1
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Mili M, Bachu V, Kuri PR, Singh NK, Goswami P. Improving synthesis and binding affinities of nucleic acid aptamers and their therapeutics and diagnostic applications. Biophys Chem 2024; 309:107218. [PMID: 38547671 DOI: 10.1016/j.bpc.2024.107218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/21/2024] [Accepted: 03/17/2024] [Indexed: 04/22/2024]
Abstract
Nucleic acid aptamers have captivated the attention of analytical and medicinal scientists globally due to their several advantages as recognition molecules over conventional antibodies because of their small size, simple and inexpensive synthesis, broad target range, and high stability in varied environmental conditions. These recognition molecules can be chemically modified to make them resistant to nuclease action in blood serum, reduce rapid renel clearance, improve the target affinity and selectivity, and make them amenable to chemically conjugate with a support system that facilitates their selective applications. This review focuses on the development of efficient aptamer candidates and their application in clinical diagnosis and therapeutic applications. Significant advances have been made in aptamer-based diagnosis of infectious and non-infectious diseases. Collaterally, the progress made in therapeutic applications of aptamers is encouraging, as evident from their use in diagnosing cancer, neurodegenerative diseases, microbial infection, and in imaging. This review also updates the progress on clinical trials of many aptamer-based products of commercial interests. The key development and critical issues on the subject have been summarized in the concluding remarks.
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Affiliation(s)
- Malaya Mili
- Department of Biosciences and Bioengineering, IIT Guwahati, 781039, Assam, India
| | - Vinay Bachu
- Department of Biosciences and Bioengineering, IIT Guwahati, 781039, Assam, India
| | - Pooja Rani Kuri
- Department of Biosciences and Bioengineering, IIT Guwahati, 781039, Assam, India
| | | | - Pranab Goswami
- Department of Biosciences and Bioengineering, IIT Guwahati, 781039, Assam, India.
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2
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Farka Z, Brandmeier JC, Mickert MJ, Pastucha M, Lacina K, Skládal P, Soukka T, Gorris HH. Nanoparticle-Based Bioaffinity Assays: From the Research Laboratory to the Market. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2307653. [PMID: 38039956 DOI: 10.1002/adma.202307653] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/16/2023] [Indexed: 12/03/2023]
Abstract
Advances in the development of new biorecognition elements, nanoparticle-based labels as well as instrumentation have inspired the design of new bioaffinity assays. This review critically discusses the potential of nanoparticles to replace current enzymatic or molecular labels in immunoassays and other bioaffinity assays. Successful implementations of nanoparticles in commercial assays and the need for rapid tests incorporating nanoparticles in different roles such as capture support, signal generation elements, and signal amplification systems are highlighted. The limited number of nanoparticles applied in current commercial assays can be explained by challenges associated with the analysis of real samples (e.g., blood, urine, or nasal swabs) that are difficult to resolve, particularly if the same performance can be achieved more easily by conventional labels. Lateral flow assays that are based on the visual detection of the red-colored line formed by colloidal gold are a notable exception, exemplified by SARS-CoV-2 rapid antigen tests that have moved from initial laboratory testing to widespread market adaption in less than two years.
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Affiliation(s)
- Zdeněk Farka
- Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Julian C Brandmeier
- Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, Universitätsstr. 31, 93053, Regensburg, Germany
| | | | - Matěj Pastucha
- Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
- TestLine Clinical Diagnostics, Křižíkova 188, Brno, 612 00, Czech Republic
| | - Karel Lacina
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Petr Skládal
- Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Tero Soukka
- Department of Life Technologies/Biotechnology, University of Turku, Kiinamyllynkatu 10, Turku, 20520, Finland
| | - Hans H Gorris
- Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
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3
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Teng X, Wang Y, You L, Wei L, Zhang C, Du Y. Screening a DNA Aptamer Specifically Targeting Integrin β3 and Partially Inhibiting Tumor Cell Migration. Anal Chem 2023; 95:12406-12418. [PMID: 37555842 PMCID: PMC10448441 DOI: 10.1021/acs.analchem.3c01995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/26/2023] [Indexed: 08/10/2023]
Abstract
Due to its key roles in malignant tumor progression and reprograming of the tumor microenvironment, integrin β3 has attracted great attention as a new target for tumor therapy. However, the structure-function relationship of integrins β3 remains incompletely understood, leading to the shortage of specific and effective targeting probes. This work uses a purified extracellular domain of integrin β3 and integrin β3-positive cells to screen aptamers, specifically targeting integrin β3 in the native conformation on live cells through the SELEX approach. Following meticulous truncation and characterization of the initial aptamer candidates, the optimized aptamer S10yh2 was produced, exhibiting a low equilibrium dissociation constant (Kd) in the nanomolar range. S10yh2 displays specific recognition of cancer cells with varying levels of integrin β3 expression and demonstrates favorable stability in serum. Subsequent analysis of docking sites revealed that S10yh2 binds to the seven amino acid residues located in the core region of integrin β3. The S10yh2 aptamer can downregulate the level of integrin heterodimer αvβ3 on integrin β3 overexpressed cancer cells and partially inhibit cell migration behavior. In summary, S10yh2 is a promising probe with a small size, simple synthesis, good stability, high binding affinity, and selectivity. It therefore holds great potential for investigating the structure-function relationship of integrins.
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Affiliation(s)
- Xiaoyan Teng
- Department
of Laboratory Medicine, Shanghai Jiao Tong
University Affiliated Sixth People’s Hospital, Shanghai 200233, China
| | - Yu Wang
- State
Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute,
Department of Oncology, Institute of Molecular Medicine, Renji Hospital,
School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Liuxia You
- Department
of Clinical Laboratory, The Second Affiliated
Hospital of Fujian Medical University, Quanzhou, Fujian 362000, China
| | - Lirong Wei
- Department
of Laboratory Medicine, Shanghai Jiao Tong
University Affiliated Sixth People’s Hospital, Shanghai 200233, China
| | - Chao Zhang
- State
Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute,
Department of Oncology, Institute of Molecular Medicine, Renji Hospital,
School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yuzhen Du
- Department
of Laboratory Medicine, Shanghai Jiao Tong
University Affiliated Sixth People’s Hospital, Shanghai 200233, China
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4
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Highly Specific Detection of Oxytocin in Saliva. Int J Mol Sci 2023; 24:ijms24054832. [PMID: 36902261 PMCID: PMC10003004 DOI: 10.3390/ijms24054832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Oxytocin is a peptide neurophysin hormone made up of nine amino acids and is used in induction of one in four births worldwide (more than 13 percent in the United States). Herein, we have developed an antibody alternative aptamer-based electrochemical assay for real-time and point-of-care detection of oxytocin in non-invasive saliva samples. This assay approach is rapid, highly sensitive, specific, and cost-effective. Our aptamer-based electrochemical assay can detect as little as 1 pg/mL of oxytocin in less than 2 min in commercially available pooled saliva samples. Additionally, we did not observe any false positive or false negative signals. This electrochemical assay has the potential to be utilized as a point-of-care monitor for rapid and real-time oxytocin detection in various biological samples such as saliva, blood, and hair extracts.
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5
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Torrini F, Scarano S, Palladino P, Minunni M. Advances and perspectives in the analytical technology for small peptide hormones analysis: A glimpse to gonadorelin. J Pharm Biomed Anal 2023; 228:115312. [PMID: 36858006 DOI: 10.1016/j.jpba.2023.115312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/07/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023]
Abstract
In the last twenty years, we have witnessed an important evolution of bioanalytical approaches moving from conventional lab bench instrumentation to simpler, easy-to-use techniques to deliver analytical responses on-site, with reduced analysis times and costs. In this frame, affinity reagents production has also jointly advanced from natural receptors to biomimetic, abiotic receptors, animal-free produced. Among biomimetic ones, aptamers, and molecular imprinted polymers (MIPs) play a leading role. Herein, our motivation is to provide insights into the evolution of conventional and innovative analytical approaches based on chromatography, immunochemistry, and affinity sensing referred to as peptide hormones. Indeed, the analysis of peptide hormones represents a current challenge for biomedical, pharmaceutical, and anti-doping analysis. Specifically, as a paradigmatic example, we report the case of gonadorelin, a neuropeptide that in recent years has drawn a lot of attention as a therapeutic drug misused in doping practices during sports competitions.
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Affiliation(s)
- Francesca Torrini
- Department of Chemistry 'Ugo Schiff', University of Florence, 50019 Sesto Fiorentino, FI, Italy.
| | - Simona Scarano
- Department of Chemistry 'Ugo Schiff', University of Florence, 50019 Sesto Fiorentino, FI, Italy
| | - Pasquale Palladino
- Department of Chemistry 'Ugo Schiff', University of Florence, 50019 Sesto Fiorentino, FI, Italy
| | - Maria Minunni
- Department of Chemistry 'Ugo Schiff', University of Florence, 50019 Sesto Fiorentino, FI, Italy.
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6
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Chen Z, Luo H, Gubu A, Yu S, Zhang H, Dai H, Zhang Y, Zhang B, Ma Y, Lu A, Zhang G. Chemically modified aptamers for improving binding affinity to the target proteins via enhanced non-covalent bonding. Front Cell Dev Biol 2023; 11:1091809. [PMID: 36910146 PMCID: PMC9996316 DOI: 10.3389/fcell.2023.1091809] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
Nucleic acid aptamers are ssDNA or ssRNA fragments that specifically recognize targets. However, the pharmacodynamic properties of natural aptamers consisting of 4 naturally occurring nucleosides (A, G, C, T/U) are generally restricted for inferior binding affinity than the cognate antibodies. The development of high-affinity modification strategies has attracted extensive attention in aptamer applications. Chemically modified aptamers with stable three-dimensional shapes can tightly interact with the target proteins via enhanced non-covalent bonding, possibly resulting in hundreds of affinity enhancements. This review overviewed high-affinity modification strategies used in aptamers, including nucleobase modifications, fluorine modifications (2'-fluoro nucleic acid, 2'-fluoro arabino nucleic acid, 2',2'-difluoro nucleic acid), structural alteration modifications (locked nucleic acid, unlocked nucleic acid), phosphate modifications (phosphorothioates, phosphorodithioates), and extended alphabets. The review emphasized how these high-affinity modifications function in effect as the interactions with target proteins, thereby refining the pharmacodynamic properties of aptamers.
