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Alkhamis O, Canoura J, Wang L, Xiao Y. Nuclease-assisted selection of slow-off rate aptamers. SCIENCE ADVANCES 2024; 10:eadl3426. [PMID: 38865469 PMCID: PMC11168469 DOI: 10.1126/sciadv.adl3426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 05/09/2024] [Indexed: 06/14/2024]
Abstract
Conventional directed evolution methods offer the ability to select bioreceptors with high binding affinity for a specific target in terms of thermodynamic properties. However, there is a lack of analogous approaches for kinetic selection, which could yield affinity reagents that exhibit slow off-rates and thus remain tightly bound to targets for extended periods. Here, we describe an in vitro directed evolution methodology that uses the nuclease flap endonuclease 1 to achieve the efficient discovery of aptamers that have slow dissociation rates. Our nuclease-assisted selection strategy can yield specific aptamers for both small molecules and proteins with off-rates that are an order of magnitude slower relative to those obtained with conventional selection methods while still retaining excellent overall target affinity in terms of thermodynamics. This new methodology provides a generalizable approach for generating slow off-rate aptamers for diverse targets, which could, in turn, prove valuable for applications including molecular devices, bioimaging, and therapy.
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Affiliation(s)
- Obtin Alkhamis
- Department of Chemistry, North Carolina State University, Raleigh, NC 27607, USA
| | - Juan Canoura
- Department of Chemistry, North Carolina State University, Raleigh, NC 27607, USA
| | - Linlin Wang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27607, USA
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2
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Olivan LA, Hand K, White RJ. Utilization of Spontaneous Alkyne-Gold Self-Assembly Chemistry as an Alternative Method for Fabricating Electrochemical Aptamer-Based Sensors. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:12117-12123. [PMID: 38826127 DOI: 10.1021/acs.langmuir.4c00972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Electrochemical aptamer-based (E-AB) sensors are a promising class of biosensors which use structure-switching redox-labeled oligonucleotides (aptamers) codeposited with passivating alkanethiol monolayers on electrode surfaces to specifically bind and detect target analytes. Signaling in E-AB sensors is an outcome of aptamer conformational changes upon target binding, with the sequence of the aptamer imparting specificity toward the analyte of interest. The change in conformation translates to a change in electron transfer between the redox label attached to the aptamer and the underlying electrode and is related to analyte concentration, allowing specific electrochemical detection of nonelectroactive analytes. E-AB sensor measurements are reagentless with time resolutions of seconds or less and may be miniaturized into the submicron range. Traditionally these sensors are fabricated using thiol-on-gold chemistry. Here we present an alternate immobilization chemistry, gold-alkyne binding, which results in an increase in sensor lifetimes under ideal conditions by up to ∼100%. We find that gold-alkyne binding is spontaneous and supports efficient E-AB sensor signaling with analytical performance characteristics similar to those of thiol generated monolayers. The surface modification differs from gold-thiol binding only in the time and aptamer concentration required to achieve similar aptamer surface coverages. In addition, alkynated aptamers differ from their thiolated analogues only by their chemical handle for surface attachment, so any existing aptamers can be easily adapted to utilize this attachment strategy.
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Affiliation(s)
- Lars Alexander Olivan
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0171, United States
| | - Kaitlyn Hand
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0171, United States
| | - Ryan J White
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0171, United States
- Department of Electrical and Computer Engineering, University of Cincinnati, Cincinnati, Ohio 45221, United States
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3
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Zhao Y, Gan Y, Chen J, Zheng H, Chang Y, Lin C. Recent reports on the sensing strategy and the On-site detection of illegal drugs. RSC Adv 2024; 14:6917-6929. [PMID: 38410368 PMCID: PMC10895702 DOI: 10.1039/d3ra06931a] [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: 10/11/2023] [Accepted: 12/13/2023] [Indexed: 02/28/2024] Open
Abstract
In this review, works on the on-site detection of illegal drugs in recent years are summarised and discussed, most of which were published within the past five years. The detection methods are categorised as colourimetric, fluorescence, Raman spectrometry, ion mobility spectrometry, electrochemistry, and mass spectrometry. Also, strategies that are possibly suitable for on-site detection and the actual instrumentation to be used in the field are listed.
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Affiliation(s)
- Yang Zhao
- Key Laboratory of Drug Monitoring and Control, Drug Intelligence and Forensic Center, Ministry of Public Security P.R.C. No. 18 Dongbeiwang West Road, Haidian District 100193 Beijing China
- Institute of Forensic Science of the Ministry of Public Security No. 17 Muxidi Nanli, West City District 100038 Beijing China
| | - Yumeng Gan
- Institute for Biomimetics and Soft Matter, Fujian Provincial Key Laboratory for Soft Functional Materials Research, College of Physical Science and Technology, Xiamen University 9 Zengcuoan West Road 361005 Xiamen China
- State Key Laboratory of Physical Chemistry of Solid Surface Xiamen China
| | - Jun Chen
- Key Laboratory of Drug Monitoring and Control, Drug Intelligence and Forensic Center, Ministry of Public Security P.R.C. No. 18 Dongbeiwang West Road, Haidian District 100193 Beijing China
| | - Hui Zheng
- Key Laboratory of Drug Monitoring and Control, Drug Intelligence and Forensic Center, Ministry of Public Security P.R.C. No. 18 Dongbeiwang West Road, Haidian District 100193 Beijing China
| | - Ying Chang
- Institute of Forensic Science of the Ministry of Public Security No. 17 Muxidi Nanli, West City District 100038 Beijing China
| | - Changxu Lin
- Institute for Biomimetics and Soft Matter, Fujian Provincial Key Laboratory for Soft Functional Materials Research, College of Physical Science and Technology, Xiamen University 9 Zengcuoan West Road 361005 Xiamen China
- State Key Laboratory of Physical Chemistry of Solid Surface Xiamen China
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4
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Davydova AS, Vorobyeva MA. Aptasensors Based on Non-Enzymatic Peroxidase Mimics: Current Progress and Challenges. BIOSENSORS 2023; 14:1. [PMID: 38275302 PMCID: PMC10813519 DOI: 10.3390/bios14010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/12/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024]
Abstract
Immunoassays based on antibodies as recognizing elements and enzymes as signal-generating modules are extensively used now in clinical lab diagnostics, food, and environmental analyses. However, the application of natural enzymes and antibodies has some drawbacks, such as relatively high manufacturing costs, thermal instability, and lot-to-lot variations that lower the reproducibility of results. Oligonucleotide aptamers are able to specifically bind their targets with high affinity and selectivity, so they represent a prospective alternative to protein antibodies for analyte recognition. Their main advantages include thermal stability and long shelf life, cost-efficient chemical synthesis, and negligible batch-to-batch variations. At the same time, a wide variety of non-protein peroxidase mimics are now available that show strong potential to replace protein enzymes. Here, we review and analyze non-protein biosensors that represent a nexus of these two concepts: aptamer-based sensors (aptasensors) with optical detection (colorimetric, luminescent, or fluorescent) based on different peroxidase mimics, such as DNAzymes, nanoparticles, or metal-organic frameworks.
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Affiliation(s)
- Anna S. Davydova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Akad. Lavrentiev, 8, 630090 Novosibirsk, Russia;
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Li J, Chen M, Ke S, Tian J, Yu H, Liu X, Yu BY. Generation of a high-affinity DNA aptamer for on-site screening of toxic aristolochic acid I in herbal medicines and botanical products. Anal Chim Acta 2023; 1264:341302. [PMID: 37230722 DOI: 10.1016/j.aca.2023.341302] [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: 02/26/2023] [Revised: 04/12/2023] [Accepted: 04/28/2023] [Indexed: 05/27/2023]
Abstract
Aristolochic Acid I (AAI) is an environmental and foodborne toxin found in the Aristolochia and Asarum species of plants that are widespread all over the world. Therefore, there is an urgent need to develop a sensitive and specific biosensor for identifying AAI. Aptamers as a powerful biorecognition element provide the most viable options for solving this problem. In this study, we used library-immobilized SELEX to isolate an AAI-specific aptamer with a KD value of 86 ± 13 nM. To verify the practicability of the selected aptamer, a label-free colorimetric aptasensor was designed. This aptasensor exhibited a low detection limit of 225 nM. Besides, it had been further applied for the determination of AAI in real samples and the recoveries ranged from 97.9% to 102.4%. In the future, AAI aptamer will provide a promising tool for safety evaluation in various fields of agriculture, food, and medication.
