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Zhong Y, Wu J, Pan X, Liu B, Wang L. Aptamer-functionalized polydiacetylene biosensor for the detection of three foodborne pathogens. ANAL SCI 2024; 40:199-211. [PMID: 37856010 DOI: 10.1007/s44211-023-00445-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 09/27/2023] [Indexed: 10/20/2023]
Abstract
Rapid, simple and sensitive screening of foodborne pathogens is of great significance to ensure food safety. In this study, an aptamer-functionalized polydiacetylene (Apta-PDA) biosensor was developed for the detection of E. coli O157:H7, S. typhimurium or V. parahaemolyticus. First, aptamers responding to the target bacteria were modified on the surface of magnetic beads by covalent binding to form MBs-oligonucleotide conjugates for bacterial enrichment. Then, an Apta-PDA biosensor was obtained by connecting the aptamers to the PDA nanovesicles using the carbodiimide method. Molecular recognition occurred in the presence of the target bacteria, whereby the aptamer folded into a sequence-defined unique structure, resulting in an MBs-Apta/bacteria/Apta-PDA sandwich structure. Due to the optical properties of PDA, the blue-red transition of the detection system could be observed by the naked eye and quantified by the colorimetric response percentage (CR%). Under optimized conditions, the detection limits of E. coli O157:H7, S. typhimurium and V. parahaemolyticus were 39, 60 and 60 CFU/ml, respectively, with a selectivity of 100% and a reaction time of 30 min. Compared with the gold standard method, the accuracy of the three target bacteria detection reached 98%, 97.5% and 97%, respectively, and the sensitivity and specificity were both greater than 90%. The entire detection process was rapid and easy to execute without any special equipment, making this technology particularly suitable for resource-poor laboratories or regions.
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Affiliation(s)
- Yuhong Zhong
- Department of Clinical Laboratory, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, People's Republic of China.
| | - Jiaqi Wu
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, 310059, People's Republic of China
| | - Xiaoyan Pan
- Department of Clinical Laboratory, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, People's Republic of China
| | - Bo Liu
- Department of Clinical Laboratory, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, People's Republic of China
| | - Lin Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, People's Republic of China
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Long Z, Bing T, Zhang X, Sheng J, Zu S, Li W, Liu X, Zhang N, Shangguan D. Structural Optimization and Interaction Study of a DNA Aptamer to L1 Cell Adhesion Molecule. Int J Mol Sci 2023; 24:ijms24108612. [PMID: 37239955 DOI: 10.3390/ijms24108612] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
The L1 cell adhesion molecule (L1CAM) plays important roles in the development and plasticity of the nervous system as well as in tumor formation, progression, and metastasis. New ligands are necessary tools for biomedical research and the detection of L1CAM. Here, DNA aptamer yly12 against L1CAM was optimized to have much stronger binding affinity (10-24 fold) at room temperature and 37 °C via sequence mutation and extension. This interaction study revealed that the optimized aptamers (yly20 and yly21) adopted a hairpin structure containing two loops and two stems. The key nucleotides for aptamer binding mainly located in loop I and its adjacent area. Stem I mainly played the role of stabilizing the binding structure. The yly-series aptamers were demonstrated to bind the Ig6 domain of L1CAM. This study reveals a detailed molecular mechanism for the interaction between yly-series aptamers and L1CAM and provides guidance for drug development and detection probe design against L1CAM.
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Affiliation(s)
- Zhenhao Long
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research and Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Bing
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research and Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Xiangru Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research and Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Sheng
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research and Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuang Zu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research and Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310013, China
| | - Weiwei Li
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310013, China
| | - Xiangjun Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research and Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nan Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research and Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Dihua Shangguan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research and Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310013, China
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Froehlich CE, He J, Haynes CL. Investigation of Charged Small Molecule-Aptamer Interactions with Surface Plasmon Resonance. Anal Chem 2023; 95:2639-2644. [PMID: 36704862 DOI: 10.1021/acs.analchem.2c04192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Investigating the interactions between small, charged molecules and aptamers using surface plasmon resonance (SPR) is limited by the inherent low response of small molecules and difficulties with nonspecific electrostatic interactions between the aptamer, analyte, and sensor surface. However, aptamers are increasingly being used in sensors for small molecule detection in critical areas like healthcare and environmental safety. The ability to probe these interactions through simple, direct SPR assays would be greatly beneficial and allow for the development of improved sensors without the need for complicated signal enhancement. However, these assays are nearly nonexistent in the current literature and are instead surpassed by sandwich or competitive binding techniques, which require additional sample preparation and reagents. In this work, we develop a method to characterize the interaction between the charged small molecule serotonin (176 Da) and an aptamer with SPR using streptavidin-biotin capture and a high-ionic-strength buffer. Additionally, other methods, such as serotonin immobilization and thiol-coupling of the aptamer, were investigated for comparison. These techniques give insight into working with small molecules and allow for quickly adapting a binding affinity assay into a direct SPR sensor.
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Dzuvor CKO, Tettey EL, Danquah MK. Aptamers as promising nanotheranostic tools in the COVID-19 pandemic era. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 14:e1785. [PMID: 35238490 PMCID: PMC9111085 DOI: 10.1002/wnan.1785] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/02/2022] [Accepted: 02/07/2022] [Indexed: 12/13/2022]
Abstract
The emergence of SARS-COV-2, the causative agent of new coronavirus disease (COVID-19) has become a pandemic threat. Early and precise detection of the virus is vital for effective diagnosis and treatment. Various testing kits and assays, including nucleic acid detection methods, antigen tests, serological tests, and enzyme-linked immunosorbent assay (ELISA), have been implemented or are being explored to detect the virus and/or characterize cellular and antibody responses to the infection. However, these approaches have inherent drawbacks such as nonspecificity, high cost, are characterized by long turnaround times for test results, and can be labor-intensive. Also, the circulating SARS-COV-2 variant of concerns, reduced antibody sensitivity and/or neutralization, and possible antibody-dependent enhancement (ADE) have warranted the search for alternative potent therapeutics. Aptamers, which are single-stranded oligonucleotides, generated artificially by SELEX (Evolution of Ligands by Exponential Enrichment) may offer the capacity to generate high-affinity neutralizers and/or bioprobes for monitoring relevant SARS-COV-2 and COVID-19 biomarkers. This article reviews and discusses the prospects of implementing aptamers for rapid point-of-care detection and treatment of SARS-COV-2. We highlight other SARS-COV-2 targets (N protein, spike protein stem-helix), SELEX augmented with competition assays and in silico technologies for rapid discovery and isolation of theranostic aptamers against COVID-19 and future pandemics. It further provides an overview on site-specific bioconjugation approaches, customizable molecular scaffolding strategies, and nanotechnology platforms to engineer these aptamers into ultrapotent blockers, multivalent therapeutics, and vaccines to boost both humoral and cellular immunity against the virus. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Diagnostic Tools > Biosensing Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease Therapeutic Approaches and Drug Discovery > Nanomedicine for Respiratory Disease.
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Affiliation(s)
- Christian K. O. Dzuvor
- Bioengineering Laboratory, Department of Chemical and Biological EngineeringMonash UniversityClaytonVictoriaAustralia
| | | | - Michael K. Danquah
- Department of Chemical EngineeringUniversity of TennesseeChattanoogaTennesseeUSA
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Yousef H, Liu Y, Zheng L. Nanomaterial-Based Label-Free Electrochemical Aptasensors for the Detection of Thrombin. BIOSENSORS 2022; 12:bios12040253. [PMID: 35448312 PMCID: PMC9025199 DOI: 10.3390/bios12040253] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/08/2022] [Accepted: 04/14/2022] [Indexed: 05/06/2023]
Abstract
Thrombin plays a central role in hemostasis and its imbalances in coagulation can lead to various pathologies. It is of clinical significance to develop a fast and accurate method for the quantitative detection of thrombin. Electrochemical aptasensors have the capability of combining the specific selectivity from aptamers with the extraordinary sensitivity from electrochemical techniques and thus have attracted considerable attention for the trace-level detection of thrombin. Nanomaterials and nanostructures can further enhance the performance of thrombin aptasensors to achieve high sensitivity, selectivity, and antifouling functions. In highlighting these material merits and their impacts on sensor performance, this paper reviews the most recent advances in label-free electrochemical aptasensors for thrombin detection, with an emphasis on nanomaterials and nanostructures utilized in sensor design and fabrication. The performance, advantages, and limitations of those aptasensors are summarized and compared according to their material structures and compositions.