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Affiliation(s)
- Zefeng Chen
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Hang Luo
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Amu Gubu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Aptacure Therapeutics Limited, Kowloon, Hong Kong SAR, China
| | - Sifan Yu
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Huarui Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Hong Dai
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Yihao Zhang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Baoting Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Yuan Ma
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen, Hong Kong SAR, China
| | - Aiping Lu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen, Hong Kong SAR, China
| | - Ge Zhang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen, Hong Kong SAR, China
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7
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Chen S, Liu TL, Dong Y, Li J. A Wireless, Regeneratable Cocaine Sensing Scheme Enabled by Allosteric Regulation of pH Sensitive Aptamers. ACS NANO 2022; 16:20922-20936. [PMID: 36468646 DOI: 10.1021/acsnano.2c08511] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
A key challenge for achieving continuous biosensing with existing technologies is the poor reusability of the biorecognition interface due to the difficulty in the dissociation of analytes from the bioreceptors upon surface saturation. In this work, we introduce a regeneratable biosensing scheme enabled by allosteric regulation of a re-engineered pH sensitive anti-cocaine aptamer. The aptamer can regain its affinity with target analytes due to proton-promoted duplex-to-triplex transition in DNA configuration followed by the release of adsorbed analytes. A Pd/PdHx electrode placed next to the sensor can enable the pH regulation of the local chemical environment via electrochemical reactions. Demonstration of a "flower-shaped", stretchable, and inductively coupled electronic system with sensing and energy harvesting capabilities provides a promising route to designing wireless devices in biointegrated forms. These advances have the potential for future development of electronic sensing platforms with on-chip regeneration capability for continuous, quantitative, and real-time monitoring of chemical and biological markers.
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Affiliation(s)
- Shulin Chen
- Department of Materials Science and Engineering, The Ohio State University, Columbus, Ohio43210, United States
| | - Tzu-Li Liu
- Department of Materials Science and Engineering, The Ohio State University, Columbus, Ohio43210, United States
| | - Yan Dong
- Department of Materials Science and Engineering, The Ohio State University, Columbus, Ohio43210, United States
| | - Jinghua Li
- Department of Materials Science and Engineering, The Ohio State University, Columbus, Ohio43210, United States
- Chronic Brain Injury Program, The Ohio State University, Columbus, Ohio43210, United States
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8
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Huang Y, Pei X, Du S, Li Z, Gu X, Sun W, Niu X. Target-induced ratiometric electrochemical aptasensor for highly sensitive detection of thrombin based on AuNPs-MXene. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107774] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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9
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Şahin S, Üstündağ Z, Caglayan MO. Spectroscopic ellipsometry-based aptasensor platform for bisphenol a detection. Talanta 2022. [DOI: 10.1016/j.talanta.2022.123885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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A sequential toggle cell-SELEX DNA aptamer for targeting Staphylococcus aureus, Streptococcus agalactiae, and Escherichia coli bacteria. J Genet Eng Biotechnol 2022; 20:95. [PMID: 35776386 PMCID: PMC9249959 DOI: 10.1186/s43141-022-00374-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/02/2022] [Indexed: 12/26/2022]
Abstract
BACKGROUND Mastitis is an inflammation of the mammary glands caused by a microbial infection. The common bacteria causing this infection in dairy farms are Staphylococcus aureus, Streptococcus agalactiae, and Escherichia coli. The aptamer is a new biosensor platform for detecting pathogens; however, its use for simultaneous detection of S. aureus, S. agalactiae, and E. coli bacteria has not been reported. This study's objective is to isolate and characterize polyclonal DNA aptamer with broad reactivity to the mastitis bacteria S. aureus, S. agalactiae, and E. coli using a sequential toggle cell-SELEX. METHODS AND RESULTS The DNA aptamer pool from SELEX 15 was inserted into the pGEM-T easy plasmid. Furthermore, the transformant clones were selected by PCR colony, plasmid isolation, and sequencing. Six DNA aptamers, consisting of S15K3, S15K4, S15K6, S15K13, S15K15, and S15K20 with a constant region and the right size of 81 bp were derived from the sequencing analysis. The secondary structure of the DNA was predicted using Mfold software. The DNA was analyzed with binding characteristics, including binding capacity and affinity (Kd), using qPCR. The results indicated aptamer S15K15 has the highest binding ability into S. agalactiae, while S15K13 performed binding capacity most to E. coli EPEC 4, and S15K3 has the highest capacity of binding to S. aureus BPA-12. CONCLUSION Aptamer S15K3 has the best binding characteristics on all three bacterial targets.
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11
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A Simple and Selective Colorimetric Aptasensor for Detection of Toxins Microcystin-LR in Fish Tissue Using a Truncated Aptamer. FOOD ANAL METHOD 2022. [DOI: 10.1007/s12161-022-02283-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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12
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Tatarko M, Spagnolo S, Oravczová V, Süle J, Hun M, Hucker A, Hianik T. Changes of Viscoelastic Properties of Aptamer-Based Sensing Layers Following Interaction with Listeria innocua. SENSORS (BASEL, SWITZERLAND) 2021; 21:5585. [PMID: 34451028 PMCID: PMC8402281 DOI: 10.3390/s21165585] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/13/2021] [Accepted: 08/18/2021] [Indexed: 02/06/2023]
Abstract
A multiharmonic quartz crystal microbalance (QCM) has been applied to study the viscoelastic properties of the aptamer-based sensing layers at the surface of a QCM transducer covered by neutravidin following interaction with bacteria Listeria innocua. Addition of bacteria in the concentration range 5 × 103-106 CFU/mL resulted in a decrease of resonant frequency and in an increase of dissipation. The frequency decrease has been lower than one would expect considering the dimension of the bacteria. This can be caused by lower penetration depth of the acoustics wave (approximately 120 nm) in comparison with the thickness of the bacterial layer (approximately 500 nm). Addition of E. coli at the surface of neutravidin as well as aptamer layers did not result in significant changes in frequency and dissipation. Using the Kelvin-Voight model the analysis of the viscoelastic properties of the sensing layers was performed and several parameters such as penetration depth, Γ, viscosity coefficient, η, and shear modulus, μ, were determined following various modifications of QCM transducer. The penetration depth decreased following adsorption of the neutravidin layer, which is evidence of the formation of a rigid protein structure. This value did not change significantly following adsorption of aptamers and Listeria innocua. Viscosity coefficient was higher for the neutravidin layer in comparison with the naked QCM transducer in a buffer. However, a further increase of viscosity coefficient took place following attachment of aptamers suggesting their softer structure. The interaction of Listeria innocua with the aptamer layer resulted in slight decrease of viscosity coefficient. The shearing modulus increased for the neutravidin layer and decreased following aptamer adsorption, while a slight increase of µ was observed after the addition of Listeria innocua.
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Affiliation(s)
- Marek Tatarko
- Department of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina F1, 842 48 Bratislava, Slovakia; (M.T.); (S.S.); (V.O.)
| | - Sandro Spagnolo
- Department of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina F1, 842 48 Bratislava, Slovakia; (M.T.); (S.S.); (V.O.)
| | - Veronika Oravczová
- Department of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina F1, 842 48 Bratislava, Slovakia; (M.T.); (S.S.); (V.O.)
| | - Judit Süle
- Hungarian Dairy Research Institute Ltd., 9200 Mosonmagyaróvár, Hungary; (J.S.); (M.H.); (A.H.)
| | - Milan Hun
- Hungarian Dairy Research Institute Ltd., 9200 Mosonmagyaróvár, Hungary; (J.S.); (M.H.); (A.H.)
| | - Attila Hucker
- Hungarian Dairy Research Institute Ltd., 9200 Mosonmagyaróvár, Hungary; (J.S.); (M.H.); (A.H.)
| | - Tibor Hianik
- Department of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina F1, 842 48 Bratislava, Slovakia; (M.T.); (S.S.); (V.O.)
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13
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Li L, Wan J, Wen X, Guo Q, Jiang H, Wang J, Ren Y, Wang K. Identification of a New DNA Aptamer by Tissue-SELEX for Cancer Recognition and Imaging. Anal Chem 2021; 93:7369-7377. [PMID: 33960774 DOI: 10.1021/acs.analchem.1c01445] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cancer has become one of the most common diseases with high mortality in humans. Early and accurate diagnosis of cancer is of great significance to enhance the survival rate of patients. Therefore, effective molecular ligands capable of selectively recognizing cancer are urgently needed. In this work, we identified a new DNA aptamer named SW1 by tissue-based systematic evolution of ligands by exponential enrichment (tissue-SELEX), in which cancerous liver tissue sections were used as the positive control and adjacent normal liver tissue sections were used as the negative control. Taking immobilized liver cancer SMMC-7721 cells as the research object, aptamer SW1 exhibited excellent affinity with a Kd value of 123.62 ± 17.53 nM, and its binding target was preliminarily determined as a non-nucleic acid substance in the nucleus. Moreover, tissue imaging results showed that SW1 explicitly recognized cancerous liver tissues with a high detection rate of 72.7% but displayed a low detection rate to adjacent normal tissues. In addition to liver cancer cells and tissues, aptamer SW1 has been demonstrated to recognize various other types of cancer cells and tissues. Furthermore, SW1-A, an optimized aptamer of SW1, maintained its excellent affinity toward liver cancer cells and tissues. Collectively, these results indicate that SW1 possesses great potential for use as an effective molecular probe for clinical diagnosis of cancer.
