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Nguyen LBT, Tan EX, Leong SX, Koh CSL, Madhumita M, Phang IY, Ling XY. Harnessing Cooperative Multivalency in Thioguanine for Surface-Enhanced Raman Scattering (SERS)-Based Differentiation of Polyfunctional Analytes Differing by a Single Functional Group. Angew Chem Int Ed Engl 2024; 63:e202410815. [PMID: 38925600 DOI: 10.1002/anie.202410815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 06/16/2024] [Accepted: 06/23/2024] [Indexed: 06/28/2024]
Abstract
Small-molecule receptors are increasingly employed to probe various functional groups for (bio)chemical analysis. However, differentiation of polyfunctional analogs sharing multiple functional groups remains challenging for conventional mono- and bidentate receptors because their insufficient number of binding sites limits interactions with the least reactive yet property-determining functional group. Herein, we introduce 6-thioguanine (TG) as a supramolecular receptor for unique tridentate receptor-analyte complexation, achieving ≥97 % identification accuracy among 16 polyfunctional analogs across three classes: glycerol derivatives, disubstituted propane, and vicinal diols. Crucially, we demonstrate distinct spectral changes induced by the tridentate interaction between TG's three anchoring points and all the analyte's functional groups, even the least reactive ones. Notably, hydrogen bond (H-bond) networks formed in the TG-analyte complexes demonstrate additive effects in binding strength originating from good bond linearity, cooperativity, and resonance, thus strengthening complexation events and amplifying the differences in spectral changes induced among analytes. It also enhances spectral consistency by selectively forming a sole configuration that is stronger than the respective analyte-analyte interaction. Finally, we achieve 95.4 % accuracy for multiplex identification of a mixture consisting of multiple polyfunctional analogs. We envisage that extension to other multidentate non-covalent interactions enables the development of interference-free small molecule-based sensors for various (bio)chemical analysis applications.
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Affiliation(s)
- Lam Bang Thanh Nguyen
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, International Joint Research Laboratory for Nano Energy Composites School of Chemical and Material Engineering, Jiangnan University, Wuxi, P. R. China, 214122
- Division of Chemistry and Biological Chemistry School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Emily Xi Tan
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, International Joint Research Laboratory for Nano Energy Composites School of Chemical and Material Engineering, Jiangnan University, Wuxi, P. R. China, 214122
- Division of Chemistry and Biological Chemistry School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Shi Xuan Leong
- Division of Chemistry and Biological Chemistry School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Charlynn Sher Lin Koh
- Division of Chemistry and Biological Chemistry School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Murugan Madhumita
- Division of Chemistry and Biological Chemistry School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - In Yee Phang
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, International Joint Research Laboratory for Nano Energy Composites School of Chemical and Material Engineering, Jiangnan University, Wuxi, P. R. China, 214122
| | - Xing Yi Ling
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, International Joint Research Laboratory for Nano Energy Composites School of Chemical and Material Engineering, Jiangnan University, Wuxi, P. R. China, 214122
- Division of Chemistry and Biological Chemistry School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
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2
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Ma X, Zhang Y, Zhu L, Wu Y, Li J, Huang K, Xu W. Aptamer and Thiol Co-Regulated Color-Shifting Fluorophores via Dynamic Through-Bond/Space Conjugation for Constructing Ratiometric RNA Sensor. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2401437. [PMID: 38932671 DOI: 10.1002/smll.202401437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 06/05/2024] [Indexed: 06/28/2024]
Abstract
Fluorophores with color-shifting characteristics have attracted enormous research interest in the quantitative application of RNA sensors. It reports here a simple synthesis, luminescent properties, and co-transcription ability of de-conjugated triphenylmethane leucomalachite green (LMG). This novel clusteroluminescence fluorophore is rapidly synthesized from malachite green (MG) in reductive transcription system containing dithiothreitol, emitting fluorescence in the UV region through space conjugation. The co-transcribed MG RNA aptamer (MGA) bound to the ligand, resulting in red fluorescence from the through-bond conjugation. Given the equilibrated color-shifting fluorophores, they are rationally employed in a 3WJ-based rolling circle transcription switch, with the target-aptamer acting as an activator to achieve steric allosterism. This one-pot system allows the target to compete continuously for allosteric sites, and the activated transcription switches continue to amplify MGA forward, achieving accurate Aflatoxin 1 quantification at the picomolar level in 1 h. Due to the programmability of this RNA sensor, the design method of target-competitive aptamers is standardized, making it universally applicable.