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Affiliation(s)
- Hibba Yousef
- Department of Biomedical Engineering, Khalifa University, Abu Dhabi 127788, United Arab Emirates;
| | - Yang Liu
- College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia;
| | - Lianxi Zheng
- Department of Mechanical Engineering, Khalifa University, Abu Dhabi 127788, United Arab Emirates
- Correspondence:
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Shabalina AV, Sharko DO, Glazyrin YE, Bolshevich EA, Dubinina OV, Kim AM, Veprintsev DV, Lapin IN, Zamay GS, Krat AV, Zamay SS, Svetlichnyi VA, Kichkailo AS, Berezovski MV. Development of Electrochemical Aptasensor for Lung Cancer Diagnostics in Human Blood. SENSORS 2021; 21:s21237851. [PMID: 34883850 PMCID: PMC8659852 DOI: 10.3390/s21237851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 11/12/2021] [Accepted: 11/18/2021] [Indexed: 02/04/2023]
Abstract
We describe the preparation and characterization of an aptamer-based electrochemical sensor to lung cancer tumor markers in human blood. The highly reproducible aptamer sensing layer with a high density (up to 70% coverage) on the gold electrode was made. Electrochemical methods and confocal laser scanning microscopy were used to study the stability of the aptamer layer structure and binding ability. A new blocking agent, a thiolated oligonucleotide with an unrelated sequence, was applied to fill the aptamer layer’s defects. Electrochemical aptasensor signal processing was enhanced using deep learning and computer simulation of the experimental data array. It was found that the combinations (coupled and tripled) of cyclic voltammogram features allowed for distinguishing between the samples from lung cancer patients and healthy candidates with a mean accuracy of 0.73. The capacitive component from the non-Faradic electrochemical impedance spectroscopy data indicated the tumor marker’s presence in a sample. These findings allowed for the creation of highly informative aptasensors for early lung cancer diagnostics.
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Affiliation(s)
- Anastasiia V. Shabalina
- Siberian Physical-Technical Institute, Tomsk State University, 634050 Tomsk, Russia; (A.V.S.); (D.O.S.); (E.A.B.); (O.V.D.); (A.M.K.); (I.N.L.); (V.A.S.)
| | - Darya O. Sharko
- Siberian Physical-Technical Institute, Tomsk State University, 634050 Tomsk, Russia; (A.V.S.); (D.O.S.); (E.A.B.); (O.V.D.); (A.M.K.); (I.N.L.); (V.A.S.)
| | - Yury E. Glazyrin
- Federal Research Center, Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science, 660036 Krasnoyarsk, Russia; (Y.E.G.); (D.V.V.); (G.S.Z.); (S.S.Z.)
- Laboratory of Biomolecular and Medical Technologies, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, 660022 Krasnoyarsk, Russia;
| | - Elena A. Bolshevich
- Siberian Physical-Technical Institute, Tomsk State University, 634050 Tomsk, Russia; (A.V.S.); (D.O.S.); (E.A.B.); (O.V.D.); (A.M.K.); (I.N.L.); (V.A.S.)
| | - Oksana V. Dubinina
- Siberian Physical-Technical Institute, Tomsk State University, 634050 Tomsk, Russia; (A.V.S.); (D.O.S.); (E.A.B.); (O.V.D.); (A.M.K.); (I.N.L.); (V.A.S.)
| | - Anastasiia M. Kim
- Siberian Physical-Technical Institute, Tomsk State University, 634050 Tomsk, Russia; (A.V.S.); (D.O.S.); (E.A.B.); (O.V.D.); (A.M.K.); (I.N.L.); (V.A.S.)
| | - Dmitry V. Veprintsev
- Federal Research Center, Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science, 660036 Krasnoyarsk, Russia; (Y.E.G.); (D.V.V.); (G.S.Z.); (S.S.Z.)
| | - Ivan N. Lapin
- Siberian Physical-Technical Institute, Tomsk State University, 634050 Tomsk, Russia; (A.V.S.); (D.O.S.); (E.A.B.); (O.V.D.); (A.M.K.); (I.N.L.); (V.A.S.)
| | - Galina S. Zamay
- Federal Research Center, Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science, 660036 Krasnoyarsk, Russia; (Y.E.G.); (D.V.V.); (G.S.Z.); (S.S.Z.)
- Laboratory of Biomolecular and Medical Technologies, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, 660022 Krasnoyarsk, Russia;
| | - Alexey V. Krat
- Laboratory of Biomolecular and Medical Technologies, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, 660022 Krasnoyarsk, Russia;
- Krasnoyarsk Regional Clinical Cancer Center Named after A.I. Kryzhanovsky, 660133 Krasnoyarsk, Russia
| | - Sergey S. Zamay
- Federal Research Center, Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science, 660036 Krasnoyarsk, Russia; (Y.E.G.); (D.V.V.); (G.S.Z.); (S.S.Z.)
- Laboratory of Biomolecular and Medical Technologies, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, 660022 Krasnoyarsk, Russia;
| | - Valery A. Svetlichnyi
- Siberian Physical-Technical Institute, Tomsk State University, 634050 Tomsk, Russia; (A.V.S.); (D.O.S.); (E.A.B.); (O.V.D.); (A.M.K.); (I.N.L.); (V.A.S.)
| | - Anna S. Kichkailo
- Federal Research Center, Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science, 660036 Krasnoyarsk, Russia; (Y.E.G.); (D.V.V.); (G.S.Z.); (S.S.Z.)
- Laboratory of Biomolecular and Medical Technologies, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, 660022 Krasnoyarsk, Russia;
- Correspondence: (A.S.K.); (M.V.B.)
| | - Maxim V. Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, AB K1N 6N5, Canada
- Correspondence: (A.S.K.); (M.V.B.)
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Vishwakarma A, Lal R, Ramya M. Aptamer-based approaches for the detection of waterborne pathogens. Int Microbiol 2021; 24:125-140. [PMID: 33404933 DOI: 10.1007/s10123-020-00154-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/13/2020] [Accepted: 12/14/2020] [Indexed: 02/06/2023]
Abstract
Waterborne ailments pose a serious threat to public health and are a huge economic burden. Lack of hygiene in drinking and recreational water is the chief source of microbial pathogens in developing countries. Poor water quality and sanitation account for more than 3.4 million deaths a year worldwide. This has urged authorities and researchers to explore different avenues of pathogen detection. There is a growing demand for rapid and reliable sensor technologies, in particular those that can detect in situ and perform in harsh conditions. Some of the major waterborne pathogens include Vibrio cholerae, Leptospira interrogans, Campylobacter jejuni, Shigella spp., enterotoxigenic Escherichia coli, Clostridium difficile, Cryptosporidium parvum, Entamoeba histolytica, and Hepatitis A virus. While conventional methods of pathogen detection like serodiagnosis and microbiological methods have been superseded by nucleic acid amplification methods, there is still potential for improvement. This review provides an insight into aptamers and their utility in the form of aptasensors. It discusses how aptamer-based approaches have emerged as a novel strategy and its advantages over more resource-intensive and complex biochemical approaches.
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Affiliation(s)
- Archana Vishwakarma
- Molecular Genetics Laboratory, Department of Genetic Engineering, College of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur 603203, Kanchipuram, Chennai, TN, India
| | - Roshni Lal
- Molecular Genetics Laboratory, Department of Genetic Engineering, College of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur 603203, Kanchipuram, Chennai, TN, India
| | - Mohandass Ramya
- Molecular Genetics Laboratory, Department of Genetic Engineering, College of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur 603203, Kanchipuram, Chennai, TN, India.
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Impedimetric Aptamer-Based Biosensors: Principles and Techniques. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 174:17-41. [PMID: 32328684 DOI: 10.1007/10_2019_113] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Aptamers are a specific class of ligands with high affinities comparable to antibodies, which are selected and synthesized in vitro. In combination with impedance spectroscopy as sensitive measurement method, we gain a class of biosensors with high potential for handheld devices and point-of-care tests. In this review, we report on recent advances in aptamer-based impedimetric biosensors. Besides giving a short summary of electrochemical measurement techniques, the most exciting innovative developments of detection strategies in the last decades are reviewed. Finally, important criteria for the comparison of aptamer-based biosensors are discussed.