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Affiliation(s)
- Lie Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Jun Wan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Xiaohong Wen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Qiuping Guo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Huishan Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Jie Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Yazhou Ren
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
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14
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Saad M, Faucher SP. Aptamers and Aptamer-Coupled Biosensors to Detect Water-Borne Pathogens. Front Microbiol 2021; 12:643797. [PMID: 33679681 PMCID: PMC7933031 DOI: 10.3389/fmicb.2021.643797] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
Aptamers can serve as efficient bioreceptors for the development of biosensing detection platforms. Aptamers are short DNA or RNA oligonucleotides that fold into specific structures, which enable them to selectively bind to target analytes. The method used to identify aptamers is Systematic Evolution of Ligands through Exponential Enrichment (SELEX). Target properties can have an impact on aptamer efficiencies. Therefore, characteristics of water-borne microbial targets must be carefully considered during SELEX for optimal aptamer development. Several aptamers have been described for key water-borne pathogens. Here, we provide an exhaustive overview of these aptamers and discuss important microbial aspects to consider when developing such aptamers.
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Affiliation(s)
- Mariam Saad
- Department of Natural Resources, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Université de Montréal, Faculté de Médecine Vétérinaire, Saint-Hyacinthe, QC, Canada
| | - Sebastien P. Faucher
- Department of Natural Resources, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Université de Montréal, Faculté de Médecine Vétérinaire, Saint-Hyacinthe, QC, Canada
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15
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Pu Y, Xiang J, Zhang X, Deng Y, Liu H, Tan W. CD36 as a Molecular Target of Functional DNA Aptamer NAFLD01 Selected against NAFLD Cells. Anal Chem 2021; 93:3951-3958. [PMID: 33596054 DOI: 10.1021/acs.analchem.0c04866] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The aim of this study was to identify the target of nonalcoholic fatty liver disease (NAFLD) cell-specific aptamer NAFLD01 and investigate its effect on lipid metabolism in vitro. A distinct membrane protein of NAFLD cells pulled down by NAFLD01 was analyzed by mass spectrometry to determine target candidates, and affinity of NAFLD01 to target-protein-silent NAFLD cells was detected to validate it. Knockdown of CD36 abolished the binding of NAFLD01, and its binding affinity was associated with membrane-bound CD36. NAFLD01 affinity for NAFLD cells was proportional to the CD36 expression level. Moreover, compared to random sequences, NAFLD01 showed better recognition for both mouse and human tissue sections of NAFLD. Importantly, NAFLD01 could ameliorate liver fat deposition through interaction with CD36 in vitro. Therefore, aptamer NAFLD01 could act as an effective and safe targeted drug for NAFLD. NAFLD01 is the first reported CD36-specific aptamer. This aptamer can improve hepatocyte steatosis via specifically binding to CD36. This study provides a molecular tool to investigate the mechanism of CD36 in NAFLD.
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Affiliation(s)
- Ying Pu
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Juan Xiang
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xinxu Zhang
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yuanyuan Deng
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Huixia Liu
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.,Cancer Hospital of the University of Chinese Academy of Sciences, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.,Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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16
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Selection and Characterization of Cell Surface Specific Aptamer and Development of Fluorescence Assay for Detection of Shigella flexneri from Water Samples. J Fluoresc 2021; 31:685-693. [PMID: 33582948 DOI: 10.1007/s10895-021-02691-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/25/2021] [Indexed: 10/22/2022]
Abstract
The present study demonstrates, development of ssDNA aptamers against whole cell of S. flexneri employing a whole bacterium-based Systemic Evolution of Ligands by Exponential Enrichment (SELEX). After ten rounds of SELEX, cell surface specific aptamer pool was cloned, sequenced and divided based on sequence similarities and secondary structure. Binding affinity of FITC labelled aptamer from different group were carried out by flow cytometry analysis. The dissociation constant (Kd) values for specific and higher binder were evaluated to range from 144 to 329 nM. Six high binding aptamers with lower dissociation constant was chosen for selectivity study. Aptamer SHI 23, SHI 37 and SHI 42 showed higher selectivity towards S. flexneri in comparison with other related bacteria. Further applicability of selected aptamer was proven by fluorescence assay for convenience detection of target cell from spiked water sample and natural contaminated water samples. Altogether, aptamer generated in this study can be alternative DNA ligands for detection of S. flexneri compared to available ligands.
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17
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Zhu Q, Liu L, Wang R, Zhou X. A split aptamer (SPA)-based sandwich-type biosensor for facile and rapid detection of streptomycin. JOURNAL OF HAZARDOUS MATERIALS 2021; 403:123941. [PMID: 33264988 DOI: 10.1016/j.jhazmat.2020.123941] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 06/12/2023]
Abstract
As antibiotic pollution is gaining prominence as a global issue, the demand for detection of streptomycin (STR), which is a widely used antibiotic with potential human health and ecological risks, has attracted increasing attention. Aptamer-based biosensors have been developed for the detection of STR in buffers and samples, however, the non-target signals due to the conformational variation of free aptamers possibly affect their sensitivity and stability. In this study, by introducing the STR-specific split aptamer (SPA), a sensitive evanescent wave fluorescent (EWF) biosensor is developed for the sandwich-type based detection of STR. The standard calibration curve obtained for STR has a detection limit of 33 nM with a linear range of 60-526 nM. This biosensor exhibited good selectivity, reliable reusability for at least 100 times measurements, and high recovery rates for spiked water samples; moreover, all detection steps are easy-to-operate and can be completed in 5 min. Therefore, it exhibits great promise for actual on-site environmental monitoring. Additionally, without introducing any other oligonucleotides or auxiliary materials, this SPA-based biosensing method shows potential as a simple, sensitive, and low-cost manner for the detection of other small molecular targets.
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Affiliation(s)
- Qian Zhu
- State Key Joint Laboratory of ESPC, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Lanhua Liu
- State Key Joint Laboratory of ESPC, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Ruoyu Wang
- State Key Joint Laboratory of ESPC, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Xiaohong Zhou
- State Key Joint Laboratory of ESPC, School of Environment, Tsinghua University, Beijing, 100084, China; National Engineering Laboratory for Advanced Technology and Equipment of Water Environment Pollution Monitoring, Changsha, 410205, China.
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18
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Mi X, Li H, Tan R, Tu Y. Dual-Modular Aptasensor for Detection of Cardiac Troponin I Based on Mesoporous Silica Films by Electrochemiluminescence/Electrochemical Impedance Spectroscopy. Anal Chem 2020; 92:14640-14647. [PMID: 33090771 DOI: 10.1021/acs.analchem.0c03130] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A simple, dual-modular aptasensor for accurate determination of cardiac troponin I (cTnI), a sensitive biomarker of acute myocardial infarction, is reported. It has the parallel output of electrochemiluminescence (ECL) and electrochemical impedance spectroscopy (EIS) based on target-gated transportation of signal probes (luminol/H2O2 or Fe(CN)63-/4-). The sensing capacity is originated from the amino-functionalized mouth margin of the nanochannels in a vertically oriented mesoporous silica film, which was in situ-grown on indium tin oxide-coated glass. With the linkage of glutaraldehyde to couple the aptamer as a trapper, it brings in the high specific target-gated response toward cTnI as decreased ECL or increased EIS. The concentration of cTnI is measurable by the ECL response within a wide linear range from 0.05 pg mL-1 to 10 ng mL-1, as well as the EIS response for a linear range between 0.05 pg mL-1 and 1 ng mL-1. Significantly, the self-verification of these two data from ECL and EIS validated each other with a satisfactory linear correlation (R2 = 0.999), thereby realizing the more reliable and accurate quantification to avoid false results. The designed strategy is an effective method for detection of cTnI, which is of great potential to apply in clinical detection.
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Affiliation(s)
- Xiaona Mi
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, Suzhou 215123, P. R. China
| | - Hui Li
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou 215004, P. R. China
| | - Rong Tan
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, Suzhou 215123, P. R. China
| | - Yifeng Tu
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, Suzhou 215123, P. R. China
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19
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Structure-switching fluorescence aptasensor for sensitive detection of chloramphenicol. Mikrochim Acta 2020; 187:505. [PMID: 32815083 DOI: 10.1007/s00604-020-04471-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 08/02/2020] [Indexed: 01/09/2023]
Abstract
The performance of chloramphenicol aptamer, including binding thermodynamics, structure switching, and binding domain, was investigated by isothermal titration calorimetry, circular dichroism, and molecular docking. Then, a new fluorescence aptasensor was developed with signal amplification mediated by exonuclease I-catalyzed reaction and hybridization chain reaction (HCR) for chloramphenicol detection. In this system, the aptamer-binding domain is blocked by the initiator of HCR, the aptamer undergoes structure switching in the presence of chloramphenicol, and DNA dissociation occurs. The released aptamer is subsequently recognized and cleaved by Exo I to set free chloramphenicol. With the Exo I-assisted chloramphenicol recycling, an increasing number of initiators were exposed from the digestion of the initiator-aptamer complex. Then, the chain-like assembly of FAM labeled H1 and H2 through HCR was triggered by the initiator, generating a long DNA polymer. Under optimum conditions, the aptasensor exhibited a log-linear range from 0.001 to 100 nM of chloramphenicol and a detection limit of 0.3 pM. Additionally, the designed biosensing platform was applied to determine chloramphenicol in milk and lake water with high accuracy. The current approach provides a new avenue to develop sensitive aptasensors with the assistance of binding mechanism between aptamer and target compounds. Graphical abstract.
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20
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Chemical Modification of Aptamers for Increased Binding Affinity in Diagnostic Applications: Current Status and Future Prospects. Int J Mol Sci 2020; 21:ijms21124522. [PMID: 32630547 PMCID: PMC7350236 DOI: 10.3390/ijms21124522] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022] Open
Abstract
Aptamers are short single stranded DNA or RNA oligonucleotides that can recognize analytes with extraordinary target selectivity and affinity. Despite their promising properties and diagnostic potential, the number of commercial applications remains scarce. In order to endow them with novel recognition motifs and enhanced properties, chemical modification of aptamers has been pursued. This review focuses on chemical modifications, aimed at increasing the binding affinity for the aptamer's target either in a non-covalent or covalent fashion, hereby improving their application potential in a diagnostic context. An overview of current methodologies will be given, thereby distinguishing between pre- and post-SELEX (Systematic Evolution of Ligands by Exponential Enrichment) modifications.