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Affiliation(s)
- Jiwei Li
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Research Center for Traceability and Standardization of TCMs, Cellular and Molecular Biology Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Meiqi Chen
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Research Center for Traceability and Standardization of TCMs, Cellular and Molecular Biology Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Sisi Ke
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Research Center for Traceability and Standardization of TCMs, Cellular and Molecular Biology Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Jiangwei Tian
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Research Center for Traceability and Standardization of TCMs, Cellular and Molecular Biology Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Haixiang Yu
- Department of Surgery, Duke University Medical Center, Durham, NC, 27710, USA.
| | - Xiufeng Liu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Research Center for Traceability and Standardization of TCMs, Cellular and Molecular Biology Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, PR China.
| | - Bo-Yang Yu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Research Center for Traceability and Standardization of TCMs, Cellular and Molecular Biology Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, PR China
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6
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Ye H, Wang M, Yu X, Ma P, Zhu P, Zhong J, He K, Guo Y. Molecular Docking Insight into the Label-Free Fluorescence Aptasensor for Ochratoxin A Detection. Molecules 2023; 28:4841. [PMID: 37375396 DOI: 10.3390/molecules28124841] [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: 05/08/2023] [Revised: 06/07/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Ochratoxin A (OTA) is the most common mycotoxin and can be found in wheat, corn and other grain products. As OTA pollution in these grain products is gaining prominence as a global issue, the demand to develop OTA detection technology has attracted increasing attention. Recently, a variety of label-free fluorescence biosensors based on aptamer have been established. However, the binding mechanisms of some aptasensors are still unclear. Herein, a label-free fluorescent aptasensor employing Thioflavin T (ThT) as donor for OTA detection was constructed based on the G-quadruplex aptamer of the OTA aptamer itself. The key binding region of aptamer was revealed by using molecular docking technology. In the absence of the OTA target, ThT fluorescent dye binds with the OTA aptamer to form an aptamer/ThT complex, and results in the fluorescence intensity being obviously enhanced. In the presence of OTA, the OTA aptamer binds to OTA because of its high affinity and specificity to form an aptamer/OTA complex, and the ThT fluorescent dye is released from the OTA aptamer into the solution. Therefore, the fluorescence intensity is significantly decreased. Molecular docking results revealed that OTA is binding to the pocket-like structure and surrounded by the A29-T3 base pair and C4, T30, G6 and G7 of the aptamer. Meanwhile, this aptasensor shows good selectivity, sensitivity and an excellent recovery rate of the wheat flour spiked experiment.
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Affiliation(s)
- Hua Ye
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Mengyuan Wang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Xi Yu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Pengfei Ma
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Ping Zhu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Jianjun Zhong
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Kuo He
- College of Agriculture and Forestry Science and Technology, Hebei North University, Zhangjiakou 075000, China
| | - Yuanxin Guo
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
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Yu H, Zhu J, Shen G, Deng Y, Geng X, Wang L. Improving aptamer performance: key factors and strategies. Mikrochim Acta 2023; 190:255. [PMID: 37300603 DOI: 10.1007/s00604-023-05836-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/16/2023] [Indexed: 06/12/2023]
Abstract
Aptamers are functional single-stranded oligonucleotide fragments isolated from randomized libraries by Systematic Evolution of Ligands by Exponential Enrichment (SELEX), exhibiting excellent affinity and specificity toward targets. Compared with traditional antibody reagents, aptamers display many desirable properties, such as low variation and high flexibility, and they are suitable for artificial and large-scale synthesis. These advantages make aptamers have a broad application potential ranging from biosensors, bioimaging to therapeutics and other areas of application. However, the overall performance of aptamer pre-selected by SELEX screening is far from being satisfactory. To improve aptamer performance and applicability, various post-SELEX optimization methods have been developed in the last decade. In this review, we first discuss the key factors that influence the performance or properties of aptamers, and then we summarize the key strategies of post-SELEX optimization which have been successfully used to improve aptamer performance, such as truncation, extension, mutagenesis and modification, splitting, and multivalent integration. This review shall provide a comprehensive summary and discussion of post-SELEX optimization methods developed in recent years. Moreover, by discussing the mechanism of each approach, we highlight the importance of choosing the proper method to perform post-SELEX optimization.
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Affiliation(s)
- Hong Yu
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Jiangxiong Zhu
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Guoqing Shen
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Yun Deng
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Xueqing Geng
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Lumei Wang
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China.
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China.
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China.
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Azzouz A, Kumar V, Hejji L, Kim KH. Advancements in nanomaterial-based aptasensors for the detection of emerging organic pollutants in environmental and biological samples. Biotechnol Adv 2023; 66:108156. [PMID: 37084799 DOI: 10.1016/j.biotechadv.2023.108156] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/16/2023] [Accepted: 04/15/2023] [Indexed: 04/23/2023]
Abstract
The combination of nanomaterials (NMs) and aptamers into aptasensors enables highly specific and sensitive detection of diverse pollutants. The great potential of aptasensors is recognized for the detection of diverse emerging organic pollutants (EOPs) in different environmental and biological matrices. In addition to high sensitivity and selectivity, NM-based aptasensors have many other advantages such as portability, miniaturization, facile use, and affordability. This work showcases the recent advances achieved in the design and fabrication of NM-based aptasensors for monitoring EOPs (e.g., hormones, phenolic contaminants, pesticides, and pharmaceuticals). On the basis of their sensing mechanisms, the covered aptasensing systems are classified as electrochemical, colorimetric, PEC, fluorescence, SERS, and ECL. Special attention has been paid to the fabrication processes, analytical achievements, and sensing mechanisms of NM-based aptasensors. Further, the practical utility of aptasensing approaches has also been assessed based on their basic performance metrics (e.g., detection limits, sensing ranges, and response times).
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Affiliation(s)
- Abdelmonaim Azzouz
- Department of Chemistry, Faculty of Science, University of Abdelmalek Essaadi, B.P. 2121, M'Hannech II, 93002 Tetouan, Morocco
| | - Vanish Kumar
- National Agri-Food Biotechnology Institute (NABI), Sector 81, SAS Nagar, Mohali, Punjab 140306, India
| | - Lamia Hejji
- Department of Chemistry, Faculty of Science, University of Abdelmalek Essaadi, B.P. 2121, M'Hannech II, 93002 Tetouan, Morocco; Department of Chemical, Environmental, and Materials Engineering, Higher Polytechnic School of Linares, University of Jaén, Campus Científico-Tecnológico, Cinturón Sur s/n, 23700 Linares, Jaén, Spain
| | - Ki-Hyun Kim
- Department of Civil and Environmental Engineering, Hanyang University, 222 Wangsimni-Ro, Seoul 04763, South Korea.
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Liu Q, Liu Y, Wan Q, Lu Q, Liu J, Ren Y, Tang J, Su Q, Luo Y. Label-Free, Reusable, Equipment-Free, and Visual Detection of Hydrogen Sulfide Using a Colorimetric and Fluorescent Dual-Mode Sensing Platform. Anal Chem 2023; 95:5920-5926. [PMID: 36989391 DOI: 10.1021/acs.analchem.2c05364] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
In this work, we have found for the first time that the fluorescence of rhodamine B (RhB) would be dramatically reduced after it bound to hemin/G-quadruplex and reacted with •OH. Based on this finding, we have designed a colorimetric and fluorescent dual-mode sensing platform for visual detection of hydrogen sulfide (H2S). The constructed sensor is based on the formation of dsDNA and the G-quadruplex structure by the cytosine-Ag+-cytosine mismatch, causing H2O2-mediated catalysis to oxidize ABTS or RhB to induce a colorimetric or fluorescent change. In the presence of H2S, the solution color for colorimetric and fluorescent assays would change from dark green to pink and from green (fluorescence off) to bright yellow (fluorescence on), respectively. This dual-mode assay showed high selectivity toward H2S over other interference materials with a low measurable detection limit value (below than 2.5 μM), and it has been successfully applied to H2S visual detection in real samples. Moreover, the dual-mode sensing strategy presented an excellent reutilization character both in colorimetric and fluorescent assays. This method was employed as a label-free, simple, fast, and equipment-free platform for H2S detection with high selectivity and reusability. This work realized naked-eye detection both in colorimetric and fluorescent analysis at a lower concentration of H2S, demonstrating a promising strategy for on-site visual detection of H2S.
