29 (a 29-base nucleotide, targeting exosite II of thrombin), and it is designed to allow consecutive hybridization of TBA15 and TBA29 to form a network of TBAs (i.e., supra-TBA15/29). The programmed hybrid-aptamers (Supra-TBA15/29) were self-assembled on GO to further boost anticoagulation activity by inhibiting thrombin activity, and thus suppress the thrombin-induced fibrin formation from fibrinogen. The Supra-TBA15/29-GO composite was formed mainly through multivalent interaction between poly(adenine) from Supra-TBA15/29 and GO. We controlled the assembly of Supra-TBA15/29 on GO by regulating the preparation temperature and the concentration ratio of Supra-TBA15/29 to GO to optimize the distance between TBA15 and TBA29 units, aptamer density, and aptamer orientation on the GO surfaces. The dose-dependent thrombin clotting time (TCT) delay caused by Supra-TBA15/29-GO was >10 times longer than that of common anticoagulant drugs including heparin, argatroban, hirudin, and warfarin. Supra-TBA15/29-GO exhibits high biocompatibility, which has been proved by in vitro cytotoxicity and hemolysis assays. In addition, the thromboelastography of whole-blood coagulation and rat-tail bleeding assays indicate the anticoagulation ability of Supra-TBA15/29-GO is superior to the most widely used anticoagulant (heparin). Our highly biocompatible Supra-TBA15/29-GO with strong multivalent interaction with thrombin [dissociation constant (K d) = 1.9 × 10-11 M] shows great potential as an effective direct thrombin inhibitor for the treatment of hemostatic disorders.
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Affiliation(s)
- Ting-Xuan Lin
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Pei-Xin Lai
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Ju-Yi Mao
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan.,Doctoral Degree Program in Marine Biotechnology, National Taiwan Ocean University, Keelung, Taiwan.,Doctoral Degree Program in Marine Biotechnology, Academia Sinica, Taipei, Taiwan
| | - Han-Wei Chu
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Binesh Unnikrishnan
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Anisha Anand
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Chih-Ching Huang
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan.,Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan.,School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan
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