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21
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Li X, Leng Y, Li X, Wang Y, Luo P, Zhang C, Wang Z, Yue X, Shen C, Chen L, Liu Z, Shi C, Xie L. The TβR II-targeted aptamer S58 prevents fibrosis after glaucoma filtration surgery. Aging (Albany NY) 2020; 12:8837-8857. [PMID: 32452828 PMCID: PMC7288943 DOI: 10.18632/aging.102997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 02/04/2020] [Indexed: 12/18/2022]
Abstract
Glaucoma filtration surgery (GFS) is an effective clinical treatment for glaucoma when intraocular pressure (IOP) control is poor. However, the occurrence of conjunctival scarring at the surgical site is the main reason for failure of the surgery. In a previous study, we isolated and developed S58, a novel nucleic acid aptamer targeting TβR II, by systematic evolution of ligands by exponential enrichment (SELEX). Here, we show how S58 sterically inhibits the TβR II interaction with TGF-β. The effects of topical S58 treatment were studied in a rabbit model of GFS. At 6 postoperative weeks, S58 reduced fibrosis and prolonged bleb survival in rabbits after GFS. Further in vitro tests showed that the levels of fibrosis in S58 treated-Human Conjunctival Fibroblasts (HConFs) were decreased and that antioxidant defense was increased. In addition, the loss of nuclear factor erythroid 2-related factor 2 (Nrf2) or the inhibition of phosphoinositide 3-kinase/protein kinase B (PI3K/Akt) reversed the anti-fibrotic effects of S58. The present work suggests that S58 could effectively improve GFS surgical outcomes by activating the intracellular antioxidant defense PI3K/Akt/Nrf2 signaling pathway.
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Affiliation(s)
- Xueru Li
- Department of Ophthalmology, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing 401120, China
| | - Yu Leng
- Department of Ophthalmology, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing 401120, China
| | - Xiangji Li
- Department of Ophthalmology, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing 401120, China
| | - Yawei Wang
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University, Chongqing 400038, China
| | - Peng Luo
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University, Chongqing 400038, China
| | - Chi Zhang
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University, Chongqing 400038, China
| | - Ziwen Wang
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University, Chongqing 400038, China
| | - Xiaofeng Yue
- Department of Ophthalmology, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing 401120, China
| | - Chongxing Shen
- Department of Ophthalmology, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing 401120, China
| | - Long Chen
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University, Chongqing 400038, China
| | - Zujuan Liu
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University, Chongqing 400038, China
| | - Chunmeng Shi
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University, Chongqing 400038, China
| | - Lin Xie
- Department of Ophthalmology, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing 401120, China
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22
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Jaria G, Calisto V, Otero M, Esteves VI. Monitoring pharmaceuticals in the aquatic environment using enzyme-linked immunosorbent assay (ELISA)-a practical overview. Anal Bioanal Chem 2020; 412:3983-4008. [PMID: 32088755 DOI: 10.1007/s00216-020-02509-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/29/2020] [Accepted: 02/11/2020] [Indexed: 12/22/2022]
Abstract
The presence of pharmaceuticals, which are considered as contaminants of emerging concern, in natural waters is currently recognized as a widespread problem. Monitoring these contaminants in the environment has been an important field of research since their presence can affect the ecosystems even at very low levels. Several analytical techniques have been developed to detect and quantify trace concentrations of these contaminants in the aquatic environment, namely high-performance liquid chromatography, gas chromatography, and capillary electrophoresis, usually coupled to different types of detectors, which need to be complemented with time-consuming and costly sample cleaning and pre-concentration procedures. Generally, the enzyme-linked immunosorbent assay (ELISA), as other immunoassay methodologies, is mostly used in biological samples (most frequently urine and blood). However, during the last years, the number of studies referring the use of ELISA for the analysis of pharmaceuticals in complex environmental samples has been growing. Therefore, this work aims to present an overview of the application of ELISA for screening and quantification of pharmaceuticals in the aquatic environment, namely in water samples and biological tissues. The experimental procedures together with the main advantages and limitations of the assay are addressed, as well as new incomes related with the application of molecular imprinted polymers to mimic antibodies in similar, but alternative, approaches. Graphical Abstract.
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Affiliation(s)
- Guilaine Jaria
- Department of Chemistry and CESAM, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Vânia Calisto
- Department of Chemistry and CESAM, University of Aveiro, 3810-193, Aveiro, Portugal.
| | - Marta Otero
- Department of Environment and Planning and CESAM, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Valdemar I Esteves
- Department of Chemistry and CESAM, University of Aveiro, 3810-193, Aveiro, Portugal
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23
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Kassahun GS, Griveau S, Juillard S, Champavert J, Ringuedé A, Bresson B, Tran Y, Bedioui F, Slim C. Hydrogel Matrix-Grafted Impedimetric Aptasensors for the Detection of Diclofenac. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:827-836. [PMID: 31910020 DOI: 10.1021/acs.langmuir.9b02031] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Driven by the growing concern about the release of untreated emerging pollutants and the need for determining small amounts of these pollutants present in the environment, novel biosensors dedicated to molecular recognition are developed. We have designed biosensors using a novel class of grafted polymers, surface-attached hydrogel thin films, on conductive transducers as a biocompatible matrix for biomolecule immobilization. We showed that they can be dedicated to the molecular recognition of diclofenac (DCL). The immobilization of the aptamer onto surface-attached hydrogel thin films by covalent attachment provides a biodegradable shelter, providing the aptamer with excellent environments to preserve its active and functional structure while allowing the detection of DCL. The grafting of the aptamer is obtained using the formation of amide bonds via the activation of carboxylic acid groups of the poly(acrylic acid) hydrogel thin film. For improved sensitivity and higher stability of the sensor, a high density of the immobilized aptamer is enabled. The aptamer-modified electrode was then incubated with DCL solutions at different concentrations. The performances of the aptasensor were investigated by electrochemical impedance spectroscopy. The change in charge-transfer resistance was found to be linear with DCL concentration in the 30 pM to 1 μM range. The detection limit was calculated to be 0.02 nM. The improvement of the limit of detection can be mainly attributed to the three-dimensional environment of the hydrogel matrix which improves the grafting density of the aptamer and the affinity of the aptamer to DCL.
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Affiliation(s)
- G S Kassahun
- Institute of Chemistry for Life and Health Sciences (iCLeHS), PSL Research University, CNRS, Chimie ParisTech , 11 Rue Pierre et Marie Curie , 75231 Paris Cedex 05, France
| | - S Griveau
- Institute of Chemistry for Life and Health Sciences (iCLeHS), PSL Research University, CNRS, Chimie ParisTech , 11 Rue Pierre et Marie Curie , 75231 Paris Cedex 05, France
| | - S Juillard
- Institute of Chemistry for Life and Health Sciences (iCLeHS), PSL Research University, CNRS, Chimie ParisTech , 11 Rue Pierre et Marie Curie , 75231 Paris Cedex 05, France
| | - J Champavert
- Institute of Chemistry for Life and Health Sciences (iCLeHS), PSL Research University, CNRS, Chimie ParisTech , 11 Rue Pierre et Marie Curie , 75231 Paris Cedex 05, France
| | - A Ringuedé
- Institut de Recherche de Chimie de Paris (IRCP), PSL Research University, CNRS, Chimie ParisTech , 11 Rue Pierre et Marie Curie , 75231 Paris Cedex 05, France
| | - B Bresson
- Soft Matter Engineering and Science, PSL Research University, UMR 7615 CNRS, ESPCI , 10 Rue Vauquelin , F-75231 Paris Cedex 05, France
| | - Y Tran
- Soft Matter Engineering and Science, PSL Research University, UMR 7615 CNRS, ESPCI , 10 Rue Vauquelin , F-75231 Paris Cedex 05, France
| | - F Bedioui
- Institute of Chemistry for Life and Health Sciences (iCLeHS), PSL Research University, CNRS, Chimie ParisTech , 11 Rue Pierre et Marie Curie , 75231 Paris Cedex 05, France
| | - C Slim
- Institute of Chemistry for Life and Health Sciences (iCLeHS), PSL Research University, CNRS, Chimie ParisTech , 11 Rue Pierre et Marie Curie , 75231 Paris Cedex 05, France
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24
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Wu X, Liu H, Han D, Peng B, Zhang H, Zhang L, Li J, Liu J, Cui C, Fang S, Li M, Ye M, Tan W. Elucidation and Structural Modeling of CD71 as a Molecular Target for Cell-Specific Aptamer Binding. J Am Chem Soc 2019; 141:10760-10769. [PMID: 31185171 DOI: 10.1021/jacs.9b03720] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Pancreatic cancer is a highly lethal malignancy associated with tissues of the pancreas. Early diagnosis and effective treatment are crucial to improving the survival rate of patients with pancreatic cancer. In a previous study, we employed the cell-SELEX strategy to obtain an ssDNA aptamer termed XQ-2d with high binding affinity for pancreatic cancer. Here, we first identify CD71 as the XQ-2d-binding target. We found that knockdown of CD71 abolished the binding of XQ-2d and that the binding affinity of XQ-2d is associated with membrane-bound CD71, rather than total CD71 levels. Competitive analysis revealed that XQ-2d shares the same binding site on CD71 with transferrin (Tf), but not anti-CD71 antibody. We then used a surface energy transfer (SET) nanoruler to measure the distance between the binding sites of XQ-2d and anti-CD71 antibody, and it was about 15 nm. Furthermore, we did molecular dynamics simulation to clarify that the spatial structure of XQ-2d and Tf competitively binding to CD71. We also engineered XQ-2d-mediated targeted therapy for pancreatic cancer, using an XQ-2d-based complex for loading doxorubicin (Dox). Because CD71 is overexpressed not only in pancreatic cancer but also in a variety of tumors, our work provides a systematic novel way of studying a potential biomarker and also promising tools for cancer diagnosis and therapy, opening new doors for effective cancer theranostics.