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HIRANO S, SAITO J, YUKAWA T, SANO D, OKAMOTO A, OKABE S, KITAJIMA M. Improvement of Electrochemical Conditions for Detecting Redox Reaction of K<sub>3</sub>[Fe(CN)<sub>6</sub>] toward the Application in Norovirus Aptasensor. ELECTROCHEMISTRY 2020. [DOI: 10.5796/electrochemistry.20-00017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Seiya HIRANO
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University
| | - Junki SAITO
- Department of Applied Chemistry, School of Engineering, The University of Tokyo
| | - Tomoki YUKAWA
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University
| | - Daisuke SANO
- Department of Frontier Science for Advanced Environment, Graduate School of Environmental Studies and Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University
| | - Akihiro OKAMOTO
- International Center for Materials Nanoarchitectonics (WPI-MANA) and Center for Sensor and Actuator Material, National Institute for Materials Science (NIMS)
- School of Chemical Sciences and Engineering, Hokkaido University
| | - Satoshi OKABE
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University
| | - Masaaki KITAJIMA
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University
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Munzar JD, Ng A, Juncker D. Duplexed aptamers: history, design, theory, and application to biosensing. Chem Soc Rev 2019; 48:1390-1419. [PMID: 30707214 DOI: 10.1039/c8cs00880a] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nucleic acid aptamers are single stranded DNA or RNA sequences that specifically bind a cognate ligand. In addition to their widespread use as stand-alone affinity binding reagents in analytical chemistry, aptamers have been engineered into a variety of ligand-specific biosensors, termed aptasensors. One of the most common aptasensor formats is the duplexed aptamer (DA). As defined herein, DAs are aptasensors containing two nucleic acid elements coupled via Watson-Crick base pairing: (i) an aptamer sequence, which serves as a ligand-specific receptor, and (ii) an aptamer-complementary element (ACE), such as a short DNA oligonucleotide, which is designed to hybridize to the aptamer. The ACE competes with ligand binding, such that DAs generate a signal upon ligand-dependent ACE-aptamer dehybridization. DAs possess intrinsic advantages over other aptasensor designs. For example, DA biosensing designs generalize across DNA and RNA aptamers, DAs are compatible with many readout methods, and DAs are inherently tunable on the basis of nucleic acid hybridization. However, despite their utility and popularity, DAs have not been well defined in the literature, leading to confusion over the differences between DAs and other aptasensor formats. In this review, we introduce a framework for DAs based on ACEs, and use this framework to distinguish DAs from other aptasensor formats and to categorize cis- and trans-DA designs. We then explore the ligand binding dynamics and chemical properties that underpin DA systems, which fall under conformational selection and induced fit models, and which mirror classical SN1 and SN2 models of nucleophilic substitution reactions. We further review a variety of in vitro and in vivo applications of DAs in the chemical and biological sciences, including riboswitches and riboregulators. Finally, we present future directions of DAs as ligand-responsive nucleic acids. Owing to their tractability, versatility and ease of engineering, DA biosensors bear a great potential for the development of new applications and technologies in fields ranging from analytical chemistry and mechanistic modeling to medicine and synthetic biology.
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Affiliation(s)
- Jeffrey D Munzar
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
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Khoshbin Z, Verdian A, Housaindokht MR, Izadyar M, Rouhbakhsh Z. Aptasensors as the future of antibiotics test kits-a case study of the aptamer application in the chloramphenicol detection. Biosens Bioelectron 2018; 122:263-283. [PMID: 30268964 DOI: 10.1016/j.bios.2018.09.060] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/08/2018] [Accepted: 09/16/2018] [Indexed: 12/31/2022]
Abstract
Antibiotics are a type of antimicrobial drug with the ubiquitous presence in foodstuff that effectively applied to treat the diseases and promote the animal growth worldwide. Chloramphenicol as one of the antibiotics with the broad action spectrum against Gram-positive and Gram-negative bacteria is widely applied for the effective treatment of infectious diseases in humans and animals. Unfortunately, the serious side effects of chloramphenicol, such as aplastic anemia, kidney damage, nausea, and diarrhea restrict its application in foodstuff and biomedical fields. Development of the sufficiently sensitive methods to detect chloramphenicol residues in food and clinical diagnosis seems to be an essential demand. Biosensors have been introduced as the promising tools to overcome the requirement. As one of the newest types of the biosensors, aptamer-based biosensors (aptasensors) are the efficient sensing platforms for the chloramphenicol monitoring. In the present review, we summarize the recent achievements of the accessible aptasensors for qualitative detection and quantitative determination of chloramphenicol as a candidate of the antibiotics. The present chloramphenicol aptasensors can be classified in two main optical and electrochemical categories. Also, the other formats of the aptasensing assays like the high performance liquid chromatography (HPLC) and microchip electrophoresis (MCE) have been reviewed. The enormous interest in utilizing the diverse nanomaterials is also highlighted in the fabrication of the chloramphenicol aptasensors. Finally, some results are presented based on the advantages and disadvantages of the studied aptasensors to achieve a promising perspective for designing the novel antibiotics test kits.
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Affiliation(s)
- Zahra Khoshbin
- 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.
| | | | - Mohammad Izadyar
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Zeinab Rouhbakhsh
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
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Zhang YB, Wang YP, Liu J. [Research advances in the role of aptamers in the diagnosis and targeted therapy of pediatric cancer]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2018; 20:421-427. [PMID: 29764582 PMCID: PMC7389069 DOI: 10.7499/j.issn.1008-8830.2018.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 03/29/2018] [Indexed: 06/08/2023]
Abstract
Aptamers are single-stranded DNA or RNA which are isolated from synthesized random oligonucleotide library in vitro via systematic evolution of ligands by exponential enrichment (SELEX) and can bind to metal ions, small molecules, carbohydrates, lipids, proteins, and others targets with high affinity and specificity. Aptamers have the advantages of simple preparation, good thermal stability, and low immunogenicity and have great potential in the medical fields such as molecular imaging, biosensing, early diagnosis of diseases, and targeted therapy. Aptamer technology may be useful for early diagnosis and targeted therapy of pediatric cancer, and may avoid the side effects of conventional chemotherapy, such as growth and development disorders and long-term organ dysfunction. This article reviews the latest research advances in the selection and application of aptamers for pediatric cancer.
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Affiliation(s)
- Yi-Bin Zhang
- Molecular Research Center, School of Life Sciences, Central South University, Changsha 410078, China.
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13
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An aptamer-based biosensor for detection of doxorubicin by electrochemical impedance spectroscopy. Anal Bioanal Chem 2017; 410:1453-1462. [PMID: 29199352 DOI: 10.1007/s00216-017-0786-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/31/2017] [Accepted: 11/24/2017] [Indexed: 12/18/2022]
Abstract
An aptamer-based biosensor was developed for the detection of doxorubicin using electrochemical impedance spectroscopy. Doxorubicin and its 14-dehydroxylated version daunorubicin are anthracyclines often used in cancer treatment. Due to their mutagenic and cardiotoxic effects, detection in groundwater is desirable. We developed a biosensor using the daunorubicin-binding aptamer as biological recognition element. The aptamer was successfully co-immobilized with mercaptohexanol on gold and a density of 1.3*1013 ± 2.4*1012 aptamer molecules per cm2 was achieved. The binding of doxorubicin to the immobilized aptamer was detected by electrochemical impedance spectroscopy. The principle is based on the inhibition of electron transfer between electrode and ferro-/ferricyanide in solution caused by the binding of doxorubicin to the immobilized aptamer. A linear relationship between the charge transfer resistance (R ct ) and the doxorubicin concentration was obtained over the range of 31 nM to 125 nM doxorubicin, with an apparent binding constant of 64 nM and a detection limit of 28 nM. With the advantages of high sensitivity, selectivity, and simple sensor construction, this method shows a high potential of impedimetric aptasensors in environmental monitoring. Graphical abstract Measurement chamber and immobilization principle for the detection of doxorubicin by electrochemical impedance spectroscopy.
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Triplex-quadruplex structural scaffold: a new binding structure of aptamer. Sci Rep 2017; 7:15467. [PMID: 29133961 PMCID: PMC5684193 DOI: 10.1038/s41598-017-15797-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/02/2017] [Indexed: 11/08/2022] Open
Abstract
Apart from the canonical Watson-Crick duplex, nucleic acids can often form other structures, e.g. G-quadruplex and triplex. These structures give nucleic acid additional functions besides coding for genetic information. Aptamers are one type of functional nucleic acids that bind to specific targets with high selectivity and affinity by folding into special tertiary structures. Despite the fact that numerous aptamers have been reported, only a few different types of aptamer structures are identified. Here we report a novel triplex-quadruplex hybrid scaffold formed by a codeine binding aptamer (CBA). CBA and its derivatives are G-rich DNA sequences. Codeine binding can induce the formation of a complex structure for this aptamer containing a G-quadruplex and a G·GC triplex, while codeine is located at the junction of the triplex and quadruplex. When split CBA into two moieties, codeine does not bind either moieties individually, but can bind them together by inducing the formation of the triplex-quadruplex scaffold. This structure formation induced by codeine binding is shown to inhibit polymerase reaction, which shows a potential application of the aptamer sequence in gene regulations.
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15
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Nambi Krishnan J, Park SH, Kim SK. Aptamer-Based Single-Step Assay by the Fluorescence Enhancement on Electroless Plated Nano Au Substrate. SENSORS (BASEL, SWITZERLAND) 2017; 17:E2044. [PMID: 28880198 PMCID: PMC5620733 DOI: 10.3390/s17092044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 08/25/2017] [Accepted: 09/02/2017] [Indexed: 01/13/2023]
Abstract
A new single-step aptamer-based surface-enhanced fluorescent optical sensor is built, by combining an aptamer-target interaction for target recognition and a fluorophore interaction for signal enhancement. The developed aptasensor is simple, sensitive, specific and stable for the detection of thrombin. A new nanometallic Au structure in the range of 100 nm was constructed through effective electroless plating method on a Cu thin film. Cu⁺ ions act as sacrificial seeds for the reduction of Au2+/3+ ions to form Au nanolawns. In order to utilize the structure for a fluorescence-based sensor, aptamer conjugated with Cy3 was immobilized on the nanogold substrate through electrostatic attraction. The Au substrate was coated with chitosan (molecular weight 1000 Da). Thrombin binding aptamer (TBA) was applied as a model system demonstrating the aptamer-based fluorescence assay on nanogold substrates. Thrice-enhanced fluorescence emission was achieved with Cy3-conjugated TBA stably immobilized on the chitosan-coated Au substrate. The intensity change was proportional to the concentration of thrombin from 10 μM to 10 pM, whereas the intensity change was ignorable for other proteins such as human serum albumin (HSA). Aptamer-based assay benefited from simple immobilization of receptors and Au nanostructure contributed in building an effective surface enhancing/positively charged substrate was proved. Such an aptasensor holding high utilities for point-of-care devices by incorporating simplicity, sensitivity and selectivity in detection, low-cost for test, small sample volumes has been developed.