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Affiliation(s)
- Qiao Liu
- Department of Pharmacology, North Sichuan Medical College, Nanchong, Sichuan 637100, P. R. China
| | - Yue Liu
- Department of Pharmacology, North Sichuan Medical College, Nanchong, Sichuan 637100, P. R. China
| | - Qing Wan
- Department of Pharmacology, North Sichuan Medical College, Nanchong, Sichuan 637100, P. R. China
| | - Qinrui Lu
- Department of Pharmacology, North Sichuan Medical College, Nanchong, Sichuan 637100, P. R. China
| | - Jun Liu
- Department of Pharmacology, North Sichuan Medical College, Nanchong, Sichuan 637100, P. R. China
| | - Yonggang Ren
- Department of Basic Medical Sciences, North Sichuan Medical College, Nanchong, Sichuan 637100, P. R. China
| | - Jiancai Tang
- Department of Basic Medical Sciences, North Sichuan Medical College, Nanchong, Sichuan 637100, P. R. China
| | - Qiang Su
- Department of Pharmacy, Nanchong Central Hospital, The Second Clinical Medical College, North Sichuan Medical College, Nanchong, Sichuan 637000, P. R. China
- Nanchong Key Laboratory of Individualized Drug Therapy, Nanchong, Sichuan 637000, P. R. China
| | - Yingping Luo
- Department of Pharmacology, North Sichuan Medical College, Nanchong, Sichuan 637100, P. R. China
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Cao Q, Jiang D, Zheng L, Xu F, Shiigi H, Shan X, Wang W, Chen Z. Dual-binding domain electrochemiluminescence biosensing platform with self-checking function for sensitive detection of synthetic cathinone in e-cigarettes. Biosens Bioelectron 2023; 224:114963. [PMID: 36603282 DOI: 10.1016/j.bios.2022.114963] [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: 10/12/2022] [Revised: 11/25/2022] [Accepted: 11/27/2022] [Indexed: 11/30/2022]
Abstract
Current single signal electrochemiluminescence (ECL) sensors are susceptible to false positive or false negative phenomena due to experimental conditions. Therefore, sensors with "self-checking" function are attracting democratic attention. In quick succession, a highly sensitive single-cathode dual ECL signal aptasensor with self-checking function to improve the shortcomings mentioned above was designed. This aptasensor used In-based metal-organic framework (MIL-68) as load and stabilizer to effectively attenuate the aggregation-induced quenching (ACQ) effect of porphyrin derivatives (Sn-TCPP) while improve ECL stability. The introduction of cooperative-binding split-aptamers" (CBSAs) aptamers increased the specificity of the aptasensor and its unique double-binding domains detection accelerated the detection efficiency. When analyzing 3,4-methylenedioxypyrovalerone (MDPV), we could calculate two concentrations based on the strength of ECL 1 and ECL 2. If the concentrations are the same, the result would be obtained; if not, it should be retested. Depending on the above operation, the results achieve self-check. It was found that the designed aptasensor could quantify the concentration of MDPV between 1.0 × 10-12 g/L and 1.0 × 10-6 g/L with the limit of detection (LOD) of 1.4 × 10-13 g/L and 2.0 × 10-13 g/L, respectively (3 σ/slope). This study not only improves the detection technology of MDPV, but also explores the dual-signal detection of porphyrin for the first time and enriches the definition of self-checking sensor.
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Affiliation(s)
- Qianying Cao
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, School of Petrochemical Engineering, Changzhou University, Changzhou, 213164, China
| | - Ding Jiang
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, School of Petrochemical Engineering, Changzhou University, Changzhou, 213164, China; Advanced Catalysis and Green Manufacturing Collaborative Innovation Center, Changzhou University, Changzhou, 213164, China
| | - Lingli Zheng
- Changzhou Institute of Mechatronic Technology, Changzhou, 213164, China
| | - Fangmin Xu
- Institute of Forensic Science, Public Security Bureau of Jiangyin, Wuxi, 214431, China
| | - Hiroshi Shiigi
- Osaka Prefecture University, Department of Applied Chemistry, Naka Ku, 1-2 Gakuen, Sakai, Osaka, 5998570, Japan
| | - Xueling Shan
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, School of Petrochemical Engineering, Changzhou University, Changzhou, 213164, China; Advanced Catalysis and Green Manufacturing Collaborative Innovation Center, Changzhou University, Changzhou, 213164, China
| | - Wenchang Wang
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, School of Petrochemical Engineering, Changzhou University, Changzhou, 213164, China; Advanced Catalysis and Green Manufacturing Collaborative Innovation Center, Changzhou University, Changzhou, 213164, China
| | - Zhidong Chen
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, School of Petrochemical Engineering, Changzhou University, Changzhou, 213164, China; Advanced Catalysis and Green Manufacturing Collaborative Innovation Center, Changzhou University, Changzhou, 213164, China.
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11
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Cai S, Chen X, Chen H, Zhang Y, Wang X, Zhou N. A fluorescent aptasensor for ATP based on functional DNAzyme/walker and terminal deoxynucleotidyl transferase-assisted formation of DNA-AgNCs. Analyst 2023; 148:799-805. [PMID: 36692002 DOI: 10.1039/d2an02006h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The development of sensitive adenosine triphosphate (ATP) sensors is imperative due to the tight relationship between the physiological conditions and ATP levels in vivo. Herein, a fluorescent aptasensor for ATP is presented, which adopts a strategy that combines a split aptamer and a DNAzyme/walker with terminal deoxynucleotidyl transferase (TDT)-assisted formation of DNA-AgNCs to realize fluorescence detection of ATP. A multifunctional oligonucleotide sequence is rationally designed, which integrates a split aptamer, a DNAzyme and a DNA walker. Both multifunctional oligonucleotide and its substrate strand are connected to the surface of Fe3O4@Au nanoparticles via Au-S bonds. The existence of ATP can induce the formation of the complete aptamer, and then activate the DNAzyme to circularly cleave the substrate strand, leaving 2',3'-cyclophosphate at the 3'end of the strand. This blocks the polymerization of dCTP to form poly(C) even in the presence of TDT and dCTP, due to the lack of free 3'-OH. In contrast, when ATP is absent, the DNAzyme/walker cannot work and then TDT catalyzes the formation of poly(C) at the free 3'-OH of the substrate strand, which is subsequently utilized as the template to prepare DNA-AgNCs. The fluorescence response derived from AgNCs thus reflects the ATP concentration. Under the optimum conditions, the aptasensor shows a linear response range from 5 nM to 10 000 nM, with a detection limit of 0.27 nM. The level of ATP in human serum can be effectively measured by the aptasensor with good recovery, indicating its application potential in medical samples.
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Affiliation(s)
- Shixin Cai
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
| | - Xin Chen
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
| | - Haohan Chen
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
| | - Yuting Zhang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
| | - Xiaoli Wang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
| | - Nandi Zhou
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
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12
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Affiliation(s)
- David Love
- United States Drug Enforcement Administration, Special Testing and Research Laboratory, USA
| | - Nicole S. Jones
- RTI International, Applied Justice Research Division, Center for Forensic Sciences, 3040 E. Cornwallis Road, Research Triangle Park, NC, 22709-2194, USA,70113th Street, N.W., Suite 750, Washington, DC, 20005-3967, USA,Corresponding author. RTI International, Applied Justice Research Division, Center for Forensic Sciences, 3040 E. Cornwallis Road, Research Triangle Park, NC, 22709-2194, USA.
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13
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R O'Steen M, M Kolpashchikov D. A self-assembling split aptamer multiplex assay for SARS-COVID19 and miniaturization of a malachite green DNA-based aptamer. SENSORS AND ACTUATORS REPORTS 2022; 4:100125. [PMID: 36373144 PMCID: PMC9635949 DOI: 10.1016/j.snr.2022.100125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/30/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Multiplex assays often rely on expensive sensors incorporating covalently linked fluorescent dyes. Herein, we developed a self-assembling aptamer-based multiplex assay. This multiplex approach utilizes a previously established split aptamer sensor in conjugation with a novel split aptamer sensor based upon a malachite green DNA aptamer. This system was capable of simultaneous fluorescent detection of two SARS COVID-19-related sequences in one sample with individual sensors that possesses a limit of detection (LOD) in the low nM range. Optimization of the Split Malachite Green (SMG) sensor yielded a minimized aptamer construct, Mini-MG, capable of inducing fluorescence of malachite green in both a DNA hairpin and sensor format.