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Affiliation(s)
- Xiaoqiu Wu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China
| | - Honglin Liu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China.,School of Food and Biological Engineering , Hefei University of Technology , Hefei , Anhui 230009 , China
| | - Dongmei Han
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China
| | - Bo Peng
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China
| | - Hui Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China
| | - Lin Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China
| | - Jianglin Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China
| | | | - Cheng Cui
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China.,Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute , University of Florida , Gainesville , Florida 32611 , United States
| | | | | | - Mao Ye
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China.,Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute , University of Florida , Gainesville , Florida 32611 , United States.,Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , China
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25
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Two colorimetric ampicillin sensing schemes based on the interaction of aptamers with gold nanoparticles. Mikrochim Acta 2019; 186:485. [PMID: 31264034 DOI: 10.1007/s00604-019-3524-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 05/19/2019] [Indexed: 10/26/2022]
Abstract
Two kinds of aptasensors for ampicillin (AMP) are described. The assay strategies include the use of gold nanoparticles (AuNPs) that were modified with (a) a thiolated aptamer (T-Apt), and (b) a non-thiolated polyadenine aptamer (polyA Apt). The AuNPs and the aptamers were brought to interaction prior to addition of AMP. T-Apt and polyA Apt are adsorbed on the AuNPs by different mechanisms. The adsorbed aptamer was able to bind the target while preventing non-specific interactions. Remarkably different optical absorbances (measured at 520 and 680 nm) are produced the absence and presence of AMP. The assay can selectively recognize AMP even in the presence of species of similar chemical structure. The T-Apt based assay has a linear response in the 1-600 nM AMP concentration range and a 0.1 nM limit of detection. The respective data for the polyA Apt assay are 1-400 nM and 0.49 nM. Graphical abstract Schematic presentation of the colorimetric aptasensor for ampicillin detection using two kinds of anti-ampicillin aptamers and gold nanoparticles. Polydiallyldimethylammonium chloride (PDDA) acts as aggregation agent.
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26
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Goud KY, Kailasa SK, Kumar V, Tsang YF, Lee SE, Gobi KV, Kim KH. Progress on nanostructured electrochemical sensors and their recognition elements for detection of mycotoxins: A review. Biosens Bioelectron 2018; 121:205-222. [PMID: 30219721 DOI: 10.1016/j.bios.2018.08.029] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/11/2018] [Accepted: 08/13/2018] [Indexed: 12/31/2022]
Abstract
Nanomaterial-embedded sensors have been developed and applied to monitor various targets. Mycotoxins are fungal secondary metabolites that can exert carcinogenic, mutagenic, teratogenic, immunotoxic, and estrogenic effects on humans and animals. Consequently, the need for the proper regulation on foodstuff and feed materials has been recognized from times long past. This review provides an overview of recent developments in electrochemical sensors and biosensors employed for the detection of mycotoxins. Basic aspects of the toxicity of mycotoxins and the implications of their detection are comprehensively discussed. Furthermore, the development of different molecular recognition elements and nanomaterials required for the detection of mycotoxins (such as portable biosensing systems for point-of-care analysis) is described. The current capabilities, limitations, and future challenges in mycotoxin detection and analysis are also addressed.
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Affiliation(s)
- K Yugender Goud
- Department of Civil and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea; Department of Chemistry, National Institute of Technology Warangal, Telangana 506004, India
| | - Suresh Kumar Kailasa
- Department of Applied Chemistry, S. V. National Institute of Technology, Surat 395007, Gujarat, India.
| | - Vanish Kumar
- Department of Applied Sciences, U.I.E.T., Panjab University, Chandigarh 160014, India
| | - Yiu Fai Tsang
- Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, New Territories, Hong Kong, China
| | - S E Lee
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | | | - Ki-Hyun Kim
- Department of Civil and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea.
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Khan A, Shams DF, Khan W, Ijaz A, Qasim M, Saad M, Hafeez A, Baig SA, Ahmed N. Prevalence of selected pharmaceuticals in surface water receiving untreated sewage in northwest Pakistan. ENVIRONMENTAL MONITORING AND ASSESSMENT 2018; 190:324. [PMID: 29728779 DOI: 10.1007/s10661-018-6683-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 04/09/2018] [Indexed: 06/08/2023]
Abstract
This study investigated the occurrence of four non-steroidal anti-inflammatory drugs (NSAIDs) and four benzodiazepines/anti-depressants (ADs) in municipal wastewater in Mardan city, Pakistan, and in River Kabul and River Indus receiving untreated sewage. Liquid chromatography with a triple quadrupole tandem mass spectrometry (LC-MS/MS) was used for the analysis of paracetamol, diclofenac, ibuprofen, and codeine (NSAIDs) and diazepam, bromazepam, lorazepam, and temazepam (ADs). Except codeine and lorazepam, all the target compounds were observed in sewage and surface water in various concentrations. In sewage, paracetamol was found at the higher end (32.4 μg/L) of the reported ranges in literature for other countries. Results of river samples showed that the target compounds were usually lower in concentration than the respective EC50 values for aquatic organisms. However, the levels for paracetamol and ibuprofen were critical depicting the consequence of untreated disposal. Environmental risk assessment by estimating the risk quotient (RQ) as the ratio of measured environmental concentration and predicted no-effect concentration showed medium to high (RQ > 1 and 0.1 < RQ < 1) risk from paracetamol and ibuprofen to aquatic organisms in River Kabul and Kalpani stream, Pakistan.
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Affiliation(s)
- Aisha Khan
- Department of Environmental Sciences, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
| | - Dilawar Farhan Shams
- Department of Environmental Sciences, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan.
| | - Waliullah Khan
- Department of Chemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Aamir Ijaz
- Department of Endocrinology, Armed Forces Institute of Pathology, Rawalpindi, Pakistan
| | - Muhammad Qasim
- Department of Environmental Sciences, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
| | - Maryam Saad
- Department of Environmental Sciences, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan.
| | - Ayesha Hafeez
- Department of Endocrinology, Armed Forces Institute of Pathology, Rawalpindi, Pakistan
| | - Shams Ali Baig
- Department of Environmental Sciences, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
| | - Nisar Ahmed
- Department of Endocrinology, Armed Forces Institute of Pathology, Rawalpindi, Pakistan
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Practical Application of Aptamer-Based Biosensors in Detection of Low Molecular Weight Pollutants in Water Sources. Molecules 2018; 23:molecules23020344. [PMID: 29414854 PMCID: PMC6017897 DOI: 10.3390/molecules23020344] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 01/30/2018] [Accepted: 01/30/2018] [Indexed: 01/08/2023] Open
Abstract
Water pollution has become one of the leading causes of human health problems. Low molecular weight pollutants, even at trace concentrations in water sources, have aroused global attention due to their toxicity after long-time exposure. There is an increased demand for appropriate methods to detect these pollutants in aquatic systems. Aptamers, single-stranded DNA or RNA, have high affinity and specificity to each of their target molecule, similar to antigen-antibody interaction. Aptamers can be selected using a method called Systematic Evolution of Ligands by EXponential enrichment (SELEX). Recent years we have witnessed great progress in developing aptamer selection and aptamer-based sensors for low molecular weight pollutants in water sources, such as tap water, seawater, lake water, river water, as well as wastewater and its effluents. This review provides an overview of aptamer-based methods as a novel approach for detecting low molecular weight pollutants in water sources.
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Srivastava M, Nirala NR, Srivastava SK, Prakash R. A comparative Study of Aptasensor Vs Immunosensor for Label-Free PSA Cancer Detection on GQDs-AuNRs Modified Screen-Printed Electrodes. Sci Rep 2018; 8:1923. [PMID: 29386538 PMCID: PMC5792442 DOI: 10.1038/s41598-018-19733-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 11/27/2017] [Indexed: 12/02/2022] Open
Abstract
Label-free and sensitive detection of PSA (Prostate Specific Antigen) is still a big challenge in the arena of prostate cancer diagnosis in males. We present a comparative study for label-free PSA aptasensor and PSA immunosensor for the PSA-specific monoclonal antibody, based on graphene quantum dots-gold nanorods (GQDs-AuNRs) modified screen-printed electrodes. GQDs-AuNRs composite has been synthesized and used as an electro-active material, which shows fast electron transfer and catalytic property. Aptamer or anti-PSA has immobilized onto the surface of modified screen printed electrodes. Three techniques are used simultaneously, viz. cyclic voltammetry (CV), differential pulse voltammetry (DPV) and electrochemical impedence spectroscopy (EIS) to investigate the analytical performance of both PSA aptasensor and PSA immunosensor with its corresponding PSA antigen. Under optimum conditions, both sensors show comparable results with an almost same limit of detection (LOD) of 0.14 ng mL-1. The results developed with aptasensor and anti-PSA is also checked through the detection of PSA in real samples with acceptable results. Our study suggests some advantages of aptasensor in terms of better stability, simplicity and cost effectiveness. Further our present work shows enormous potential of our developed sensors for real application using voltammetric and EIS techniques simultaneous to get reliable detection of the disease.
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Affiliation(s)
- Monika Srivastava
- School of Materials Science and Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, 221005, India
| | - Narsingh R Nirala
- School of Materials Science and Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, 221005, India
| | - S K Srivastava
- School of Materials Science and Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, 221005, India
- Department of Physics, Banaras Hindu University, Varanasi, 221005, India
| | - Rajiv Prakash
- School of Materials Science and Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, 221005, India.
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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: 28] [Impact Index Per Article: 4.0] [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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Ramlal S, Mondal B, Lavu PS, N B, Kingston J. Capture and detection of Staphylococcus aureus with dual labeled aptamers to cell surface components. Int J Food Microbiol 2017; 265:74-83. [PMID: 29132030 DOI: 10.1016/j.ijfoodmicro.2017.11.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/22/2017] [Accepted: 11/04/2017] [Indexed: 11/18/2022]
Abstract
In the present study, a high throughput whole cell SELEX method has been applied successfully in selecting specific aptamers against whole cells of Staphylococcus aureus, a potent food poisoning bacterium. A total ten rounds of SELEX and three rounds of intermittent counter SELEX, was performed to obtain specific aptamers. Obtained oligonucleotide pool were cloned, sequenced and then grouped into different families based on their primary sequence homology and secondary structure similarity. FITC labeled sequences from different families were selected for further characterization via flow cytometry analysis. The dissociation constant (Kd) values of specific and higher binders ranged from 34 to 128nM. Binding assays to assess the selectivity of aptamer RAB10, RAB 20, RAB 28 and RAB 35 demonstrated high affinity against S. aureus and low binding affinity for other bacteria. To demonstrate the potential use of the aptamer a sensitive dual labeled sandwich detection system was developed using aptamer RAB10 and RAB 35 with a detection limit of 102CFU/mL. Furthermore detection from mixed cell population and spiked sample emphasized the robustness as well as applicability of the developed method. Altogether, the established assay could be a reliable detection tool for the routine investigation of Staphylococcus aureus in samples from food and clinical sources.