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Affiliation(s)
- Jegatha Nambi Krishnan
- Center for BioMicrosystems, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Sungbuk-gu, Seoul 136-791, Korea.
- School of Micro Nano System Engineering, Korea University of Science and Technology, Daejeon 305-333, Korea.
- School of Chemical Engineering, Birla Institute of Technology and Science, Pilani, K. K. Birla Goa Campus, Zuari Nagar, Goa 403-726, India.
| | - Sang-Hwi Park
- Center for BioMicrosystems, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Sungbuk-gu, Seoul 136-791, Korea.
- School of Micro Nano System Engineering, Korea University of Science and Technology, Daejeon 305-333, Korea.
| | - Sang Kyung Kim
- Center for BioMicrosystems, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Sungbuk-gu, Seoul 136-791, Korea.
- School of Micro Nano System Engineering, Korea University of Science and Technology, Daejeon 305-333, Korea.
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17
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Rhouati A, Catanante G, Nunes G, Hayat A, Marty JL. Label-Free Aptasensors for the Detection of Mycotoxins. SENSORS 2016; 16:s16122178. [PMID: 27999353 PMCID: PMC5191157 DOI: 10.3390/s16122178] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/08/2016] [Accepted: 12/14/2016] [Indexed: 01/13/2023]
Abstract
Various methodologies have been reported in the literature for the qualitative and quantitative monitoring of mycotoxins in food and feed samples. Based on their enhanced specificity, selectivity and versatility, bio-affinity assays have inspired many researchers to develop sensors by exploring bio-recognition phenomena. However, a significant problem in the fabrication of these devices is that most of the biomolecules do not generate an easily measurable signal upon binding to the target analytes, and signal-generating labels are required to perform the measurements. In this context, aptamers have been emerged as a potential and attractive bio-recognition element to design label-free aptasensors for various target analytes. Contrary to other bioreceptor-based approaches, the aptamer-based assays rely on antigen binding-induced conformational changes or oligomerization states rather than binding-assisted changes in adsorbed mass or charge. This review will focus on current designs in label-free conformational switchable design strategies, with a particular focus on applications in the detection of mycotoxins.
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Affiliation(s)
- Amina Rhouati
- BAE Laboratory, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, Perpignan 66860, France.
- Ecole Nationale Supérieure de Biotechnologie, Constantine 25100, Algeria.
| | - Gaelle Catanante
- BAE Laboratory, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, Perpignan 66860, France.
| | - Gilvanda Nunes
- Technological Chemistry Department, Federal University of Maranhão, CCET/UFMA, Av. Portugueses, Cidade Universitária do Canga, 65080-040 São Luis, Brazil.
| | - Akhtar Hayat
- BAE Laboratory, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, Perpignan 66860, France.
- Interdisciplinary Research Centre in Biomedical Materials (IRCBM) COMSATS Institute of Information Technology (CIIT), Lahore 54000, Pakistan.
| | - Jean-Louis Marty
- BAE Laboratory, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, Perpignan 66860, France.
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Pauwels D, Pilehvar S, Geboes B, Hubin A, De Wael K, Breugelmans T. A new multisine-based impedimetric aptasensing platform. Electrochem commun 2016. [DOI: 10.1016/j.elecom.2016.07.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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19
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Meirinho SG, Dias LG, Peres AM, Rodrigues LR. Voltammetric aptasensors for protein disease biomarkers detection: A review. Biotechnol Adv 2016; 34:941-953. [PMID: 27235188 DOI: 10.1016/j.biotechadv.2016.05.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 05/20/2016] [Accepted: 05/22/2016] [Indexed: 12/14/2022]
Abstract
An electrochemical aptasensor is a compact analytical device where the bioreceptor (aptamer) is coupled to a transducer surface to convert a biological interaction into a measurable signal (current) that can be easily processed, recorded and displayed. Since the discovery of the Systematic Evolution of Ligands by Enrichment (SELEX) methodology, the selection of aptamers and their application as bioreceptors has become a promising tool in the design of electrochemical aptasensors. Aptamers present several advantages that highlight their usefulness as bioreceptors such as chemical stability, cost effectiveness and ease of modification towards detection and immobilization at different transducer surfaces. In this review, a special emphasis is given to the potential use of electrochemical aptasensors for the detection of protein disease biomarkers using voltammetry techniques. Methods for the immobilization of aptamers onto electrode surfaces are discussed, as well as different electrochemical strategies that can be used for the design of aptasensors.
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Affiliation(s)
- Sofia G Meirinho
- Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Luís G Dias
- ESA, Instituto Politécnico de Bragança, Campus Santa Apolónia, 5300-253 Bragança, Portugal; CQ-VR, Centro de Química - Vila Real, University of Trás-os-Montes e Alto Douro, Apartado 1013, 5001-801 Vila Real, Portugal
| | - António M Peres
- Laboratory of Separation and Reaction Enginerring - Laboratory of Catalysis and Materials (LSRE-LCM), ESA, Instituto Politécnico de Bragança, Campus Santa Apolónia, 5300-253 Bragança, Portugal
| | - Lígia R Rodrigues
- Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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20
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Shangguan J, Li Y, He D, He X, Wang K, Zou Z, Shi H. A combination of positive dielectrophoresis driven on-line enrichment and aptamer-fluorescent silica nanoparticle label for rapid and sensitive detection of Staphylococcus aureus. Analyst 2016; 140:4489-97. [PMID: 25963028 DOI: 10.1039/c5an00535c] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Staphylococcus aureus (S. aureus) is an important human pathogen that causes several diseases ranging from superficial skin infections to life-threatening diseases. Here, a method combining positive dielectrophoresis (pDEP) driven on-line enrichment and aptamer-fluorescent silica nanoparticle label has been developed for the rapid and sensitive detection of S. aureus in microfluidic channels. An aptamer, having high affinity to S. aureus, is used as the molecular recognition tool and immobilized onto chloropropyl functionalized fluorescent silica nanoparticles through a click chemistry approach to obtain S. aureus aptamer-nanoparticle bioconjugates (Apt(S.aureus)/FNPs). The pDEP driven on-line enrichment technology was used for accumulating the Apt(S.aureus)/FNP labeled S. aureus. After incubating with S. aureus, the mixture of Apt(S.aureus)/FNP labeled S. aureus and Apt(S.aureus)/FNPs was directly introduced into the pDEP-based microfluidic system. By applying an AC voltage in a pDEP frequency region, the Apt(S.aureus)/FNP labelled S. aureus moved to the electrodes and accumulated in the electrode gap, while the free Apt(S.aureus)/FNPs flowed away. The signal that came from the Apt(S.aureus)/FNP labelled S. aureus in the focused detection areas was then detected. Profiting from the specificity of aptamer, signal amplification of FNP label and pDEP on-line enrichment, this assay can detect as low as 93 and 270 cfu mL(-1)S. aureus in deionized water and spiked water samples, respectively, with higher sensitivities than our previously reported Apt(S.aureus)/FNP based flow cytometry. Moreover, without the need for separation and washing steps usually required for FNP label involved bioassays, the total assay time including sample pretreatment was within 2 h.
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Affiliation(s)
- Jingfang Shangguan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha 410082, China.
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21
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Shahrokhian S, Salimian R, Kalhor HR. A simple label-free electrochemical DNA biosensor based on carbon nanotube–DNA interaction. RSC Adv 2016. [DOI: 10.1039/c5ra20907b] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A DNA biosensor based on π–π interactions between DNA and MWCNTs was developed in which the MWCNTs play the role of a conductive indicator.