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Affiliation(s)
- Martin R O'Steen
- Chemistry Department, University of Central Florida, Orlando, FL, USA
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, Orlando, FL, USA
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
- National Center for Forensic Science, University of Central Florida, Orlando, FL, USA
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14
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Are aptamer-based biosensing approaches a good choice for female fertility monitoring? A comprehensive review. Biosens Bioelectron 2022; 220:114881. [DOI: 10.1016/j.bios.2022.114881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/23/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022]
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15
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Qi S, Dong X, Sun Y, Zhang Y, Duan N, Wang Z. Split aptamer remodeling-initiated target-self-service 3D-DNA walker for ultrasensitive detection of 17β-estradiol. JOURNAL OF HAZARDOUS MATERIALS 2022; 439:129590. [PMID: 35872451 DOI: 10.1016/j.jhazmat.2022.129590] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/29/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
DNA walker machines, as one of the dynamic DNA nanodevices, have attracted extensive interest in the field of analysis due to their inherent superiority. Herein, we reported a split aptamer remodeling-initiated target-self-service 3D-DNA walker for ultrasensitive, specific, and high-signal-background ratio determination of 17β-estradiol (E2) in food samples. Two split probes (STWS-a and STWS-b) were rationally designed that can undergo structural reassembled to serve as walking strands (STWS) under the induction of the target. Meanwhile, an intact E6-DNAzyme region was formed and activated at the tail of STWS. The activated E6-DNAzyme then continuously drives the 3D-DNA walker for signal amplification and specific detection of E2. Under optimal conditions, the proposed DNA walker-based biosensor exhibited excellent linearity in the range of 1 pM to 50 nM with a low limit of detection (LOD) of 0.28 pM, and good precision (2.7%) for 11 replicate determinations of 1 nM of E2. Furthermore, the developed DNA walker-based biosensor achieved excellent sensitive analysis of E2 in the complex food matrix with recoveries of 95.6-106.5%. This newly proposed split aptamer-based strategy has the advantages of ultrasensitive, high signal-to-background ratio, and high stability. Noteworthy, the successful operation of the DNA walker initiated by the split aptamer expands the principles of DNA walker design and provides a universal signal amplification platform for trace analysis.
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Affiliation(s)
- Shuo Qi
- State Key Laboratory of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiaoze Dong
- State Key Laboratory of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yuhan Sun
- State Key Laboratory of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yin Zhang
- Key Laboratory of Meat Processing of Sichuan, Chengdu University, Chengdu 610106, China
| | - Nuo Duan
- State Key Laboratory of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Meat Processing of Sichuan, Chengdu University, Chengdu 610106, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China; Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi 214122, China.
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16
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Hernández-Contreras J, Parra M, Gil S, Costero AM, Arroyo P, Sancenón F, Martínez-Máñez R, Sáez JA, Gaviña P. Colorimetric and fluorescent detection of synthetic cathinones in oral fluid with meso-aryl BODIPYs and Cu(ii). RSC Adv 2022; 12:28580-28585. [PMID: 36330338 PMCID: PMC9583296 DOI: 10.1039/d2ra05188e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/03/2022] [Indexed: 11/05/2022] Open
Abstract
Synthetic cathinones are a class of new psychoactive substances whose consumption has increased a lot and is widespread throughout the world. Thus, there is currently a need for rapid and simple detection of these drugs. In particular, detection of synthetic cathinones in oral fluid in drivers can be of great importance in preventing traffic accidents. Herein, we report two probes, based on BODIPY derivatives combined with Cu(ii), which are able to detect these drugs both in water and in oral fluid, by changes in color and fluorescence. The determined limits of detection for ephedrone (as a model drug) are lower than the usual concentrations in saliva after intake of this type of drug. The sensing mechanism seems to be related to the cathinone induced reduction of Cu(ii) to Cu(i) with concomitants changes in the BODIPY structure.
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Affiliation(s)
- Jordi Hernández-Contreras
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València Doctor Moliner 50, Burjassot Valencia 46100 Spain
| | - Margarita Parra
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València Doctor Moliner 50, Burjassot Valencia 46100 Spain .,Departamento de Química Orgánica, Universitat de València Doctor Moliner 50, Burjassot Valencia 46100 Spain.,CIBER de Bioingeniería, Biometariales y Nanomedicina (CIBER-BBN) Spain
| | - Salvador Gil
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València Doctor Moliner 50, Burjassot Valencia 46100 Spain .,Departamento de Química Orgánica, Universitat de València Doctor Moliner 50, Burjassot Valencia 46100 Spain.,CIBER de Bioingeniería, Biometariales y Nanomedicina (CIBER-BBN) Spain
| | - Ana M Costero
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València Doctor Moliner 50, Burjassot Valencia 46100 Spain .,Departamento de Química Orgánica, Universitat de València Doctor Moliner 50, Burjassot Valencia 46100 Spain.,CIBER de Bioingeniería, Biometariales y Nanomedicina (CIBER-BBN) Spain
| | - Pau Arroyo
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València Doctor Moliner 50, Burjassot Valencia 46100 Spain .,Departamento de Química Orgánica, Universitat de València Doctor Moliner 50, Burjassot Valencia 46100 Spain
| | - Félix Sancenón
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València Doctor Moliner 50, Burjassot Valencia 46100 Spain .,CIBER de Bioingeniería, Biometariales y Nanomedicina (CIBER-BBN) Spain.,Departamento de Química, Universitat Politècnica de València Camino de Vera s/n Valencia 46022 Spain
| | - Ramón Martínez-Máñez
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València Doctor Moliner 50, Burjassot Valencia 46100 Spain .,CIBER de Bioingeniería, Biometariales y Nanomedicina (CIBER-BBN) Spain.,Departamento de Química, Universitat Politècnica de València Camino de Vera s/n Valencia 46022 Spain
| | - José A Sáez
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València Doctor Moliner 50, Burjassot Valencia 46100 Spain .,Departamento de Química Orgánica, Universitat de València Doctor Moliner 50, Burjassot Valencia 46100 Spain
| | - Pablo Gaviña
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València Doctor Moliner 50, Burjassot Valencia 46100 Spain .,Departamento de Química Orgánica, Universitat de València Doctor Moliner 50, Burjassot Valencia 46100 Spain.,CIBER de Bioingeniería, Biometariales y Nanomedicina (CIBER-BBN) Spain
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17
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Li T, Wang Y, Zhang Y, Zhou G, Li L. An entropy-driven signal-off DNA circuit for label-free, visual detection of small molecules with enhanced accuracy. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:1140-1147. [PMID: 35224592 DOI: 10.1039/d1ay01939b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
An entropy-driven DNA circuit offers an efficient means of sensitive analyte detection with signal amplification. In this article, we rationally engineered an aptamer-based entropy-driven signal-off DNA circuit for colorimetric detection of small molecules. The proposed signal-off DNA circuit is activated by target small molecule binding to drive the collapse of G-quadruplex DNAzyme, accompanied by the colour change of the detection solution from dark blue to light blue. Entropy-driven recycling hybridization significantly magnified the input signal of the target small molecule. Such an assay enables naked-eye detection of adenosine triphosphate and oxytetracycline at concentrations as low as 0.5 μM and 1 μM respectively. Moreover, when compared with the signal-on DNA circuit, the entropy-driven signal-off DNA circuit for colorimetric detection has two advantages. Firstly, unlike in the signal-on DNA circuit, the unavoidable formation of waste complexes in the absence of a target in the signal-off DNA circuit has no influence on target detection performance as its background signal is only determined by the substrate complex. Secondly, the signal-on DNA circuit cannot distinguish false-positive signals generated by invasive catalysts (e.g., HRP, serum, Fe3O4), while the signal-off DNA circuit can distinguish those signals as undesired signals. Overall, the signal-off DNA circuit affords a novel strategy for sensitive and accurate detection of small molecules.