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Affiliation(s)
- Shylaja Ramlal
- Microbiology Division, Defence Food Research Laboratory, Siddarthanagar, Mysore, Karnataka 570011, India.
| | - Bhairab Mondal
- Microbiology Division, Defence Food Research Laboratory, Siddarthanagar, Mysore, Karnataka 570011, India
| | - Padma Sudharani Lavu
- Microbiology Division, Defence Food Research Laboratory, Siddarthanagar, Mysore, Karnataka 570011, India
| | - Bhavanashri N
- Microbiology Division, Defence Food Research Laboratory, Siddarthanagar, Mysore, Karnataka 570011, India
| | - Joseph Kingston
- Microbiology Division, Defence Food Research Laboratory, Siddarthanagar, Mysore, Karnataka 570011, India
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Kim JY, Park JH, Kim MI, Lee HH, Kim HL, Jeong KS, Moon SO, Kang PW, Park KW, Lee YH, Chun BW. Identification of female-specific blood stains using a 17β-estradiol-targeted aptamer-based sensor. Int J Legal Med 2017; 132:91-98. [PMID: 29086052 DOI: 10.1007/s00414-017-1718-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/11/2017] [Indexed: 01/08/2023]
Abstract
Blood stain evidence obtained from a violent crime scene provides decisive clues that can enable a case to be solved through forensic analyses such as genetic identification. However, collected samples usually contain a mixture of biological material from different sources, making genetic identification difficult. To address this issue, we developed an activatable aptamer sensor targeting 17β-estradiol for detection of female-specific blood in mixed samples. With the sensor, we were able to detect blood originating from females using a variable light source (495 nm). The sensor was especially sensitive to blood from young females (10-40 years) but not to blood from older females (≥ 50 years). Genomic DNA was extracted from the female blood specimens identified by this method and used for quantification and short tandem repeat genotyping. We confirmed that there was no fluorescence interference from the aptamer sensor. These results indicate that this novel aptamer sensor can be used to analyze evidentiary blood samples and thereby facilitate subsequent genetic identification.
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Affiliation(s)
- Joo-Young Kim
- Crime-scene DNA Section, National Forensic Service, Gwangju Institute, Gwangju, 57231, Republic of Korea
| | - Jung-Hyun Park
- Mibyeong Research Center, Korea Institute of Oriental Medicine, Daejeon, 34054, Republic of Korea
| | - Man Il Kim
- Crime-scene DNA Section, National Forensic Service, Gwangju Institute, Gwangju, 57231, Republic of Korea
| | - Hye Hyeon Lee
- Crime-scene DNA Section, National Forensic Service, Gwangju Institute, Gwangju, 57231, Republic of Korea
| | - Hye Lim Kim
- Crime-scene DNA Section, National Forensic Service, Gwangju Institute, Gwangju, 57231, Republic of Korea
| | - Kyu-Sik Jeong
- Forensic DNA Division, National Forensic Service, Wonju, 26460, Republic of Korea
| | - Sang-Ok Moon
- Crime-scene DNA Section, National Forensic Service, Gwangju Institute, Gwangju, 57231, Republic of Korea
| | - Pil-Won Kang
- Crime-scene DNA Section, National Forensic Service, Gwangju Institute, Gwangju, 57231, Republic of Korea
| | - Ki-Won Park
- Forensic DNA Division, National Forensic Service, Wonju, 26460, Republic of Korea
| | - Yang-Han Lee
- Forensic DNA Division, National Forensic Service, Wonju, 26460, Republic of Korea
| | - Byung-Won Chun
- Forensic DNA Division, National Forensic Service, Wonju, 26460, Republic of Korea.
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Xu M, Gao Z, Zhou Q, Lin Y, Lu M, Tang D. Terbium ion-coordinated carbon dots for fluorescent aptasensing of adenosine 5'-triphosphate with unmodified gold nanoparticles. Biosens Bioelectron 2016; 86:978-984. [PMID: 27498324 DOI: 10.1016/j.bios.2016.07.105] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 07/28/2016] [Accepted: 07/29/2016] [Indexed: 01/11/2023]
Abstract
This work reports on a novel time-resolved fluorescent aptasensing platform for the quantitative monitoring of adenosine 5'-triphosphate (ATP) by interaction of dispersive/agglomerate gold nanoparticles (AuNPs) with terbium ion-coordinated carbon dots (Tb-CDs). To construct such a fluorescent nanoprobe, Tb-CDs with high-efficient fluorescent intensity are first synthesized by the microwave method with terbium ions (Tb(3+)). The aptasensing system consists of ATP aptamer, AuNP and Tb-CD. The dispersive/agglomerate gold nanoparticles are acquired through the reaction of the aptamer with target ATP. Upon target ATP introduction, the aptamers bind with the analytes to form new aptamer-ATP complexes and coat on the surface of AuNPs to inhibit their aggregation in the high salt solution. In this case, the fluorescent signal of Tb-CDs is quenched by the dispersive AuNPs on the basis of the fluorescence resonance energy transfer (FRET). At the absence of target analyte, gold nanoparticles tend to aggregate in the high salt state even if the aptamers are present. Thus, the added Tb-CDs maintain their intrinsic fluorescent intensity. Experimental results indicated that the aptasensing system exhibited good fluorescent responses toward ATP in the dynamic range from 40nM to 4.0μM with a detection limit of 8.5nM at 3sblank criterion. The repeatability and intermediate precision is less than 9.5% at three concentrations including 0.04, 0.4 and 2.0μM ATP. The selectivity was acceptable toward guanosine 5'-triphosphate, uridine 5'-triphosphate and cytidine 5'-triphosphate. The methodology was applied to evaluate the blank human serum spiked with target ATP, and the recoveries (at 3 concentration levels) ranged between 97.0% and 103.7%. Importantly, this detection scheme is rapid, simple, cost-effective, and does not require extensive sample preparation or separation.
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Affiliation(s)
- Mingdi Xu
- Key Laboratory of Analysis and Detection for Food Safety (MOE&Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou, 350108 PR China
| | - Zhuangqiang Gao
- Key Laboratory of Analysis and Detection for Food Safety (MOE&Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou, 350108 PR China
| | - Qian Zhou
- Key Laboratory of Analysis and Detection for Food Safety (MOE&Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou, 350108 PR China
| | - Youxiu Lin
- Key Laboratory of Analysis and Detection for Food Safety (MOE&Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou, 350108 PR China
| | - Minghua Lu
- Institute of Environmental and Analytical Science, School of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan, 475004 PR China.
| | - Dianping Tang
- Key Laboratory of Analysis and Detection for Food Safety (MOE&Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou, 350108 PR China.
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Menger M, Yarman A, Erdőssy J, Yildiz HB, Gyurcsányi RE, Scheller FW. MIPs and Aptamers for Recognition of Proteins in Biomimetic Sensing. BIOSENSORS 2016; 6:E35. [PMID: 27438862 PMCID: PMC5039654 DOI: 10.3390/bios6030035] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/04/2016] [Accepted: 07/11/2016] [Indexed: 12/12/2022]
Abstract
Biomimetic binders and catalysts have been generated in order to substitute the biological pendants in separation techniques and bioanalysis. The two major approaches use either "evolution in the test tube" of nucleotides for the preparation of aptamers or total chemical synthesis for molecularly imprinted polymers (MIPs). The reproducible production of aptamers is a clear advantage, whilst the preparation of MIPs typically leads to a population of polymers with different binding sites. The realization of binding sites in the total bulk of the MIPs results in a higher binding capacity, however, on the expense of the accessibility and exchange rate. Furthermore, the readout of the bound analyte is easier for aptamers since the integration of signal generating labels is well established. On the other hand, the overall negative charge of the nucleotides makes aptamers prone to non-specific adsorption of positively charged constituents of the sample and the "biological" degradation of non-modified aptamers and ionic strength-dependent changes of conformation may be challenging in some application.
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Affiliation(s)
- Marcus Menger
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, Potsdam D-14476, Germany.
| | - Aysu Yarman
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 25-26, Potsdam D-14476, Germany.
- Turkish-German University, Faculty of Science, Molecular Biotechnology, Sahinkaya Cad. No. 86, Bekoz, Istanbul 34820, Turkey.
| | - Júlia Erdőssy
- MTA-BME "Lendület" Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4, Budapest H-1111, Hungary.
| | - Huseyin Bekir Yildiz
- Department of Materials Science and Nanotechnology Engineering, KTO Karatay University, Konya 42020, Turkey.
| | - Róbert E Gyurcsányi
- MTA-BME "Lendület" Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4, Budapest H-1111, Hungary.
| | - Frieder W Scheller
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, Potsdam D-14476, Germany.
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 25-26, Potsdam D-14476, Germany.
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36
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Aptamer-based biosensor for label-free detection of ethanolamine by electrochemical impedance spectroscopy. Anal Chim Acta 2016; 936:222-8. [PMID: 27566359 DOI: 10.1016/j.aca.2016.06.056] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 06/28/2016] [Accepted: 06/30/2016] [Indexed: 11/22/2022]
Abstract
A label-free sensing assay for ethanolamine (EA) detection based on G-quadruplex-EA binding interaction is presented by using G-rich aptamer DNA (Ap-DNA) and electrochemical impedance spectroscopy (EIS). The presence of K(+) induces the Ap-DNA to form a K(+)-stabilized G-quadruplex structure which provides binding sites for EA. The sensing mechanism was further confirmed by circular dichroism (CD) spectroscopy and EIS measurement. As a result, the charge transfer resistance (RCT) is strongly increased as demonstrated by using the ferro/ferricyanide ([Fe(CN)6](3-/4-)) as a redox probe. Under the optimized conditions, a linear relationship between ΔRCT and EA concentration was obtained over the range of 0.16 nM and 16 nM EA, with a detection limit of 0.08 nM. Interference by other selected chemicals with similar structure was negligible. Analytical results of EA spiked into tap water and serum by the sensor suggested the assay could be successfully applied to real sample analysis. With the advantages of high sensitivity, selectivity and simple sensor construction, this method is potentially suitable for the on-site monitoring of EA contamination.