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Affiliation(s)
- Saeed Shahrokhian
- Department of Chemistry
- Sharif University of Technology
- Tehran 11155-9516
- Iran
- Institute for Nanoscience and Technology
| | - Razieh Salimian
- Department of Chemistry
- Sharif University of Technology
- Tehran 11155-9516
- Iran
| | - Hamid Reza Kalhor
- Department of Chemistry
- Sharif University of Technology
- Tehran 11155-9516
- Iran
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22
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Aptamers as Synthetic Receptors for Food Quality and Safety Control. BIOSENSORS FOR SUSTAINABLE FOOD - NEW OPPORTUNITIES AND TECHNICAL CHALLENGES 2016. [DOI: 10.1016/bs.coac.2016.03.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Wu Q, Shen H, Shen H, Sun Y, Song L. Study on sensing strategy and performance of a microfluidic chemiluminescence aptazyme sensor. Talanta 2015; 150:531-8. [PMID: 26838440 DOI: 10.1016/j.talanta.2015.12.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 12/04/2015] [Accepted: 12/10/2015] [Indexed: 11/30/2022]
Abstract
Aptamers are analogous to antibodies in their range of target recognition. G-quadruplex DNAzymes exhibit peroxidase-like activity toward certain specific reactions. Despite aptazyme sensors, based on aptamer and DNAzyme conjugates, have the potential to replace many conventional immune-biosensors; the mechanism concerning high background interference has scarcely been discussed. In this work, by taking a couple of aptazyme sensors with oligonucleotide sequences of adenosine aptamer and CatG4 DNAzyme, the sensing strategy dealing with the thermodynamic equilibrium of the functional oligonucleotide distribution had been studied. Oligonucleotide arrangement and cation condition were found important in modulating the shifting between Watson-Crick duplex and Hoogsteen G-quadruplex, which ultimately influenced sample and background signals. Notably, benefit from the microfluidic chemiluminescence detection, the developed aptazyme sensor achieved an absolute detection limit of 12 pmol adenosine with just 2 μL of pretreated sample solution consumption and satisfactory selectivity. The results have implication for better design of aptazyme sensor in the future.
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Affiliation(s)
- Qiwang Wu
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Haihui Shen
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Hong Shen
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China.
| | - Yue Sun
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Lifang Song
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
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24
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van den Kieboom CH, van der Beek SL, Mészáros T, Gyurcsányi RE, Ferwerda G, de Jonge MI. Aptasensors for viral diagnostics. Trends Analyt Chem 2015; 74:58-67. [PMID: 32287539 PMCID: PMC7112930 DOI: 10.1016/j.trac.2015.05.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We discuss progress in aptamer-based detection of viruses. We consider the use of aptasensors for point-of-care diagnostics of viruses. Aptamers have distinct advantages over antibodies for virus recognition. There is strong demand for multiplexed diagnostic measurement of pathogens.
Novel viral diagnostic tools need to be affordable, fast, accurate and easy to use with sensitivity and specificity equivalent or superior to current standards. At present, viral diagnostics are based on direct detection of viral components or indirect detection by measuring antibodies generated in response to viral infection. While sensitivity of detection and quantification are still important challenges, we expect major advances from new assay formats and synthetic binding molecules, such as aptamers. Compared to traditional antibody-based detection, aptamers could provide faster adaptation to continuously evolving virus strains and higher discriminating capacity between specific virus serotypes. Aptamers are very stable and easily modifiable, so are ideal molecules for detection and chemical sensing applications. Here, we review the use of aptasensors for detection of viral pathogens and consider the feasibility of aptasensors to become standard devices for point-of-care diagnostics of viruses.
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Affiliation(s)
- Corné H van den Kieboom
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Center, Nijmegen, Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Tamás Mészáros
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary.,MTA-BME Research Group for Technical Analytical Chemistry, Budapest University of Technology and Economics, Budapest, Hungary
| | - Róbert E Gyurcsányi
- MTA-BME Lendület Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Budapest, Hungary
| | - Gerben Ferwerda
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Marien I de Jonge
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Center, Nijmegen, Netherlands
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Acquah C, Danquah MK, Agyei D, Moy CKS, Sidhu A, Ongkudon CM. Deploying aptameric sensing technology for rapid pandemic monitoring. Crit Rev Biotechnol 2015; 36:1010-1022. [PMID: 26381238 DOI: 10.3109/07388551.2015.1083940] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The genome of virulent strains may possess the ability to mutate by means of antigenic shift and/or antigenic drift as well as being resistant to antibiotics with time. The outbreak and spread of these virulent diseases including avian influenza (H1N1), severe acute respiratory syndrome (SARS-Corona virus), cholera (Vibrio cholera), tuberculosis (Mycobacterium tuberculosis), Ebola hemorrhagic fever (Ebola Virus) and AIDS (HIV-1) necessitate urgent attention to develop diagnostic protocols and assays for rapid detection and screening. Rapid and accurate detection of first cases with certainty will contribute significantly in preventing disease transmission and escalation to pandemic levels. As a result, there is a need to develop technologies that can meet the heavy demand of an all-embedded, inexpensive, specific and fast biosensing for the detection and screening of pathogens in active or latent forms to offer quick diagnosis and early treatments in order to avoid disease aggravation and unnecessary late treatment costs. Nucleic acid aptamers are short, single-stranded RNA or DNA sequences that can selectively bind to specific cellular and biomolecular targets. Aptamers, as new-age bioaffinity probes, have the necessary biophysical characteristics for improved pathogen detection. This article seeks to review global pandemic situations in relation to advances in pathogen detection systems. It particularly discusses aptameric biosensing and establishes application opportunities for effective pandemic monitoring. Insights into the application of continuous polymeric supports as the synthetic base for aptamer coupling to provide the needed convective mass transport for rapid screening is also presented.
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Affiliation(s)
- Caleb Acquah
- a Curtin Sarawak Research Institute, Curtin University , Sarawak 98009 , Malaysia.,b Department of Chemical Engineering , Curtin University , Sarawak 98009 , Malaysia
| | - Michael K Danquah
- b Department of Chemical Engineering , Curtin University , Sarawak 98009 , Malaysia
| | - Dominic Agyei
- c Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences Deakin University , Geelong-Waurn Ponds , Australia
| | - Charles K S Moy
- d Faculty of Engineering and Science , Curtin University , Sarawak 98009 , Malaysia
| | - Amandeep Sidhu
- a Curtin Sarawak Research Institute, Curtin University , Sarawak 98009 , Malaysia.,e Faculty of Health Sciences , Curtin University , Perth 6102 , Australia , and
| | - Clarence M Ongkudon
- f Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu , Sabah, 88400 , Malaysia
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Wang B, Lou Z, Park B, Kwon Y, Zhang H, Xu B. Surface conformations of an anti-ricin aptamer and its affinity for ricin determined by atomic force microscopy and surface plasmon resonance. Phys Chem Chem Phys 2015; 17:307-14. [PMID: 25181753 DOI: 10.1039/c4cp03190c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We used atomic force microscopy (AFM) and surface plasmon resonance (SPR) to study the surface conformations of an anti-ricin aptamer and its specific binding affinity for ricin molecules. The effect of surface modification of the Au(111) substrate on the aptamer affinity was also estimated. The AFM topography images had a resolution high enough to distinguish different aptamer conformations. The specific binding site on the aptamer molecule was clearly located by the AFM recognition images. The aptamer on a Au(111) surface modified with carboxymethylated-dextran (CD) showed both similarities to and differences from the one without CD modification. The influence of CD modification was evaluated using AFM images of various aptamer conformations on the Au(111) surface. The affinity between ricin and the anti-ricin aptamer was estimated using the off-rate values measured using AFM and SPR. The SPR measurements of the ricin sample were conducted in the range from 83.3 pM to 8.33 nM, and the limit of detection was estimated as 25 pM (1.5 ng mL(-1)). The off-rate values of the ricin-aptamer interactions were estimated using both single-molecule dynamic force spectroscopy (DFS) and SPR as (7.3 ± 0.4) × 10(-4) s(-1) and (1.82 ± 0.067) × 10(-2) s(-1), respectively. The results show that single-molecule measurements can obtain different reaction parameters from bulk solution measurements. In AFM single-molecule measurements, the various conformations of the aptamer immobilized on the gold surface determined the availability of each specific binding site to the ricin molecules. The SPR bulk solution measurements averaged the signals from specific and non-specific interactions. AFM images and DFS measurements provide more specific information on the interactions of individual aptamer and ricin molecules.
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Affiliation(s)
- B Wang
- Single Molecule Study Laboratory, Faculty of Engineering and Nanoscale Science and Engineering Center, University of Georgia, Athens, GA 30602, USA.
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Acquah C, Danquah MK, Yon JLS, Sidhu A, Ongkudon CM. A review on immobilised aptamers for high throughput biomolecular detection and screening. Anal Chim Acta 2015; 888:10-8. [PMID: 26320953 DOI: 10.1016/j.aca.2015.05.050] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 05/20/2015] [Accepted: 05/22/2015] [Indexed: 02/07/2023]
Abstract
The discovery of Systematic Evolution of Ligands by Exponential Enrichment (SELEX) assay has led to the generation of aptamers from libraries of nucleic acids. Concomitantly, aptamer-target recognition and its potential biomedical applications have become a major research endeavour. Aptamers possess unique properties that make them superior biological receptors to antibodies with a plethora of target molecules. Some specific areas of opportunities explored for aptamer-target interactions include biochemical analysis, cell signalling and targeting, biomolecular purification processes, pathogen detection and, clinical diagnosis and therapy. Most of these potential applications rely on the effective immobilisation of aptamers on support systems to probe target species. Hence, recent research focus is geared towards immobilising aptamers as oligosorbents for biodetection and bioscreening. This article seeks to review advances in immobilised aptameric binding with associated successful milestones and respective limitations. A proposal for high throughput bioscreening using continuous polymeric adsorbents is also presented.