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Affiliation(s)
- Tuqiang Li
- School of Petrochemical Engineering, Changzhou University, Changzhou 213016, China.
| | - Yulan Wang
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, China
| | - Yanan Zhang
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, China
| | - Guobao Zhou
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, China
| | - Lei Li
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, China
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18
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Han Y, Liu X, Zhao Q, Gao Y, Zhou D, Long W, Wang Y, Song Y. Aptazyme-induced cascade amplification integrated with a volumetric bar-chart chip for highly sensitive detection of aflatoxin B1 and adenosine triphosphate. Analyst 2022; 147:2500-2507. [DOI: 10.1039/d2an00650b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A triple-channel volumetric bar-chart chip based on aptazyme-induced cascade signal amplification empowers visual readout of aflatoxin B1 and adenosine triphosphate concentration.
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Affiliation(s)
- Yuanyue Han
- Key Laboratory of Flexible Electronics & Institute of Advanced Materials, Jiangsu National Synergistic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, China
| | - Xinli Liu
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China
| | - Qiao Zhao
- Key Laboratory of Flexible Electronics & Institute of Advanced Materials, Jiangsu National Synergistic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, China
| | - Yanfeng Gao
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China
| | - Dongtao Zhou
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China
| | - Wenxiu Long
- Key Laboratory of Flexible Electronics & Institute of Advanced Materials, Jiangsu National Synergistic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, China
| | - Yuzhen Wang
- Key Laboratory of Flexible Electronics & Institute of Advanced Materials, Jiangsu National Synergistic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, China
| | - Yujun Song
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China
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19
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Castelli FA, Rosati G, Moguet C, Fuentes C, Marrugo-Ramírez J, Lefebvre T, Volland H, Merkoçi A, Simon S, Fenaille F, Junot C. Metabolomics for personalized medicine: the input of analytical chemistry from biomarker discovery to point-of-care tests. Anal Bioanal Chem 2022; 414:759-789. [PMID: 34432105 PMCID: PMC8386160 DOI: 10.1007/s00216-021-03586-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 12/30/2022]
Abstract
Metabolomics refers to the large-scale detection, quantification, and analysis of small molecules (metabolites) in biological media. Although metabolomics, alone or combined with other omics data, has already demonstrated its relevance for patient stratification in the frame of research projects and clinical studies, much remains to be done to move this approach to the clinical practice. This is especially true in the perspective of being applied to personalized/precision medicine, which aims at stratifying patients according to their risk of developing diseases, and tailoring medical treatments of patients according to individual characteristics in order to improve their efficacy and limit their toxicity. In this review article, we discuss the main challenges linked to analytical chemistry that need to be addressed to foster the implementation of metabolomics in the clinics and the use of the data produced by this approach in personalized medicine. First of all, there are already well-known issues related to untargeted metabolomics workflows at the levels of data production (lack of standardization), metabolite identification (small proportion of annotated features and identified metabolites), and data processing (from automatic detection of features to multi-omic data integration) that hamper the inter-operability and reusability of metabolomics data. Furthermore, the outputs of metabolomics workflows are complex molecular signatures of few tens of metabolites, often with small abundance variations, and obtained with expensive laboratory equipment. It is thus necessary to simplify these molecular signatures so that they can be produced and used in the field. This last point, which is still poorly addressed by the metabolomics community, may be crucial in a near future with the increased availability of molecular signatures of medical relevance and the increased societal demand for participatory medicine.
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Affiliation(s)
- Florence Anne Castelli
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
- MetaboHUB, Gif-sur-Yvette, France
| | - Giulio Rosati
- Institut Català de Nanociència i Nanotecnologia (ICN2), Edifici ICN2 Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Christian Moguet
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
| | - Celia Fuentes
- Institut Català de Nanociència i Nanotecnologia (ICN2), Edifici ICN2 Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Jose Marrugo-Ramírez
- Institut Català de Nanociència i Nanotecnologia (ICN2), Edifici ICN2 Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Thibaud Lefebvre
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
- Centre de Recherche sur l'Inflammation/CRI, Université de Paris, Inserm, Paris, France
- CRMR Porphyrie, Hôpital Louis Mourier, AP-HP Nord - Université de Paris, Colombes, France
| | - Hervé Volland
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
| | - Arben Merkoçi
- Institut Català de Nanociència i Nanotecnologia (ICN2), Edifici ICN2 Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Stéphanie Simon
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
| | - François Fenaille
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
- MetaboHUB, Gif-sur-Yvette, France
| | - Christophe Junot
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France.
- MetaboHUB, Gif-sur-Yvette, France.
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20
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Guan C, Zhu X, Feng C. DNA Nanodevice-Based Drug Delivery Systems. Biomolecules 2021; 11:1855. [PMID: 34944499 PMCID: PMC8699395 DOI: 10.3390/biom11121855] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/06/2021] [Accepted: 12/06/2021] [Indexed: 12/20/2022] Open
Abstract
DNA, a natural biological material, has become an ideal choice for biomedical applications, mainly owing to its good biocompatibility, ease of synthesis, modifiability, and especially programmability. In recent years, with the deepening of the understanding of the physical and chemical properties of DNA and the continuous advancement of DNA synthesis and modification technology, the biomedical applications based on DNA materials have been upgraded to version 2.0: through elaborate design and fabrication of smart-responsive DNA nanodevices, they can respond to external or internal physical or chemical stimuli so as to smartly perform certain specific functions. For tumor treatment, this advancement provides a new way to solve the problems of precise targeting, controllable release, and controllable elimination of drugs to a certain extent. Here, we review the progress of related fields over the past decade, and provide prospects for possible future development directions.
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Affiliation(s)
- Chaoyang Guan
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China;
| | - Xiaoli Zhu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China;
- Department of Clinical Laboratory Medicine, Shanghai Tenth People’s Hospital of Tongji University, Shanghai 200072, China
| | - Chang Feng
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China;
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21
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Yu H, Alkhamis O, Canoura J, Liu Y, Xiao Y. Advances and Challenges in Small‐Molecule DNA Aptamer Isolation, Characterization, and Sensor Development. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202008663] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Haixiang Yu
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Obtin Alkhamis
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Juan Canoura
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Yingzhu Liu
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Yi Xiao
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
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22
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Yu H, Alkhamis O, Canoura J, Liu Y, Xiao Y. Advances and Challenges in Small-Molecule DNA Aptamer Isolation, Characterization, and Sensor Development. Angew Chem Int Ed Engl 2021; 60:16800-16823. [PMID: 33559947 PMCID: PMC8292151 DOI: 10.1002/anie.202008663] [Citation(s) in RCA: 154] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 11/16/2021] [Indexed: 12/12/2022]
Abstract
Aptamers are short oligonucleotides isolated in vitro from randomized libraries that can bind to specific molecules with high affinity, and offer a number of advantages relative to antibodies as biorecognition elements in biosensors. However, it remains difficult and labor-intensive to develop aptamer-based sensors for small-molecule detection. Here, we review the challenges and advances in the isolation and characterization of small-molecule-binding DNA aptamers and their use in sensors. First, we discuss in vitro methodologies for the isolation of aptamers, and provide guidance on selecting the appropriate strategy for generating aptamers with optimal binding properties for a given application. We next examine techniques for characterizing aptamer-target binding and structure. Afterwards, we discuss various small-molecule sensing platforms based on original or engineered aptamers, and their detection applications. Finally, we conclude with a general workflow to develop aptamer-based small-molecule sensors for real-world applications.
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Affiliation(s)
- Haixiang Yu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Obtin Alkhamis
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Juan Canoura
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Yingzhu Liu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Yi Xiao
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
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23
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Screening and application of a broad-spectrum aptamer for acyclic guanosine analogues. Anal Bioanal Chem 2021; 413:4855-4863. [PMID: 34110440 DOI: 10.1007/s00216-021-03446-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/16/2021] [Accepted: 05/31/2021] [Indexed: 10/21/2022]
Abstract
Acyclic guanosine analogues, a class of widely used antiviral drugs, can cause chronic toxicity and virus resistance. Therefore, it is essential to establish rapid and accurate methods to detect acyclic guanosine analogues. In this study, five acyclic guanosine analogues (acyclovir, famciclovir, ganciclovir, penciclovir, and valaciclovir) were used as positive targets to obtain broad-spectrum aptamers through Capture-SELEX technology. Real-time quantitative PCR (Q-PCR) was used to monitor the aptamer SELEX process. After the sixteen rounds of selection against mixed targets, sequences were obtained by high-throughput sequencing (HTS). Furthermore, a broad-spectrum aptamer, named CIV6, was found as the higher performance aptamer that was suitable for five acyclic guanosine analogues by graphene oxide (GO) polarization and fluorescence assay. Finally, the aptamer CIV6 was used to construct GO fluorescence assay to detect five acyclic guanosine analogues. The limits of detection (LOD) of acyclovir, famciclovir, ganciclovir, penciclovir, and valaciclovir were 0.48 ng·mL-1, 0.53 ng·mL-1, 0.50 ng·mL-1, 0.56 ng·mL-1, and 0.38 ng·mL-1, respectively.