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Affiliation(s)
- Xuan Ma
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Yangzi Zhang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Longjiao Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Yifan Wu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Jun Li
- College of Food Science, Hebei Normal University of Science and Technology, Hebei, 066004, China
| | - Kunlun Huang
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Wentao Xu
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
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3
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Osman EA, Rynes TP, Wang YL, Mruk K, McKeague M. Non-invasive single cell aptasensing in live cells and animals. Chem Sci 2024; 15:4770-4778. [PMID: 38550682 PMCID: PMC10967030 DOI: 10.1039/d3sc05735f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/18/2024] [Indexed: 04/04/2024] Open
Abstract
We report a genetically encoded aptamer biosensor platform for non-invasive measurement of drug distribution in cells and animals. We combined the high specificity of aptamer molecular recognition with the easy-to-detect properties of fluorescent proteins. We generated six encoded aptasensors, showcasing the platform versatility. The biosensors display high sensitivity and specificity for detecting their specific drug target over related analogs. We show dose dependent response of biosensor performance reaching saturating drug uptake levels in individual live cells. We designed our platform for integration into animal genomes; thus, we incorporated aptamer biosensors into zebrafish, an important model vertebrate. The biosensors enabled non-invasive drug biodistribution imaging in whole animals across different timepoints. To our knowledge, this is the first example of an aptamer biosensor-expressing transgenic vertebrate that is carried through generations. As such, our encoded platform addresses the need for non-invasive whole animal biosensing ideal for pharmacokinetic-pharmacodynamic analyses that can be expanded to other organisms and to detect diverse molecules of interest.
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Affiliation(s)
- Eiman A Osman
- Department of Chemistry, Faculty of Science, McGill University Montreal QC H3A 0B8 Canada
| | - Thomas P Rynes
- Department of Pharmacology and Toxicology, Brody School of Medicine, East Carolina University Greenville NC 27834 USA
| | - Y Lucia Wang
- Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University Montreal QC H3G 1Y6 Canada
| | - Karen Mruk
- Department of Pharmacology and Toxicology, Brody School of Medicine, East Carolina University Greenville NC 27834 USA
| | - Maureen McKeague
- Department of Chemistry, Faculty of Science, McGill University Montreal QC H3A 0B8 Canada
- Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University Montreal QC H3G 1Y6 Canada
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4
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Xu X, Lu Y, Liu D, Zhang L, Zheng L, Nie G. Highly efficient photoelectrochemical aptasensor based on CdS/CdTe QDs co-sensitized TiO 2 nanoparticles designed for thrombin detection. Mikrochim Acta 2024; 191:216. [PMID: 38517549 DOI: 10.1007/s00604-024-06279-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/22/2024] [Indexed: 03/24/2024]
Abstract
A photoelectrochemical (PEC) sensor for the sensitive detection of thrombin (TB) was established. Co-sensitized combination of TiO2 nanoparticles combined with modified cadmium sulfide and cadmium telluride quantum dots (CdS/CdTe QDs) was utilized as a photoactive material. Successful growth of CdS/CdTe quantum dots on mesoporous TiO2 films occured by successive ion-layer adsorption and reaction. This interesting formation of co-sensitive structure is conducive to enhancing the photocurrent response by improving the use rate of light energy. Additionally, the step-level structure of CdS/CdTe QDs and TiO2 NPs shows a wide range of visible light absorption, facilitating the dissociation of excitons into free electrons and holes. Consequently, the photoelectric response of the PEC analysis platform is significantly enhanced. This constructed PEC aptasensor shows good detection of thrombin with a low detection limit (0.033 pM) and a wide linear range (0.0001-100 nM) in diluted actual human serum samples. In addition, this PEC aptasensor also has the characteristics of good stability and good reproducibility, which provides a novel insight for the quantitative measurement of other similar analytes.