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Affiliation(s)
- Caleb Acquah
- Curtin Sarawak Research Institute, Curtin University, Sarawak, 98009, Malaysia; Department of Chemical Engineering, Curtin University, Sarawak, 98009, Malaysia
| | - Michael K Danquah
- Department of Chemical Engineering, Curtin University, Sarawak, 98009, Malaysia.
| | - John L S Yon
- Department of Chemical Engineering, Curtin University, Sarawak, 98009, Malaysia
| | - Amandeep Sidhu
- Curtin Sarawak Research Institute, Curtin University, Sarawak, 98009, Malaysia; Faculty of Health Sciences, Curtin University, Perth, 6109, Australia
| | - Clarence M Ongkudon
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, 88400, Malaysia
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Wang C, Kim J, Zhu Y, Yang J, Lee GH, Lee S, Yu J, Pei R, Liu G, Nuckolls C, Hone J, Lin Q. An aptameric graphene nanosensor for label-free detection of small-molecule biomarkers. Biosens Bioelectron 2015; 71:222-229. [PMID: 25912678 DOI: 10.1016/j.bios.2015.04.025] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 03/27/2015] [Accepted: 04/10/2015] [Indexed: 11/18/2022]
Abstract
This paper presents an aptameric graphene nanosensor for detection of small-molecule biomarkers. To address difficulties in direct detection of small molecules associated with their low molecular weight and electrical charge, we incorporate an aptamer-based competitive affinity assay in a graphene field effect transistor (FET), and demonstrate the utility of the nanosensor with dehydroepiandrosterone sulfate (DHEA-S), a small-molecule steroid hormone, as the target analyte. In the competitive affinity assay, DHEA-S specifically binds to aptamer molecules pre-hybridized to their complementary DNA anchor molecules immobilized on the graphene surface. This results in the competitive release of the strongly charged aptamer from the DNA anchor and hence a change in electrical properties of the graphene, which can be measured to achieve the detection of DHEA-S. We present experimental data on the label-free, specific and quantitative detection of DHEA-S at clinically appropriate concentrations with an estimated detection limit of 44.7 nM, and analyze the trend observed in the experiments using molecular binding kinetics theory. These results demonstrate the potential of our nanosensor in the detection of DHEA-S and other small molecules in biomedical applications.
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Affiliation(s)
- Cheng Wang
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA; Department of Microelectronic Engineering, Nankai University, Tianjin 300071, China
| | - Jinho Kim
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA
| | - Yibo Zhu
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA
| | - Jaeyoung Yang
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA
| | - Gwan-Hyoung Lee
- Department of Materials Science and Engineering, Yonsei University, Seoul 120749, Republic of Korea
| | - Sunwoo Lee
- Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | - Jaeeun Yu
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Renjun Pei
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, Jiangsu 215123, China
| | - Guohua Liu
- Department of Microelectronic Engineering, Nankai University, Tianjin 300071, China
| | - Colin Nuckolls
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - James Hone
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA.
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Billinge ER, Platt M. Multiplexed, label-free detection of biomarkers using aptamers and Tunable Resistive Pulse Sensing (AptaTRPS). Biosens Bioelectron 2015; 68:741-748. [PMID: 25682502 DOI: 10.1016/j.bios.2015.02.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/06/2015] [Indexed: 12/26/2022]
Abstract
Diagnostics that are capable of detecting multiple biomarkers are improving the accuracy and efficiency of bioassays. In previous work we have demonstrated the potential of an aptamer-based sensor (aptasensor) utilising Tunable Resistive Pulse Sensing (TRPS). Here, we have advanced the technique identifying key experimental designs for potential POC assays. The assay utilised superparamagnetic beads, and using TRPS monitored their translocations through a pore. If the surfaces of the beads are modified with an aptamer, the frequency of beads (translocations/min) through the pore can be related to the concentration of specific proteins in the solution. Herein, we have demonstrated the successful use of TRPS to observe the binding of two proteins, to their specific aptamers simultaneously. We describe a series of experiments illustrating key factors which we believe are integral to bead-based assays and demonstrate a general method for a multiplexed assay. In summary, we have explored the effects of beads size, concentration, potential bias, pH and aptamer affinity to enhance the sensitivity and practically of a TRPS aptasensor. The method utilises the fact the binding of the aptamer to the protein results in a change in charge density on the bead surface, the isoelectric point of the protein then dominates the mobility of the beads, creating a multiplexed assay termed AptaTRPS. By alteration of the applied potential to the instrument it is possible to produce a positive signal in a simple multiplexed assay.
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Affiliation(s)
- Emily R Billinge
- Centre of Analytical Sciences, Department of Chemistry, School of Science, Loughborough University, Loughborough, Leicestershire LE11 3TU, United Kingdom
| | - Mark Platt
- Centre of Analytical Sciences, Department of Chemistry, School of Science, Loughborough University, Loughborough, Leicestershire LE11 3TU, United Kingdom.
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Trashin S, de Jong M, Breugelmans T, Pilehvar S, De Wael K. Label-Free Impedance Aptasensor for Major Peanut Allergen Ara h 1. ELECTROANAL 2014. [DOI: 10.1002/elan.201400365] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Pérez-Ruiz E, Kemper M, Spasic D, Gils A, van Ijzendoorn LJ, Lammertyn J, Prins MWJ. Probing the force-induced dissociation of aptamer-protein complexes. Anal Chem 2014; 86:3084-91. [PMID: 24579568 DOI: 10.1021/ac404107s] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Aptamers are emerging as powerful synthetic bioreceptors for fundamental research, diagnostics, and therapeutics. For further advances, it is important to gain a better understanding of how aptamers interact with their targets. In this work, we have used magnetic force-induced dissociation experiments to study the dissociation process of two different aptamer-protein complexes, namely for hIgE and Ara h 1. The measurements show that both complexes exhibit dissociation with two distinct regimes: the dissociation rate depends weakly on the applied force at high forces but depends stronger on force at low forces. We attribute these observations to the existence of at least one intermediate state and at least two energy barriers in the aptamer-protein interaction. The measured spontaneous dissociation rate constants were validated with SPR using both Biacore and fiber optic technology. This work demonstrates the potential of the magnetic force-induced dissociation approach for an in-depth study of the dissociation kinetics of aptamer-protein bonds, which is not possible with SPR technologies. The results will help in the development and expansion of aptamers as bioaffinity probes.
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Affiliation(s)
- Elena Pérez-Ruiz
- Department of Biosystems - MeBioS, KU Leuven-University of Leuven , Leuven, Belgium
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Au nanoparticle-DNAzyme dual catalyst system for sensitively colorimetric detection of thrombin. Chem Res Chin Univ 2013. [DOI: 10.1007/s40242-013-3039-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Zelada-Guillén GA, Blondeau P, Rius FX, Riu J. Carbon nanotube-based aptasensors for the rapid and ultrasensitive detection of bacteria. Methods 2013; 63:233-8. [PMID: 23872060 DOI: 10.1016/j.ymeth.2013.07.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 05/08/2013] [Accepted: 07/02/2013] [Indexed: 11/15/2022] Open
Abstract
In this paper we present a new generation of potentiometric biosensors based on carbon nanotubes (transducer layer of the biosensor) and aptamers (sensing layer of the biosensor) for the ultralow and selective detection of microorganisms. We show that with these aptasensors we were able to detect a few CFU of the target bacteria almost in real-time, both in buffered and in real samples.
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Affiliation(s)
- Gustavo A Zelada-Guillén
- Universitat Rovira i Virgili, Department of Analytical and Organic Chemistry, C/ Marcel·lí Domingo s/n, 43007 Tarragona, Catalonia, Spain
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Xiao P, Lv X, Wang S, Iqbal J, Qing H, Li Q, Deng Y. An aptamer-based trypsin reactor for on-line protein digestion with electrospray ionization tandem mass spectrometry. Anal Biochem 2013; 441:123-32. [PMID: 23831476 DOI: 10.1016/j.ab.2013.06.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 06/16/2013] [Accepted: 06/17/2013] [Indexed: 01/13/2023]
Abstract
An immobilized trypsin reactor that was based on aptamers has been developed and applied for the first time for proteomic digestion. Briefly, 25 single-stranded DNA aptamers that were specific for trypsin were obtained after SELEX (systematic evolution of ligands by exponential enrichment) selection. TApt.23 (no. 23 trypsin aptamer), which had the lowest dissociation constant (Kd) value (0.0123 μM), was amino-modified and subsequently grafted to an amino-modified silica surface with glutaraldehyde. The results indicated that 14.65±0.35 μg of trypsin could be immobilized on 10mg of TApt.23-silica when an optimized borate buffer was used. Subsequently, a trypsin reactor was fabricated by using a PEEKsil micro column. Compared with in-solution digestion, the aptamer-based trypsin reactor exhibited similar results for protein identification but used a much shorter digestion time (∼30 min). An on-line analysis platform, which included a trypsin reactor coupled to a high-performance liquid chromatography tandem mass spectrometry device, was built through a 6-port valve and achieved efficient protein digestion compared with in-solution and off-line methods. Compared with irreversible covalent enzyme immobilization, the aptamer-based carrier enables more rapid and convenient immobilized trypsin elution as well as re-immobilization of the enzyme. This superior reactor demonstrated that an aptamer could become a more widely used method for enzyme immobilization and other applications.