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24
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He S, Liu M, Yin F, Liu J, Ge Z, Li F, Li M, Shi J, Wang L, Mao X, Zuo X, Li Q. Programming folding cooperativity of the dimeric i-motif with DNA frameworks for sensing small pH variations. Chem Commun (Camb) 2021; 57:3247-3250. [PMID: 33646233 DOI: 10.1039/d1cc00266j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The response sensitivity of a molecular sensor is determined by the folding cooperativity of its responsive module. Using an H+-responsive dimeric DNA i-motif as a model, we demonstrate the enhancement of its folding cooperativity through preorganization by a DNA framework, and with it we fabricate robust intracellular pH sensors with high response sensitivity.
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Affiliation(s)
- Shiliang He
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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25
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Cozma I, McConnell EM, Brennan JD, Li Y. DNAzymes as key components of biosensing systems for the detection of biological targets. Biosens Bioelectron 2021; 177:112972. [DOI: 10.1016/j.bios.2021.112972] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 01/01/2021] [Accepted: 01/02/2021] [Indexed: 12/11/2022]
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26
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Schram J, Parrilla M, Sleegers N, Van Durme F, van den Berg J, van Nuijs ALN, De Wael K. Electrochemical profiling and liquid chromatography-mass spectrometry characterization of synthetic cathinones: From methodology to detection in forensic samples. Drug Test Anal 2021; 13:1282-1294. [PMID: 33624933 DOI: 10.1002/dta.3018] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/21/2021] [Accepted: 02/22/2021] [Indexed: 12/15/2022]
Abstract
The emergence of new psychoactive drugs in the market demands rapid and accurate tools for the on-site classification of illegal and legal compounds with similar structures. Herein, a novel method for the classification of synthetic cathinones (SCs) is presented based on their electrochemical profile. First, the electrochemical profile of five common SC (i.e., mephedrone, ethcathinone, methylone, butylone, and 4-chloro-alpha-pyrrolidinovalerophenone) is collected to build calibration curves using square wave voltammetry on graphite screen-printed electrodes (SPEs). Second, the elucidation of the oxidation pathways, obtained by liquid chromatography-high-resolution mass spectrometry, allows the pairing of the oxidation products to the SC electrochemical profile, providing a selective and robust classification. Additionally, the effect of common adulterants and illicit drugs on the electrochemical profile of the SC is explored. Interestingly, a cathodic pretreatment of the SPE allows the selective detection of each SC in presence of electroactive adulterants. Finally, the electrochemical approach is validated with gas chromatography-mass spectrometry by analyzing 26 confiscated samples from seizures and illegal webshops. Overall, the electrochemical method exhibits a successful classification of SC including structural derivatives, a crucial attribute in an ever-diversifying drug market.
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Affiliation(s)
- Jonas Schram
- AXES Research Group, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium.,NANOlab Center of Excellence, University of Antwerp, Antwerp, Belgium
| | - Marc Parrilla
- AXES Research Group, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium.,NANOlab Center of Excellence, University of Antwerp, Antwerp, Belgium
| | - Nick Sleegers
- AXES Research Group, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium.,NANOlab Center of Excellence, University of Antwerp, Antwerp, Belgium
| | - Filip Van Durme
- Drugs and Toxicology Department, National Institute for Criminalistics and Criminology (NICC), Brussels, Belgium
| | - Jorrit van den Berg
- Team Illicit Drugs, The Netherlands Forensic Institute (NFI), The Hague, The Netherlands
| | | | - Karolien De Wael
- AXES Research Group, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium.,NANOlab Center of Excellence, University of Antwerp, Antwerp, Belgium
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27
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Kolpashchikov DM, Spelkov AA. Binary (Split) Light‐up Aptameric Sensors. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.201914919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Dmitry M. Kolpashchikov
- Chemistry Department University of Central Florida Orlando FL 32816-2366 USA
- Burnett School of Biomedical Sciences University of Central Florida Orlando FL 32816 USA
| | - Alexander A. Spelkov
- Laboratory of Solution Chemistry of Advanced Materials and Technologies ITMO University 9 Lomonosova Str. St. Petersburg 191002 Russian Federation
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28
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Wu H, Chen X, Zhang M, Wang X, Chen Y, Qian C, Wu J, Xu J. Versatile detection with CRISPR/Cas system from applications to challenges. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2020.116150] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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29
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Bezerra AB, Kurian ASN, Easley CJ. Nucleic-Acid Driven Cooperative Bioassays Using Probe Proximity or Split-Probe Techniques. Anal Chem 2021; 93:198-214. [PMID: 33147015 PMCID: PMC7855502 DOI: 10.1021/acs.analchem.0c04364] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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30
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Chang CC, Yeh CY. Using Simple-Structured Split Aptamer for Gold Nanoparticle-based Colorimetric Detection of Estradiol. ANAL SCI 2020; 37:479-484. [PMID: 33281139 DOI: 10.2116/analsci.20scp07] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Demand for the detection of estradiol, which is a naturally occurring hormone, has been increasing. Gold nanoparticle-based colorimetric aptasensors have been developed for estradiol detection; however, the long sequence of aptamers due to the formation of the secondary structure likely affects the sensitivity of the aptasensors. Herein, a sensitive colorimetric biosensor is developed for label-free detection of estradiol by using an estradiol-specific split aptamer. The results demonstrate that a superior response is observed when a split aptamer with a high free energy of the secondary structure (ΔG > -3 kcal/mol) is used, in comparison to that observed using a split aptamer with a low free energy of the secondary structure (ΔG < -3 kcal/mol) at 27°C. After selecting the appropriate split aptamer, the standard calibration curve obtained for estradiol has a detection limit of 6.7 nM, with a linear range of 6.7 nM - 66.7 μM in the logarithmic scale. Furthermore, this assay is sensitive, easy-to-operate, inexpensive, and non-time-consuming (provides results within 50 min), thereby showing potential for clinical applications (detection of other small molecular targets).
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Affiliation(s)
- Chia-Chen Chang
- Department of Medical Biotechnology and Laboratory Sciences, College of Medicine, Chang Gung University.,Kidney Research Center, Department of Nephrology, Chang Gung Memorial Hospital
| | - Chung-Yu Yeh
- Department of Medical Biotechnology and Laboratory Sciences, College of Medicine, Chang Gung University
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31
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Qi X, Yan X, Zhao Y, Li L, Wang S. Highly sensitive and specific detection of small molecules using advanced aptasensors based on split aptamers: A review. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.116069] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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32
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Alkhamis O, Yang W, Farhana R, Yu H, Xiao Y. Label-free profiling of DNA aptamer-small molecule binding using T5 exonuclease. Nucleic Acids Res 2020; 48:e120. [PMID: 33053182 PMCID: PMC7672472 DOI: 10.1093/nar/gkaa849] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 09/04/2020] [Accepted: 09/24/2020] [Indexed: 12/15/2022] Open
Abstract
In vitro aptamer isolation methods can yield hundreds of potential candidates, but selecting the optimal aptamer for a given application is challenging and laborious. Existing aptamer characterization methods either entail low-throughput analysis with sophisticated instrumentation, or offer the potential for higher throughput at the cost of providing a relatively increased risk of false-positive or -negative results. Here, we describe a novel method for accurately and sensitively evaluating the binding between DNA aptamers and small-molecule ligands in a high-throughput format without any aptamer engineering or labeling requirements. This approach is based on our new finding that ligand binding inhibits aptamer digestion by T5 exonuclease, where the extent of this inhibition correlates closely with the strength of aptamer-ligand binding. Our assay enables accurate and efficient screening of the ligand-binding profiles of individual aptamers, as well as the identification of the best target binders from a batch of aptamer candidates, independent of the ligands in question or the aptamer sequence and structure. We demonstrate the general applicability of this assay with a total of 106 aptamer-ligand pairs and validate these results with a gold-standard method. We expect that our assay can be readily expanded to characterize small-molecule-binding aptamers in an automated, high-throughput fashion.