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Affiliation(s)
- Xuejiao Xu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, State Key Laboratory Base of Eco-Chemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, People's Republic of China
| | - Yan Lu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, State Key Laboratory Base of Eco-Chemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, People's Republic of China
| | - Dandan Liu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, State Key Laboratory Base of Eco-Chemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, People's Republic of China
| | - Lu Zhang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, State Key Laboratory Base of Eco-Chemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, People's Republic of China
| | - Lu Zheng
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, State Key Laboratory Base of Eco-Chemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, People's Republic of China
| | - Guangming Nie
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, State Key Laboratory Base of Eco-Chemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, People's Republic of China.
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5
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Yang K, Alkhamis O, Canoura J, Bryant A, Gong EM, Barbu M, Taylor S, Nikic D, Banerjee S, Xiao Y, Stojanovic MN, Landry DW. Exploring the Landscape of Aptamers: From Cross-Reactive to Selective to Specific, High-Affinity Receptors for Cocaine. JACS AU 2024; 4:760-770. [PMID: 38425914 PMCID: PMC10900216 DOI: 10.1021/jacsau.3c00781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 03/02/2024]
Abstract
We reported over 20 years ago MNS-4.1, the first DNA aptamer with a micromolar affinity for cocaine. MNS-4.1 is based on a structural motif that is very common in any random pool of oligonucleotides, and it is actually a nonspecific hydrophobic receptor with wide cross-reactivity with alkaloids and steroids. Despite such weaknesses preventing broad applications, this aptamer became widely used in proof-of-concept demonstrations of new formats of biosensors. We now report a series of progressively improved DNA aptamers recognizing cocaine, with the final optimized receptors having low nanomolar affinity and over a thousand-fold selectivity over the initial cross-reactants. In the process of optimization, we tested different methods to eliminate cross-reactivities and improve affinity, eventually achieving properties that are comparable to those of the reported monoclonal antibody candidates for the therapy of overdose. Multiple aptamers that we now report share structural motifs with the previously reported receptor for serotonin. Further mutagenesis studies revealed a palindromic, highly adaptable, broadly cross-reactive hydrophobic motif that could be rebuilt through mutagenesis, expansion of linker regions, and selections into receptors with exceptional affinities and varying specificities.
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Affiliation(s)
- Kyungae Yang
- Department
of Medicine, Columbia University Irving
Medical Center, New York, New York 10032, United States
| | - Obtin Alkhamis
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Juan Canoura
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Alexandra Bryant
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Edward M. Gong
- Department
of Medicine, Columbia University Irving
Medical Center, New York, New York 10032, United States
| | - Mihaela Barbu
- Department
of Medicine, Columbia University Irving
Medical Center, New York, New York 10032, United States
| | - Steven Taylor
- Department
of Medicine, Columbia University Irving
Medical Center, New York, New York 10032, United States
| | - Dragan Nikic
- Department
of Medicine, Columbia University Irving
Medical Center, New York, New York 10032, United States
| | - Saswata Banerjee
- Department
of Medicine, Columbia University Irving
Medical Center, New York, New York 10032, United States
| | - Yi Xiao
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Milan N. Stojanovic
- Department
of Medicine, Columbia University Irving
Medical Center, New York, New York 10032, United States
- Departments
of Biomedical Engineering and Systems Biology, Columbia University, New York, New York 10032, United States
| | - Donald W. Landry
- Department
of Medicine, Columbia University Irving
Medical Center, New York, New York 10032, United States
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6
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Alkhamis O, Canoura J, Wu Y, Emmons NA, Wang Y, Honeywell KM, Plaxco KW, Kippin TE, Xiao Y. High-Affinity Aptamers for In Vitro and In Vivo Cocaine Sensing. J Am Chem Soc 2024; 146:3230-3240. [PMID: 38277259 DOI: 10.1021/jacs.3c11350] [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] [Indexed: 01/28/2024]
Abstract
The ability to quantify cocaine in biological fluids is crucial for both the diagnosis of intoxication and overdose in the clinic as well as investigation of the drug's pharmacological and toxicological effects in the laboratory. To this end, we have performed high-stringency in vitro selection to generate DNA aptamers that bind cocaine with nanomolar affinity and clinically relevant specificity, thus representing a dramatic improvement over the current-generation, micromolar-affinity, low-specificity cocaine aptamers. Using these novel aptamers, we then developed two sensors for cocaine detection. The first, an in vitro fluorescent sensor, successfully detects cocaine at clinically relevant levels in 50% human serum without responding significantly to other drugs of abuse, endogenous substances, or a diverse range of therapeutic agents. The second, an electrochemical aptamer-based sensor, supports the real-time, seconds-resolved measurement of cocaine concentrations in vivo in the circulation of live animals. We believe the aptamers and sensors developed here could prove valuable for both point-of-care and on-site clinical cocaine detection as well as fundamental studies of cocaine neuropharmacology.