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Affiliation(s)
- Peng Xiao
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China; Division of Metrology in Chemistry, National Institute of Metrology, Beijing 100013, China
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Xiao P, Lv X, Man Y, Qing H, Li Q, Deng Y. Rapid and Efficient Proteolysis for Protein Analysis by an Aptamer-Based Immobilized Chymotrypsin Microreactor. ANAL LETT 2013. [DOI: 10.1080/00032719.2012.733902] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Li B, Ellington* AD. Electrochemical Techniques as Powerful Readout Methods for Aptamer-based Biosensors. DNA CONJUGATES AND SENSORS 2012. [DOI: 10.1039/9781849734936-00211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Aptamers are single-stranded nucleic acids that can be selected in vitro with special folding structures to bind to many different small-molecule, protein, and cellular targets. Over the past two decades, aptamers have become novel promising recognition elements for the fabrication of biosensors. These ‘aptasensors’ have several advantages over antibodies in that they are relatively easy to synthesise or modify in vitro, and can be appended with linkers and reporters for adaptation to various sensing strategies. In this chapter, we introduce the various electrochemical techniques that can be used as powerful readout methods for aptasensors, providing a brief introduction to aptamers and related electrochemical techniques, and then a detailed description of various branches within the field, including labelled strategies, unlabelled strategies, and enzyme-amplified strategies. For each type of approach, several basic and improved design principles will be addressed. It is hoped that, through this discussion, readers will get a sense of how several variables (aptamers, targets and redox reporters) are successfully combined with electrochemical techniques in order to produce a series of sensing platforms with high selectivity and sensitivity.
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Affiliation(s)
- Bingling Li
- Institute for Cellular and Molecular Biology Center for Systems and Synthetic Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712 USA
| | - Andrew D. Ellington*
- Institute for Cellular and Molecular Biology Center for Systems and Synthetic Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712 USA
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Waveguide-mode sensors as aptasensors. SENSORS 2012; 12:2136-51. [PMID: 22438756 PMCID: PMC3304158 DOI: 10.3390/s120202136] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 02/07/2012] [Accepted: 02/08/2012] [Indexed: 12/28/2022]
Abstract
Aptamers are artificial nucleic acid ligands that can be generated by in vitro selection through partition and amplification. Aptamers can be generated against a wide range of biomolecules through the formation of versatile stem-loop structures. Because aptamers are potential substitutes for antibodies and drugs, the development of an aptamer-based sensor (aptasensor) is mandatory for diagnosis. We previously reported that waveguide-mode sensors are useful in the analysis of a wide range of biomolecular interactions, including aptamers. The advantages of the waveguide-mode sensor that we developed include physical and chemical stability and that higher sensitivity can be achieved with ease by perforating the waveguide layer or using colored materials such as dyes or metal nanoparticles as labels. Herein, we provide an overview of the strategies and applications for aptamer-based analyses using waveguide-mode sensors.
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Properties of an LNA-modified ricin RNA aptamer. Biochem Biophys Res Commun 2012; 419:60-5. [PMID: 22326915 DOI: 10.1016/j.bbrc.2012.01.127] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 01/26/2012] [Indexed: 11/21/2022]
Abstract
'Locked nucleic acids' (LNAs) are sugar modified nucleic acids containing the 2'-O-4'C-methylene-β-D-ribofuranoses. The substitution of RNAs with LNAs leads to an enhanced thermostability. Aptamers are nucleic acids, which are selected for specific target binding from a large library pool by the 'SELEX' method. Introduction of modified nucleic acids into aptamers can improve their stability. The stem region of a ricin A chain RNA aptamer was substituted by locked nucleic acids. Different constructs of the LNA-substituted aptamers were examined for their thermostability, binding activity, folding and RNase sensitivity as compared to the natural RNA counterpart. The LNA-modified aptamers were active in target binding, while the loop regions and the adjacent stem nucleotides remained unsubstituted. The thermostability and RNase resistance of LNA substituted aptamers were enhanced as compared to the native RNA aptamer. This study supports the approach to substitute the aptamer stem region by LNAs and to leave the loop region unmodified, which is responsible for ligand binding. Thus, LNAs possess an encouraging potential for the development of new stabilized nucleic acids and will promote future diagnostic and therapeutic applications.
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Zelada-Guillén GA, Sebastián-Avila JL, Blondeau P, Riu J, Rius FX. Label-free detection of Staphylococcus aureus in skin using real-time potentiometric biosensors based on carbon nanotubes and aptamers. Biosens Bioelectron 2011; 31:226-32. [PMID: 22154169 DOI: 10.1016/j.bios.2011.10.021] [Citation(s) in RCA: 150] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2011] [Revised: 10/10/2011] [Accepted: 10/13/2011] [Indexed: 11/16/2022]
Abstract
In this paper we report the first biosensor that is able to detect Staphylococcus aureus in real-time. A network of single-walled carbon nanotubes (SWCNTs) acts as an ion-to-electron potentiometric transducer and anti-S. aureus aptamers are the recognition element. Carbon nanotubes were functionalized with aptamers using two different approaches: (1) non-covalent adsorption of drop-casted pyrenil-modified aptamers onto the external walls of the SWCNTs; and (2) covalent bond formation between amine-modified aptamers and carboxylic groups previously introduced by oxidation at the ends of the SWCNTs. Both of these approaches yielded functional biosensors but there were large differences in the minimum detectable bacteria concentration and sensitivity values. With covalent functionalization, the minimum concentration detected was 8×10(2)colony-forming units (CFU)/mL and the sensitivity was 0.36 mV/Decade. With the non-covalent approach, the sensitivity was higher (1.52 mV/Decade) but the minimum concentration detected was greatly affected (10(7) CFU/mL). In both cases, potential as a function of Decade of bacteria concentration was linear. Functional biosensors were used to test real samples from freshly excised pig skin, contaminated with the target microorganism, as a surrogate for human skin.
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Affiliation(s)
- Gustavo A Zelada-Guillén
- Department of Analytical and Organic Chemistry, Universitat Rovira i Virgili, Campus Sescelades, C/Marcel·lí Domingo s/n, 43007 Tarragona, Spain.
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Rodrigues Ribeiro Teles FS, Pires de Távora Tavira LA, Pina da Fonseca LJ. Biosensors as rapid diagnostic tests for tropical diseases. Crit Rev Clin Lab Sci 2011; 47:139-69. [PMID: 21155631 DOI: 10.3109/10408363.2010.518405] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Effective diagnosis of infectious pathogens is essential for disease identification and subsequent adequate treatment, to prevent drug resistance and to adopt suitable public health interventions for the prevention and control of epidemic outbreaks. Particular situations under which medical diagnostics operate in tropical environments make the use of new easy-to-use diagnostic tools the preferred (or even unique) option. These diagnostic tests and devices, usually based on biosensing methods, are being increasingly exploited as promising alternatives to classical, "heavy" lab instrumentation for clinical diagnosis, allowing simple, inexpensive and point-of-care testing. However, in many developing countries the lack of accessibility and affordability for many commercial diagnostic tests remains a major cause of high disease burden in such regions. We present a comprehensive overview about the problems of conventional medical diagnosis of infectious pathologies in tropical regions, while pointing out new methods and analytical tools for in-the-field and decentralized diagnosis of current major infectious tropical diseases. The review includes not only biosensor-based rapid diagnostic tests approved by regulatory entities and already commercialized, but also those at the early stages of research.