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Affiliation(s)
- Obtin Alkhamis
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
| | - Weijuan Yang
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
| | - Rifat Farhana
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
| | - Haixiang Yu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
| | - Yi Xiao
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
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33
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Li S, Zheng Y, Zou Q, Liao G, Liu X, Zou L, Yang X, Wang Q, Wang K. Engineering and Application of a Myoglobin Binding Split Aptamer. Anal Chem 2020; 92:14576-14581. [PMID: 33052657 DOI: 10.1021/acs.analchem.0c02869] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Given that a split aptamer provides a chance for the development of a sandwich assay for targets with only one aptamer, it has received extensive attention in biosensing. However, due to the lack of binding mechanisms and reliable methods, there were still a few split aptamers that bind to proteins. In this work, cardiac biomarker myoglobin (Myo) was selected as a model, a new strategy of engineering split aptamers was explored with atomic force spectroscopy (AFM), and split aptamers against target protein could be achieved by choosing the optimal binding probability between split aptamers and target. Then, the obtained split aptamers were designed for Myo detection based on dynamic light scattering (DLS). The results demonstrated that the obtained split aptamers could be used to detect targets in human serum. The strategy of engineering split aptamers has the advantages of being intuitive and reliable and could be a general strategy for obtaining split aptamers.
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Affiliation(s)
- Shaoyuan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P. R. China
| | - Yan Zheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P. R. China
| | - Qingqing Zou
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P. R. China
| | - Guofu Liao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P. R. China
| | - Xiaofeng Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P. R. China
| | - Liyuan Zou
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P. R. China
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P. R. China
| | - Qing Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P. R. China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P. R. China
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34
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Kolpashchikov DM, Spelkov AA. Binary (Split) Light-up Aptameric Sensors. Angew Chem Int Ed Engl 2020; 60:4988-4999. [PMID: 32208549 DOI: 10.1002/anie.201914919] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Indexed: 12/12/2022]
Abstract
This Minireview discusses the design and applications of binary (also known as split) light-up aptameric sensors (BLAS). BLAS consist of two RNA or DNA strands and a fluorogenic organic dye added as a buffer component. When associated, the two strands form a dye-binding site, followed by an increase in fluorescence of the aptamer-bound dye. The design is cost-efficient because it uses short oligonucleotides and does not require conjugation of organic dyes with nucleic acids. In some applications, BLAS design is preferable over monolithic sensors because of simpler assay optimization and improved selectivity. RNA-based BLAS can be expressed in cells and used for the intracellular monitoring of biological molecules. BLAS have been used as reporters of nucleic acid association events in RNA nanotechnology and nucleic-acid-based molecular computation. Other applications of BLAS include the detection of nucleic acids, proteins, and cancer cells, and potentially they can be tailored to report a broad range of biological analytes.
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Affiliation(s)
- Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, Orlando, FL, 32816-2366, USA.,Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, 32816, USA
| | - Alexander A Spelkov
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., St. Petersburg, 191002, Russian Federation
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35
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Coria‐Oriundo LL, Ceretti H, Roupioz Y, Battaglini F. Redox Polyelectrolyte Modified Gold Nanoparticles Enhance the Detection of Adenosine in an Electrochemical Split‐Aptamer Assay. ChemistrySelect 2020. [DOI: 10.1002/slct.202002488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Lucy L. Coria‐Oriundo
- INQUIMAE (CONICET) Departamento de Química Inorgánica Analítica y Química Física Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Ciudad Universitaria, Pabellón 2 C1428EHA Buenos Aires Argentina
- Facultad de Ciencias Universidad Nacional de Ingeniería Av. Túpac Amaru 210 Lima 25, Perú
| | - Helena Ceretti
- Universidad Nacional de Gral. Sarmiento, J. M. Gutiérrez 1150 B1613GSX, Los Polvorines, Prov. de Buenos Aires Argentina
| | - Yoann Roupioz
- Univ. Grenoble Alpes CNRS CEA SyMMES 38000 Grenoble France
| | - Fernando Battaglini
- INQUIMAE (CONICET) Departamento de Química Inorgánica Analítica y Química Física Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Ciudad Universitaria, Pabellón 2 C1428EHA Buenos Aires Argentina
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36
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A split aptamer sensing platform for highly sensitive detection of theophylline based on dual-color fluorescence colocalization and single molecule photobleaching. Biosens Bioelectron 2020; 166:112461. [PMID: 32745928 DOI: 10.1016/j.bios.2020.112461] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/16/2020] [Accepted: 07/16/2020] [Indexed: 01/19/2023]
Abstract
A new split aptamer sensing platform is developed for highly sensitive and selective detection of theophylline based on single molecule photobleaching (SMPB) technique. The sensing system contains two probes. One is formed by one streptavidin and four biotinylated RNA fragments labelled with fluorescein isothiocyanate (FITC). Each biotinylated RNA fragment contains two repeating aptamer fragments. The other probe is the complementary aptamer fragment labelled with Cy5 dye. The existence of theophylline can trigger the first probe to bind as many as eight Cy5-labelled probes. The average combined number depends on the theophylline concentration and can be measured by SMPB technique. In the sensing system, the dual-color fluorescence colocalization is performed by the red fluorophore (Cy5) and green fluorophore (FITC), in which the red fluorophore is utilized for quantitative counting of photobleaching steps, while the green fluorophore serves as a counting reference to increase detection efficiency. On basis of the principle, an ultra-sensitive sensing platform of theophylline is created with a low limit of detection (LOD) of 0.092 nM. This work provides not only a highly sensitive method for theophylline detection but also a novel perspective for the applications of SMPB technology to construct biosensors.
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37
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He L, Chen F, Zhang D, Xie S, Xu S, Wang Z, Zhang L, Cui C, Liu Y, Tan W. Transducing Complex Biomolecular Interactions by Temperature-Output Artificial DNA Signaling Networks. J Am Chem Soc 2020; 142:14234-14239. [DOI: 10.1021/jacs.0c05453] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Lei He
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Fengming Chen
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Dailiang Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Sitao Xie
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Shujuan Xu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and 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 and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Zhimin Wang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Lili Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Cheng Cui
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and 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 and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Yanlan Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, 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 and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
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38
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Sun X, Liu Y, Liu L, Yin F, Liu R, Guo T, Li X, Xue Q. Label-free amplified fluorescence detection of DNA biomarkers based on KFP polymerase-driven double strand displacement reactions and magnetic nanoprobes. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:3092-3097. [PMID: 32930168 DOI: 10.1039/d0ay00338g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Developing a sensitive, low-cost and general sensing platform for the analysis of a DNA biomarker and its mutation is important for early cancer screening. In our work, the tumor suppressor gene-p53 DNA was chosen as the model DNA biomarker due to its vital role in preventing oncogene cancer-inhibiting activity through mediating cellular proliferation and apoptosis. Compared with tumor biopsy, the quantification of p53 DNA and its mutation in biofluids (such as urine) is more convenient due to its simple operation and non-invasiveness. Herein, a label-free amplified fluorescence assay has been developed for p53 DNA in urine samples through the KFP polymerase-driven double strand displacement reactions and a magnetic nanoprobe. First, the ssDNA probe (RP) was designed with antisense sequences for p53 DNA and the Nb.BbvCI endonuclease recognition site. In the presence of p53 DNA, the formed dsDNA between RP and p53 DNA served as an engaging primer to initiate the first strand displacement reaction (SDA) under the action of KFP DNA polymerase and Nb.BbvCI, generating abundant short ssDNA (primer). Subsequently, the resulting primers will initiate the downstream SDA through the primer-hairpin DNA (HPa) binding, opening up, and extension of HPb and HPc under the action of KFP DNA polymerase. In the process of this final DNA polymerization reaction, the primer hybridized on HPa is released and goes on to initiate another round, forming plenty of duplex Y-shaped DNA. With the integration of SYBR Green I (SG I) into these duplex DNA, the amplified label-free fluorescence detection platform for p53 DNA can be achieved. Moreover, a biotin modified nanoprobe (bio-CP) was used to capture the superfluous HP. By performing the separation function, the binding of superfluous HP and SG could be avoided and a low background can be acquired. Benefiting from the abundant SG intercalation sites of Y-shaped DNA and low background signals, this method showed excellent sensitivity with a detection limit of 0.012 nM, and the p53 DNA in urine samples was evaluated, offering a powerful tool for biomedical research and clinical diagnosis.