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37
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Lee KC, Chiang HL, Chiu WR, Chen YC. Molecular recognition between insulin and dextran encapsulated gold nanoparticles. J Mol Recognit 2016; 29:528-535. [PMID: 27195946 DOI: 10.1002/jmr.2552] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 04/13/2016] [Accepted: 04/14/2016] [Indexed: 01/13/2023]
Abstract
Insulin is a peptide hormone that can regulate the metabolism of carbohydrates and lipids. This hormone is closely related to glucose-uptake in cells and can control blood glucose levels. Dextran is a polysaccharide composed of glucose units. In this study, we discovered that dextran-encapsulated gold nanoparticles (AuNPs@Dextran) and nanoclusters (AuNCs@Dextran) can be used to recognize insulin. The dissociation constant of insulin toward AuNPs@Dextran was estimated to be ∼5.3 × 10-6 M. The binding site on insulin toward the dextran on the nanoprobes was explored as well. It was found that the sequence of numbers 1-22 on the insulin B chain can interact with the dextran encapsulated nanoprobes. Additionally, we also demonstrated that the dextran-encapsulated nanoprobes could be used as concentration probes to selectively enrich trace amounts of insulin (∼1 pM) from serum samples. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Kai-Chieh Lee
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Hsiang-Ling Chiang
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Wei-Ru Chiu
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Yu-Chie Chen
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu, 300, Taiwan.
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Patel KA, Sethi R, Dhara AR, Roy I. Challenges with osmolytes as inhibitors of protein aggregation: Can nucleic acid aptamers provide an answer? Int J Biol Macromol 2016; 100:75-88. [PMID: 27156694 DOI: 10.1016/j.ijbiomac.2016.05.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 02/07/2023]
Abstract
Protein aggregation follows some common motifs. Whether in the formation of inclusion bodies in heterologous overexpression systems or inclusions in protein conformational diseases, or aggregation during storage or transport of protein formulations, aggregates form cross beta-sheet structures and stain with amyloidophilic dyes like Thioflavin T and Congo Red, irrespective of the concerned protein. Traditionally, osmolytes are used to stabilize proteins against stress conditions. They are employed right from protein expression, through production and purification, to formulation and administration. As osmolytes interact with the solvent, the differential effect of the stress condition on the solvent mostly determines the effect of the osmolyte on protein stability. Nucleic acid aptamers, on the other hand, are highly specific for their targets. When selected against monomeric, natively folded proteins, they bind to them with very high affinity. This binding inhibits the unfolding of the protein and/or monomer-monomer interaction which are the initial common steps of protein aggregation. Thus, by changing the approach to a protein-centric model, aptamers are able to function as universal stabilizers of proteins. The review discusses cases where osmolytes were unable to provide stabilization to proteins against different stress conditions, a gap which the aptamers seem to be able to fill.
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Affiliation(s)
- Kinjal A Patel
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Ratnika Sethi
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Anita R Dhara
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Ipsita Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160 062, India.
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Tan SY, Acquah C, Sidhu A, Ongkudon CM, Yon LS, Danquah MK. SELEX Modifications and Bioanalytical Techniques for Aptamer-Target Binding Characterization. Crit Rev Anal Chem 2016; 46:521-37. [PMID: 26980177 DOI: 10.1080/10408347.2016.1157014] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The quest to improve the detection of biomolecules and cells in health and life sciences has led to the discovery and characterization of various affinity bioprobes. Libraries of synthetic oligonucleotides (ssDNA/ssRNA) with randomized sequences are employed during Systematic Evolution of Ligands by Exponential Enrichment (SELEX) to select highly specific affinity probes called aptamers. With much focus on the generation of aptamers for a variety of target molecules, conventional SELEX protocols have been modified to develop new and improved SELEX protocols yielding highly specific and stable aptamers. Various techniques have been used to analyze the binding interactions between aptamers and their cognate molecules with associated merits and limitations. This article comprehensively reviews research advancements in the generation of aptamers, analyses physicochemical conditions affecting their binding characteristics to cellular and biomolecular targets, and discusses various field applications of aptameric binding. Biophysical techniques employed in the characterization of the molecular and binding features of aptamers to their cognate targets are also discussed.
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Affiliation(s)
- Sze Y Tan
- a Department of Chemical Engineering , Curtin University , Sarawak , Malaysia.,b Curtin Sarawak Research Institute , Curtin University , Sarawak , Malaysia
| | - Caleb Acquah
- a Department of Chemical Engineering , Curtin University , Sarawak , Malaysia.,b Curtin Sarawak Research Institute , Curtin University , Sarawak , Malaysia
| | - Amandeep Sidhu
- b Curtin Sarawak Research Institute , Curtin University , Sarawak , Malaysia.,c Faculty of Health Sciences , Curtin University , Perth , Australia
| | - Clarence M Ongkudon
- d Biotechnology Research Institute , University Malaysia Sabah , Kota Kinabalu , Sabah , Malaysia
| | - L S Yon
- a Department of Chemical Engineering , Curtin University , Sarawak , Malaysia
| | - Michael K Danquah
- a Department of Chemical Engineering , Curtin University , Sarawak , Malaysia.,b Curtin Sarawak Research Institute , Curtin University , Sarawak , Malaysia
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Reinemann C, Freiin von Fritsch U, Rudolph S, Strehlitz B. Generation and characterization of quinolone-specific DNA aptamers suitable for water monitoring. Biosens Bioelectron 2015; 77:1039-47. [PMID: 26547431 DOI: 10.1016/j.bios.2015.10.069] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 10/22/2015] [Accepted: 10/26/2015] [Indexed: 12/17/2022]
Abstract
Quinolones are antibiotics that are accredited in human and veterinary medicine but are regularly used in high quantities also in industrial livestock farming. Since these compounds are often only incompletely metabolized, significant amounts contaminate the aquatic environment and negatively impact on a variety of different ecosystems. Although there is increasing awareness of problems caused by pharmaceutical pollution, available methods for the detection and elimination of numerous pharmaceutical residues are currently inefficient or expensive. While this also applies to antibiotics that may lead to multi-drug resistance in pathogenic bacteria, aptamer-based technologies potentially offer alternative approaches for sensitive and efficient monitoring of pharmaceutical micropollutants. Using the Capture-SELEX procedure, we here describe the selection of an aptamer pool with enhanced binding qualities for fluoroquinolones, a widely used group of antibiotics in both human and veterinary medicine. The selected aptamers were shown to detect various quinolones with high specificity, while specific binding activities to structurally unrelated drugs were not detectable. The quinolone-specific aptamers bound to ofloxacin, one of the most frequently prescribed fluoroquinolone, with high affinity (KD=0.1-56.9 nM). The functionality of quinolone-specific aptamers in real water samples was demonstrated in local tap water and in effluents of sewage plants. Together, our data suggest that these aptamers may be applicable as molecular receptors in biosensors or as catcher molecules in filter systems for improved monitoring and treatment of polluted water.
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Affiliation(s)
- C Reinemann
- UFZ - Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany.
| | - U Freiin von Fritsch
- UFZ - Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - S Rudolph
- UFZ - Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - B Strehlitz
- UFZ - Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
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41
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Kun Á, Szathmáry E. Fitness Landscapes of Functional RNAs. Life (Basel) 2015; 5:1497-517. [PMID: 26308059 PMCID: PMC4598650 DOI: 10.3390/life5031497] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 07/26/2015] [Accepted: 08/03/2015] [Indexed: 11/16/2022] Open
Abstract
The notion of fitness landscapes, a map between genotype and fitness, was proposed more than 80 years ago. For most of this time data was only available for a few alleles, and thus we had only a restricted view of the whole fitness landscape. Recently, advances in genetics and molecular biology allow a more detailed view of them. Here we review experimental and theoretical studies of fitness landscapes of functional RNAs, especially aptamers and ribozymes. We find that RNA structures can be divided into critical structures, connecting structures, neutral structures and forbidden structures. Such characterisation, coupled with theoretical sequence-to-structure predictions, allows us to construct the whole fitness landscape. Fitness landscapes then can be used to study evolution, and in our case the development of the RNA world.
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Affiliation(s)
- Ádám Kun
- Parmenides Center for the Conceptual Foundations of Science, Kirchplatz 1, 82049 Munich/Pullach, Germany.
- MTA-ELTE-MTMT Ecology Research Group, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
- Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, Eötvös University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
| | - Eörs Szathmáry
- Parmenides Center for the Conceptual Foundations of Science, Kirchplatz 1, 82049 Munich/Pullach, Germany.
- Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, Eötvös University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
- MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
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42
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Soh JH, Lin Y, Rana S, Ying JY, Stevens MM. Colorimetric Detection of Small Molecules in Complex Matrixes via Target-Mediated Growth of Aptamer-Functionalized Gold Nanoparticles. Anal Chem 2015. [PMID: 26197040 DOI: 10.1021/acs.analchem.5b00875] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A versatile and sensitive colorimetric assay that allows the rapid detection of small-molecule targets using the naked eye is demonstrated. The working principle of the assay integrates aptamer-target recognition and the aptamer-controlled growth of gold nanoparticles (Au NPs). Aptamer-target interactions modulate the amount of aptamer strands adsorbed on the surface of aptamer-functionalized Au NPs via desorption of the aptamer strands when target molecules bind with the aptamer. Depending on the resulting aptamer coverage, Au NPs grow into morphologically varied nanostructures, which give rise to different colored solutions. Au NPs with low aptamer coverage grow into spherical NPs, which produce red-colored solutions, whereas Au NPs with high aptamer coverage grow into branched NPs, which produce blue-colored solutions. We achieved visible colorimetric response and nanomolar detection limits for the detection of ochratoxin A (1 nM) in red wine samples, as well as cocaine (1 nM) and 17β-estradiol (0.2 nM) in spiked synthetic urine and saliva, respectively. The detection limits were well within clinically and physiologically relevant ranges, and below the maximum food safety limits. The assay is highly sensitive, specific, and able to detect an array of analytes rapidly without requiring sophisticated equipment, making it relevant for many applications, such as high-throughput drug and clinical screening, food sampling, and diagnostics. Furthermore, the assay is easily adapted as a chip-based platform for rapid and portable target detection.