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Electrochemical detection of thrombin based on aptamer and ferrocenylhexanethiol loaded silica nanocapsules. Biosens Bioelectron 2011; 26:3536-41. [PMID: 21376563 DOI: 10.1016/j.bios.2011.01.041] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Revised: 01/19/2011] [Accepted: 01/31/2011] [Indexed: 11/23/2022]
Abstract
A sensitive and specific electrochemical assay for detection of thrombin based on aptamer and ferrocenylhexanethiol loaded silica nanocapsules (FcSH/SiNCs) amplification is described. In the protocol, a double aptamer sandwich structure was formed in the presence of thrombin, in which an aptamer-labeled FcSH/SiNCs for electrochemical detection, and a streptavidin-coated magnetic bead immobilized aptamer for rapid and specific separation of target protein. After separated from the sample mixture under a magnetic field, the sandwich complex was treated with NaOH to release the loaded ferrocenylhexanethiol (FcSH) from the silica nanocapsules (SiNCs). Differential pulse voltammetry (DPV) was employed to detect the released FcSH, which was related to the concentration of the thrombin. The method took advantage of sandwich binding of two affinity aptamers for increased specificity, high payload of FcSH in SiNCs for signal amplification, magnetic beads for fast magnetic separation. The peak current of released FcSH had a good linear relationship with the thrombin concentration in the range of 0.1-5 nmol/L, and the detection limit of thrombin in the method was 0.06 nmol/L. The detection was also specific for thrombin without being affected by other proteins, such as immunoglobulin G, bovine serum albumin, lysozyme and human serum albumin. The method has been used to detect thrombin in human serum albumin with minimum background interference.
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Nguyen TH, Steinbock LJ, Butt HJ, Helm M, Berger R. Measuring single small molecule binding via rupture forces of a split aptamer. J Am Chem Soc 2011; 133:2025-7. [PMID: 21287983 DOI: 10.1021/ja1092002] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The rupture force of a split (bipartite) aptamer that forms binding pockets for adenosine monophosphate (AMP) was measured by atomic force spectroscopy. Changes in the rupture force were observed in the presence of AMP, while this effect was absent when mutant aptamers or inosine were used. Thus, changes in the rupture force were a direct consequence of specific binding of AMP to the split aptamer. The split aptamer concept allowed the detection of nonlabeled AMP and enabled us to determine the dissociation constant on a single-molecule level.
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Radi AE. Electrochemical Aptamer-Based Biosensors: Recent Advances and Perspectives. INTERNATIONAL JOURNAL OF ELECTROCHEMISTRY 2011; 2011:1-17. [DOI: 10.4061/2011/863196] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
Abstract
This paper reviews the advancements of a wide range of electrochemical aptamer-based biosensors, electrochemical aptasensors, for target analytes monitoring. Methods for immobilizing aptamers onto an electrode surface are discussed. Aptasensors are presented according to their detection strategies. Many of these are simply electrochemical, aptamer-based equivalents of traditional immunochemical approaches, sandwich and competition assays employing electroactive signaling moieties. Others, exploiting the unusual physical properties of aptamers, are signal-on (positive readout signal) and signal-off (negative readout signal) aptasensors based on target binding-induced conformational change of aptamers. Aptamer label-free devices are also discussed.
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Affiliation(s)
- Abd-Elgawad Radi
- Department of Chemistry, Faculty of Science, Mansoura University, Dumyat 34517, Egypt
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45
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Pagba CV, Lane SM, Wachsmann-Hogiu S. Conformational changes in quadruplex oligonucleotide structures probed by Raman spectroscopy. BIOMEDICAL OPTICS EXPRESS 2010; 2:207-17. [PMID: 21339867 PMCID: PMC3038437 DOI: 10.1364/boe.2.000207] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 12/07/2010] [Accepted: 12/18/2010] [Indexed: 05/02/2023]
Abstract
Quadruplex structures are higher order structures formed by guanine-rich oligonucleotides. In the present study, temperature-induced conformational changes in the quadruplex structures of aptamers and other guanine-rich oligonucleotides are probed by Raman spectroscopy. In particular, dramatic changes in the fingerprint region are observed in the spectra of thrombin binding aptamer at higher temperatures. These changes are accompanied by a decrease in the intensity of the 1480 cm(-1) peak (attributed to C8 = N7-H2), which is diagnostic of the quadruplex structure. We also show that these changes can be reversed (to a certain extent) by addition of K(+) ions.
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Affiliation(s)
- Cynthia V. Pagba
- Center for Biophotonics Science and Technology, University of California Davis, 2700 Stockton Blvd., Suite 1400, Sacramento, CA 95817
| | - Stephen M. Lane
- Center for Biophotonics Science and Technology, University of California Davis, 2700 Stockton Blvd., Suite 1400, Sacramento, CA 95817
- Department of Neurological Surgery, University of California Davis, 4860 Y Street, Sacramento, CA 95817
| | - Sebastian Wachsmann-Hogiu
- Center for Biophotonics Science and Technology, University of California Davis, 2700 Stockton Blvd., Suite 1400, Sacramento, CA 95817
- Department of Pathology and Internal Medicine, University of California Davis, 4400 V Street, Sacramento, CA 95817
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Chen YY, Tseng CW, Chang HY, Hung YL, Huang CC. Gold nanoparticle-based colorimetric assays for coagulation-related proteins and their inhibition reactions. Biosens Bioelectron 2010; 26:3160-6. [PMID: 21215609 DOI: 10.1016/j.bios.2010.12.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 12/04/2010] [Accepted: 12/09/2010] [Indexed: 01/14/2023]
Abstract
In this paper, we describe two simple, label-free, homogenous assays using gold nanoparticles (Au NPs)-one to detect coagulation-related proteins and the other to screen inhibition reactions. The first nanosensor functions on the basis of the fact that thrombin catalyzes fibrinogen to form long-chain fibrins, which then induce aggregation of Au NPs. We applied this sensor to study the interactions of thrombin, inhibitors, cofactors, and antidotes. We further used thrombin-conjugated Au NPs (Thr-Au NPs) to analyze the levels of fibrinogen in plasma samples via fibrinogen-induced aggregation of Thr-Au NPs. The limit of detection (LOD; S/N=3) of this sensor for fibrinogen in plasma was 10nM. The Thr-Au NP probe provided quantitative results for fibrinogen in plasma samples that correlated (R(2)=0.97) with those obtained using a clinical von Clauss clotting rate assay. In addition, the Thr-Au NP-based sensor could be used to monitor thrombin concentrations in plasma samples under physiological conditions. Compared with conventional assays, these label-free assays offer several advantages, such as rapid and simple readout by the naked eye or by UV-vis absorption spectroscopy.
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Affiliation(s)
- Yi-You Chen
- Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
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47
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Impedimetric aptasensor for tobramycin detection in human serum. Biosens Bioelectron 2010; 26:2354-60. [PMID: 21051217 DOI: 10.1016/j.bios.2010.10.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 09/15/2010] [Accepted: 10/06/2010] [Indexed: 11/24/2022]
Abstract
An RNA aptamer is proposed as a recognition element for the detection of tobramycin in human serum. A displacement assay was developed using faradaic-electrochemical impedance spectroscopy (F-EIS) as a detection technique. Two modified aptamers, a partially (ATA) and a fully O-methylated aptamer (FATA) were evaluated and compared. The affinity constant, K(D), for both aptamers was estimated by F-EIS resulting virtually identical within the experimental error. The selectivity towards other aminoglycosides was also studied. The analytical characteristics were evaluated in aqueous solution using both aptamers and FATA was selected for human serum experiments. Using a 1:0.5 dilution of the serum, a linear range between 3 μM and 72.1 μM was obtained, which included the therapeutic range of the antibiotic.
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Li B, Dong S, Wang E. Homogeneous analysis: label-free and substrate-free aptasensors. Chem Asian J 2010; 5:1262-72. [PMID: 20408164 DOI: 10.1002/asia.200900660] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this Focus Review, we introduce a kind of "label-free" and "substrate-free" (LFSF) aptasensor that carries out the whole sensing process in a homogeneous solution. This means that commonly used covalent label; separation, and immobilization steps in biosensors are successfully avoided, which simplifies the sensing operations to the greatest degree. After brief description about the advantages of aptamers and "LFSF" aptasensors, the main content of the review is divided into fluorescent aptasenors, calorimetric aptasensors, and hemin-aptamer-DNAzyme "LFSF" aptasensors, which are three most widely developed sensing systems in this field. It is hoped that this review can provide an overall scene about how aptamers function as ideal recognition elements in smart analysis.
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Affiliation(s)
- Bingling Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022 P. R. China
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Zhang J, Zhang B, Wu Y, Jia S, Fan T, Zhang Z, Zhang C. Fast determination of the tetracyclines in milk samples by the aptamer biosensor. Analyst 2010; 135:2706-10. [PMID: 20714519 DOI: 10.1039/c0an00237b] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel aptamer biosensor for fast tetracyclines determination was established and illustrated in this paper. The tetracyclines aptamer as a specific affinity molecule was immobilized on the surface of the glassy carbon (GC) electrodes. It can specifically bind tetracyclines quickly in milk and other samples without sample treatment. Subsequently, the electrochemical signals are produced and measured accurately. The linear relationship between the currents and the tetracyclines concentration is 0.1-100 ng ml(-1). The sensitivity limit of the device is 1 ng ml(-1). The detection time is 5 min.
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Affiliation(s)
- Juankun Zhang
- Tianjin Key Lab of Industrial Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P. R. China.
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50
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Nishizawa S, Sato Y, Xu Z, Morita K, Li M, Teramae N. Abasic site-based DNA aptamers for analytical applications. Supramol Chem 2010. [DOI: 10.1080/10610278.2010.484865] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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