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Affiliation(s)
- Xia Sun
- Department of Chemistry, Liaocheng University, Liao Cheng 252059, China.
| | - Yeling Liu
- Department of Chemistry, Liaocheng University, Liao Cheng 252059, China.
| | - Liqi Liu
- Department of Chemistry, Liaocheng University, Liao Cheng 252059, China.
| | - Fei Yin
- Department of Chemistry, Liaocheng University, Liao Cheng 252059, China.
| | - Ruixin Liu
- Department of Chemistry, Liaocheng University, Liao Cheng 252059, China.
| | - Tianyu Guo
- Department of Art and Science, University of Vermont, 05405, Burlington, Vermont, USA
| | - Xia Li
- Department of Chemistry, Liaocheng University, Liao Cheng 252059, China.
| | - Qingwang Xue
- Department of Chemistry, Liaocheng University, Liao Cheng 252059, China.
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39
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Debiais M, Lelievre A, Smietana M, Müller S. Splitting aptamers and nucleic acid enzymes for the development of advanced biosensors. Nucleic Acids Res 2020; 48:3400-3422. [PMID: 32112111 PMCID: PMC7144939 DOI: 10.1093/nar/gkaa132] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/12/2020] [Accepted: 02/18/2020] [Indexed: 12/16/2022] Open
Abstract
In analogy to split-protein systems, which rely on the appropriate fragmentation of protein domains, split aptamers made of two or more short nucleic acid strands have emerged as novel tools in biosensor set-ups. The concept relies on dissecting an aptamer into a series of two or more independent fragments, able to assemble in the presence of a specific target. The stability of the assembled structure can further be enhanced by functionalities that upon folding would lead to covalent end-joining of the fragments. To date, only a few aptamers have been split successfully, and application of split aptamers in biosensing approaches remains as promising as it is challenging. Further improving the stability of split aptamer target complexes and with that the sensitivity as well as efficient working modes are important tasks. Here we review functional nucleic acid assemblies that are derived from aptamers and ribozymes/DNAzymes. We focus on the thrombin, the adenosine/ATP and the cocaine split aptamers as the three most studied DNA split systems and on split DNAzyme assemblies. Furthermore, we extend the subject into split light up RNA aptamers used as mimics of the green fluorescent protein (GFP), and split ribozymes.
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Affiliation(s)
- Mégane Debiais
- Institut des Biomolécules Max Mousseron, University of Montpellier, CNRS, ENCSM, Montpellier, France
| | - Amandine Lelievre
- University Greifswald, Institute for Biochemistry, Greifswald, Germany
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron, University of Montpellier, CNRS, ENCSM, Montpellier, France
| | - Sabine Müller
- University Greifswald, Institute for Biochemistry, Greifswald, Germany
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40
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Chen J, Tang J, Meng HM, Liu Z, Wang L, Geng X, Wu Y, Qu L, Li Z. Recognition triggered assembly of split aptamers to initiate a hybridization chain reaction for wash-free and amplified detection of exosomes. Chem Commun (Camb) 2020; 56:9024-9027. [DOI: 10.1039/d0cc02337j] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A novel split aptamer-based system was developed for the amplified detection of exosomes in situ assisted by a target-induced HCR.
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Affiliation(s)
- Juan Chen
- College of Chemistry
- Green Catalysis Center
- Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications
- Zhengzhou University
- Zhengzhou 450001
| | - Jinlu Tang
- School of Basic Medical Sciences
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Hong-Min Meng
- College of Chemistry
- Green Catalysis Center
- Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications
- Zhengzhou University
- Zhengzhou 450001
| | - Zhuo Liu
- College of Chemistry
- Green Catalysis Center
- Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications
- Zhengzhou University
- Zhengzhou 450001
| | - Lin Wang
- The Academy of Medical Sciences
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Xin Geng
- College of Chemistry
- Green Catalysis Center
- Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications
- Zhengzhou University
- Zhengzhou 450001
| | - Yanan Wu
- College of Chemistry
- Green Catalysis Center
- Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications
- Zhengzhou University
- Zhengzhou 450001
| | - Lingbo Qu
- College of Chemistry
- Green Catalysis Center
- Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications
- Zhengzhou University
- Zhengzhou 450001
| | - Zhaohui Li
- College of Chemistry
- Green Catalysis Center
- Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications
- Zhengzhou University
- Zhengzhou 450001
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Connelly RP, Verduzco C, Farnell S, Yishay T, Gerasimova YV. Toward a Rational Approach to Design Split G-Quadruplex Probes. ACS Chem Biol 2019; 14:2701-2712. [PMID: 31599573 DOI: 10.1021/acschembio.9b00634] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Hybridization probes have become an indispensable tool for nucleic acid analysis. Systematic efforts in probe optimization resulted in their improved binding affinity, turn-on ratios, and ability to discriminate single nucleotide substitutions (SNSs). The use of split (or multicomponent) probes is a promising strategy to improve probe selectivity and enable an analysis of folded analytes. Here, we developed criteria for the rational design of a split G-quadruplex (G4) peroxidase-like deoxyribozyme (sPDz) probe that provides a visual output signal. The sPDz probe consists of two DNA strands that hybridize to the abutting positions of a DNA/RNA target and form a G4 structure catalyzing, in the presence of a hemin cofactor, H2O2-mediated oxidation of organic compounds into their colored oxidation products. We have demonstrated that probe design becomes complicated in the case of target sequences containing clusters (two or more) of cytosine residues and developed strategies to overcome the challenges to achieving high signal-to-noise and excellent SNS discrimination. Specifically, to improve selectivity, a conformational constraint that stabilizes the probe's dissociated state is beneficial. If the signal intensity is compromised, introduction of flexible non-nucleotide linkers between the G4-forming and target-recognizing elements of the probe helps to decrease the steric hindrance for G4 PDz formation observed as a signal increase. Varying the modes of G4 core splitting is another instrument for the optimal sPDz design. The suggested algorithm was successfully utilized for the design of the sPDz probe interrogating a fragment of the Influenza A virus genome (subtype H1N1), which can be of practical use for flu diagnostics and surveillance.
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Affiliation(s)
- Ryan P. Connelly
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, Florida 32816, United States
| | - Charles Verduzco
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, Florida 32816, United States
| | - Serena Farnell
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, Florida 32816, United States
| | - Tamar Yishay
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, Florida 32816, United States
| | - Yulia V. Gerasimova
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, Florida 32816, United States
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Mao X, Li Q, Zuo X, Fan C. Catalytic Nucleic Acids for Bioanalysis. ACS APPLIED BIO MATERIALS 2019; 3:2674-2685. [PMID: 35025402 DOI: 10.1021/acsabm.9b00928] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Xiuhai Mao
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chunhai Fan
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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Alkhamis O, Canoura J, Yu H, Liu Y, Xiao Y. Innovative engineering and sensing strategies for aptamer-based small-molecule detection. Trends Analyt Chem 2019; 121. [PMID: 32863483 DOI: 10.1016/j.trac.2019.115699] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Aptamers are nucleic acid-based affinity reagents that have gained widespread attention as biorecognition elements for the detection of targets such as ions, small molecules, and proteins. Over the past three decades, the field of aptamer-based sensing has grown considerably. However, the advancement of aptamer-based small-molecule detection has fallen short of the high demand for such sensors in applications such as diagnostics, environmental monitoring, and forensics. This is due to two challenges: the complexity of developing generalized sensing platforms and the poor sensitivities of assays targeting small molecules. This paper will review new approaches for the streamlined development of high-performance aptamer-based sensors for small-molecule detection. We here provide historical context, explore the current state-of-the art, and offer future directions-with emphasis placed on new aptamer engineering methods, the use of cooperative binding, and label-free approaches using fully-folded, high-affinity aptamers for small-molecule sensing.
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Affiliation(s)
- Obtin Alkhamis
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, USA, 33199
| | - Juan Canoura
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, USA, 33199
| | - Haixiang Yu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, USA, 33199
| | - Yingzhu Liu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, USA, 33199
| | - Yi Xiao
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, USA, 33199
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