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Affiliation(s)
- Obtin Alkhamis
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27607, United States
| | - Juan Canoura
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27607, United States
| | - Yuyang Wu
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Nicole A Emmons
- Department of Psychological and Brain Sciences, University of California, Santa Barbara, California 93106, United States
| | - Yuting Wang
- Department of Psychological and Brain Sciences, University of California, Santa Barbara, California 93106, United States
| | - Kevin M Honeywell
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Kevin W Plaxco
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Tod E Kippin
- Department of Psychological and Brain Sciences, University of California, Santa Barbara, California 93106, United States
| | - Yi Xiao
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27607, United States
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7
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Shi L, Jin Y, Liu J. Intramolecular aptamer switches. Analyst 2024; 149:745-750. [PMID: 38193253 DOI: 10.1039/d3an02022c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Aptamer switches as effective biosensing tools have become a focal point of research in engineered aptasensors. Intramolecular aptamer switches are more versatile, affordable, and simpler than classical "open-close" and strand displacement-based aptamer switches. Recently, many new aptamers with an overall hairpin structure have been reported. In this study, intramolecular aptamer switches were developed by adding new base pairs to the end of aptamers. The additional nucleotides can pair with the internal domains of the aptamer, causing a change in its conformation from the original secondary structure without a target. When a target binds to an aptamer, a marked change in the structure of the aptamer is expected. As models for testing this intramolecular aptamer switch idea, aptamers of oxytetracycline (OTC), 17β-estradiol (E2), and adenosine were employed. When the additional base pairs are too long, binding the target to the aptamer becomes more challenging. This research offers valuable insights into the development of intramolecular aptamer switches and their potential applications in biosensor design.
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Affiliation(s)
- Lu Shi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada.
| | - Yan Jin
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada.
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8
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Canoura J, Liu Y, Alkhamis O, Xiao Y. Aptamer-Based Fentanyl Detection in Biological Fluids. Anal Chem 2023; 95:18258-18267. [PMID: 38033203 DOI: 10.1021/acs.analchem.3c04104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
Fentanyl is a widely abused analgesic and anesthetic drug with a narrow therapeutic window that creates easy opportunities for overdose and death. Rapid, accurate, and sensitive fentanyl detection in biosamples is crucial for therapeutic drug monitoring and overdose diagnosis. Unfortunately, current methods are limited to either sophisticated laboratory-based tests or antibody-based immunoassays, which are prone to false results and are mainly used with urine samples. Here, we have utilized library-immobilized SELEX to isolate new aptamers─nucleic acid-based bioreceptors that are well-suited for biosensing─that can specifically bind fentanyl under physiological conditions. We isolated multiple aptamers with nanomolar affinity and excellent specificity against dozens of interferents and incorporated one of these into an electrochemical aptamer-based sensor that can rapidly detect fentanyl at clinically relevant concentrations in 50% diluted serum, urine, and saliva. Given the excellent performance of these sensors, we believe that they could serve as the basis for point-of-care devices for monitoring fentanyl during medical procedures and determining fentanyl overdose.
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Affiliation(s)
- Juan Canoura
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina , 27607, United States
| | - Yingzhu Liu
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina , 27607, United States
| | - Obtin Alkhamis
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina , 27607, United States
| | - Yi Xiao
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina , 27607, United States
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