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Affiliation(s)
- Jun Hui Soh
- †Department of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, London, U.K.,‡Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore
| | - Yiyang Lin
- †Department of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, London, U.K
| | - Subinoy Rana
- †Department of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, London, U.K
| | - Jackie Y Ying
- ‡Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore
| | - Molly M Stevens
- †Department of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, London, U.K
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43
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Müller A, König B. Vesicular aptasensor for the detection of thrombin. Chem Commun (Camb) 2015; 50:12665-8. [PMID: 25205174 DOI: 10.1039/c4cc05221h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Self-assembled phospholipid vesicles are functionalized with thrombin-binding aptamers using a thiol-click reaction. The resulting aptasensors signal the binding of the analyte to the vesicle surface by changes of the emission properties of membrane co-embedded reporter dyes.
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Affiliation(s)
- Andreas Müller
- Institut für Organische Chemie, Universität Regensburg, 93040 Regensburg, Germany.
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44
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Nelissen FHT, Goossens EPM, Tessari M, Heus HA. Enzymatic preparation of multimilligram amounts of pure single-stranded DNA samples for material and analytical sciences. Anal Biochem 2015; 475:68-73. [PMID: 25637680 DOI: 10.1016/j.ab.2015.01.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 01/17/2015] [Accepted: 01/19/2015] [Indexed: 12/15/2022]
Abstract
We present a method for high-yield production of multimilligram amounts of pure single-stranded DNA employing rolling circle amplification (RCA) and processing by restriction enzymes. Pure and homogeneous samples are produced with minimal handling time, reagents, and waste products. The RCA method is more than twice as efficient in dNTP incorporation than conventional polymerase chain reaction in producing end product. The validity and utility of the method are demonstrated in the production of a uniformly (13)C/(15)N-labeled 38-nt cocaine aptamer DNA used in nanosensing devices.
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Affiliation(s)
- Frank H T Nelissen
- Department of Biophysical Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Elles P M Goossens
- Department of Biophysical Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Marco Tessari
- Department of Biophysical Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Hans A Heus
- Department of Biophysical Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands.
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45
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Williams RM, Kulick AR, Yedlapalli S, Battistella L, Hajiran CJ, Sooter LJ. In vitro selection of a single-stranded DNA molecular recognition element specific for bromacil. J Nucleic Acids 2014; 2014:102968. [PMID: 25400940 PMCID: PMC4225842 DOI: 10.1155/2014/102968] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Revised: 09/14/2014] [Accepted: 09/14/2014] [Indexed: 02/05/2023] Open
Abstract
Bromacil is a widely used herbicide that is known to contaminate environmental systems. Due to the hazards it presents and inefficient detection methods, it is necessary to create a rapid and efficient sensing device. Towards this end, we have utilized a stringent in vitro selection method to identify single-stranded DNA molecular recognition elements (MRE) specific for bromacil. We have identified one MRE with high affinity (K d = 9.6 nM) and specificity for bromacil compared to negative targets of selection and other pesticides. The selected ssDNA MRE will be useful as the sensing element in a field-deployable bromacil detection device.
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Affiliation(s)
- Ryan M. Williams
- Department of Basic Pharmaceutical Sciences, West Virginia University, 1 Medical Center Drive, P.O. Box 9530, Morgantown, WV 26506, USA
- Memorial Sloan Kettering Cancer Center, Molecular Pharmacology & Chemistry Program, 1275 York Avenue, New York, NY 10065, USA
| | - Amanda R. Kulick
- Department of Basic Pharmaceutical Sciences, West Virginia University, 1 Medical Center Drive, P.O. Box 9530, Morgantown, WV 26506, USA
| | - Srilakshmi Yedlapalli
- Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, WV 26506, USA
| | - Louisa Battistella
- Department of Basic Pharmaceutical Sciences, West Virginia University, 1 Medical Center Drive, P.O. Box 9530, Morgantown, WV 26506, USA
| | - Cyrus J. Hajiran
- Department of Basic Pharmaceutical Sciences, West Virginia University, 1 Medical Center Drive, P.O. Box 9530, Morgantown, WV 26506, USA
| | - Letha J. Sooter
- Department of Basic Pharmaceutical Sciences, West Virginia University, 1 Medical Center Drive, P.O. Box 9530, Morgantown, WV 26506, USA
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46
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Dziuba D, Pohl R, Hocek M. Bodipy-labeled nucleoside triphosphates for polymerase synthesis of fluorescent DNA. Bioconjug Chem 2014; 25:1984-95. [PMID: 25290695 DOI: 10.1021/bc5003554] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
New fluorescent nucleosides and nucleoside triphosphate (dNTPs) analogs bearing the F-Bodipy fluorophore linked through a short, flexible nonconjugate tether were synthesized. The Bodipy-labeled dNTPs were substrates for several DNA polymerases which incorporated them into DNA in primer extension, nicking enzyme amplification reaction, and polymerase chain reaction. The fluorescence of F-Bodipy is not quenched upon incorporation in DNA and can be detected both in solutions and on gels.
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Affiliation(s)
- Dmytro Dziuba
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center , Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
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47
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Tian J, Yuan PX, Shan D, Ding SN, Zhang GY, Zhang XJ. Biosensing platform based on graphene oxide via self-assembly induced by synergic interactions. Anal Biochem 2014; 460:16-21. [DOI: 10.1016/j.ab.2014.05.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 05/18/2014] [Accepted: 05/20/2014] [Indexed: 11/16/2022]
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48
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Williams RM, Crihfield CL, Gattu S, Holland LA, Sooter LJ. In vitro selection of a single-stranded DNA molecular recognition element against atrazine. Int J Mol Sci 2014; 15:14332-47. [PMID: 25196435 PMCID: PMC4159853 DOI: 10.3390/ijms150814332] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/11/2014] [Accepted: 08/08/2014] [Indexed: 01/11/2023] Open
Abstract
Widespread use of the chlorotriazine herbicide, atrazine, has led to serious environmental and human health consequences. Current methods of detecting atrazine contamination are neither rapid nor cost-effective. In this work, atrazine-specific single-stranded DNA (ssDNA) molecular recognition elements (MRE) were isolated. We utilized a stringent Systematic Evolution of Ligands by Exponential Enrichment (SELEX) methodology that placed the greatest emphasis on what the MRE should not bind to. After twelve rounds of SELEX, an atrazine-specific MRE with high affinity was obtained. The equilibrium dissociation constant (Kd) of the ssDNA sequence is 0.62 ± 0.21 nM. It also has significant selectivity for atrazine over atrazine metabolites and other pesticides found in environmentally similar locations and concentrations. Furthermore, we have detected environmentally relevant atrazine concentrations in river water using this MRE. The strong affinity and selectivity of the selected atrazine-specific ssDNA validated the stringent SELEX methodology and identified a MRE that will be useful for rapid atrazine detection in environmental samples.
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Affiliation(s)
- Ryan M Williams
- Department of Pharmaceutical Sciences, West Virginia University, 1 Medical Center Drive, PO Box 9530, Morgantown, WV 26506, USA.
| | - Cassandra L Crihfield
- Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, USA.
| | - Srikanth Gattu
- Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, USA.
| | - Lisa A Holland
- Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, USA.
| | - Letha J Sooter
- Department of Pharmaceutical Sciences, West Virginia University, 1 Medical Center Drive, PO Box 9530, Morgantown, WV 26506, USA.
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49
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Zhao N, Pei SN, Parekh P, Salazar E, Zu Y. Blocking interaction of viral gp120 and CD4-expressing T cells by single-stranded DNA aptamers. Int J Biochem Cell Biol 2014; 51:10-8. [PMID: 24661998 DOI: 10.1016/j.biocel.2014.03.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 02/26/2014] [Accepted: 03/13/2014] [Indexed: 01/29/2023]
Abstract
To investigate the potential clinical application of aptamers to prevention of HIV infection, single-stranded DNA (ssDNA) aptamers specific for CD4 were developed using the systematic evolution of ligands by exponential enrichment approach and next generation sequencing. In contrast to RNA-based aptamers, the developed ssDNA aptamers were stable in human serum up to 12h. Cell binding assays revealed that the aptamers specifically targeted CD4-expressing cells with high binding affinity (Kd=1.59nM), a concentration within the range required for therapeutic application. Importantly, the aptamers selectively bound CD4 on human cells and disrupted the interaction of viral gp120 to CD4 receptors, which is a prerequisite step of HIV-1 infection. Functional studies showed that the aptamer polymers significantly blocked binding of viral gp120 to CD4-expressing cells by up to 70% inhibition. These findings provide a new approach to prevent HIV-1 transmission using oligonucleotide aptamers.
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Affiliation(s)
- Nianxi Zhao
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, and Cancer Pathology Laboratory, Houston Methodist Research Institute, 6565 Fannin Street, Houston, TX 77030, USA
| | - Sung-nan Pei
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, and Cancer Pathology Laboratory, Houston Methodist Research Institute, 6565 Fannin Street, Houston, TX 77030, USA
| | - Parag Parekh
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, and Cancer Pathology Laboratory, Houston Methodist Research Institute, 6565 Fannin Street, Houston, TX 77030, USA
| | - Eric Salazar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, and Cancer Pathology Laboratory, Houston Methodist Research Institute, 6565 Fannin Street, Houston, TX 77030, USA
| | - Youli Zu
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, and Cancer Pathology Laboratory, Houston Methodist Research Institute, 6565 Fannin Street, Houston, TX 77030, USA.
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50
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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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