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Jia L, Wang Y, Jiang M, Yuan W, Jin Y, Yan W, Ze X, Chen Y, Niu L. An ultrasensitive dual-mode stagey for 17β-estradiol assay: Photoelectrochemical and colorimetric biosensor based on a WSe 2/TiO 2-modified electrode coupled with nucleic acid amplification. Anal Chim Acta 2024; 1319:342966. [PMID: 39122278 DOI: 10.1016/j.aca.2024.342966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/22/2024] [Accepted: 07/10/2024] [Indexed: 08/12/2024]
Abstract
BACKGROUND The abuse of 17β-estradiol(E2) has aroused wide concern in environmental and biomedical fields, which severely affects the endocrine function of human and animals. Therefore, an ultrasensitive and accurate assay of E2 is critically important. Traditional chromatography or immunoassay techniques exhibited good sensitivity and selectivity, but expensive instruments and antibodies may pose cost and stability issues, as well as difficulties in meeting on-site detection requirements. Ultrasensitive, reliable, and on-site detection of E2 at trace level remains a challenge. Hence, developing a simple, ultrasensitive assay to simultaneously achieve accurate detection and rapid visual analysis of E2 is extremely crucial. RESULTS We developed a versatile dual-mode photoelectrochemical (PEC) and colorimetric biosensor based on isothermal nucleic acid amplification strategy for the ultrasensitive and accurate detection of E2. The method modified titanium dioxide (TiO2) with tungsten selenide (WSe2) nanoflowers to synthesize WSe2/TiO2 heterostructures as a substrate for signal amplification and nanoprobe modification. Isothermal nucleic acid amplification strategy has been proven to be a powerful tool for strong signal amplification. The presence of a target triggered the nucleic acid amplification reaction, and produced a large amount of tDNA that competed with G-quadruplex immobilized on the electrode surface. The remaining G-quadruplex/hemin catalyzed the 4-chloro-1-naphthol (4-CN) to form biocatalytic precipitation (BCP) and ABTS-H2O2 chromogenic reaction, thus, the dual-mode platform was capable of achieving PEC-colorimetric ultrasensitive detection based on the catalytic activity of G-quadruplex/hemin DNAzyme. Within optimal conditions, the dual-mode biosensor exhibited a remarkable detection limit as low as 0.026 pM. SIGNIFICANCE Benefiting from the superior performance of WSe2/TiO2 and the power signal amplification of isothermal nucleic acid amplification strategy, this aptasensor achieved the ultrasensitive detection of E2. The independent transmission paths of photoelectrochemical and colorimetric provide mutual support and flexible switching, significantly enhancing the overall sensitivity and accuracy of the detection strategy, which can meet the needs for E2 precise quantification and rapid on-site detection.
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Affiliation(s)
- Licong Jia
- School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China; Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, 050017, PR China
| | - Yipeng Wang
- School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Meng Jiang
- School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Wei Yuan
- School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Yan Jin
- School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Wen Yan
- School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Xi Ze
- School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China
| | - Yuan Chen
- Department of Pediatrics, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, PR China.
| | - Lingmei Niu
- School of Public Health, Hebei Medical University, Shijiazhuang, 050017, PR China; Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, 050017, PR China; Institute of Medicine and Health, Hebei Medical University, Shijiazhuang, 050017, PR China; Hebei Key Laboratory of Forensic Medicine, Hebei Province, Shijiazhuang, 050017, PR China.
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2
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Kumar S, Mohan A, Sharma NR, Kumar A, Girdhar M, Malik T, Verma AK. Computational Frontiers in Aptamer-Based Nanomedicine for Precision Therapeutics: A Comprehensive Review. ACS OMEGA 2024; 9:26838-26862. [PMID: 38947800 PMCID: PMC11209897 DOI: 10.1021/acsomega.4c02466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/09/2024] [Accepted: 05/28/2024] [Indexed: 07/02/2024]
Abstract
In the rapidly evolving landscape of nanomedicine, aptamers have emerged as powerful molecular tools, demonstrating immense potential in targeted therapeutics, diagnostics, and drug delivery systems. This paper explores the computational features of aptamers in nanomedicine, highlighting their advantages over antibodies, including selectivity, low immunogenicity, and a simple production process. A comprehensive overview of the aptamer development process, specifically the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) process, sheds light on the intricate methodologies behind aptamer selection. The historical evolution of aptamers and their diverse applications in nanomedicine are discussed, emphasizing their pivotal role in targeted drug delivery, precision medicine and therapeutics. Furthermore, we explore the integration of artificial intelligence (AI), machine learning (ML), Internet of Things (IoT), Internet of Medical Things (IoMT), and nanotechnology in aptameric development, illustrating how these cutting-edge technologies are revolutionizing the selection and optimization of aptamers for tailored biomedical applications. This paper also discusses challenges in computational methods for advancing aptamers, including reliable prediction models, extensive data analysis, and multiomics data incorporation. It also addresses ethical concerns and restrictions related to AI and IoT use in aptamer research. The paper examines progress in computer simulations for nanomedicine. By elucidating the importance of aptamers, understanding their superiority over antibodies, and exploring the historical context and challenges, this review serves as a valuable resource for researchers and practitioners aiming to harness the full potential of aptamers in the rapidly evolving field of nanomedicine.
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Affiliation(s)
- Shubham Kumar
- School
of Bioengineering and Biosciences, Lovely
Professional University, Phagwara, Punjab 144001, India
| | - Anand Mohan
- School
of Bioengineering and Biosciences, Lovely
Professional University, Phagwara, Punjab 144001, India
| | - Neeta Raj Sharma
- School
of Bioengineering and Biosciences, Lovely
Professional University, Phagwara, Punjab 144001, India
| | - Anil Kumar
- Gene
Regulation Laboratory, National Institute
of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Madhuri Girdhar
- Division
of Research and Development, Lovely Professional
University, Phagwara 144401, Punjab, India
| | - Tabarak Malik
- Department
of Biomedical Sciences, Institute of Health, Jimma University, MVJ4+R95 Jimma, Ethiopia
| | - Awadhesh Kumar Verma
- School
of Bioengineering and Biosciences, Lovely
Professional University, Phagwara, Punjab 144001, India
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3
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Shi C, Yang D, Ma X, Pan L, Shao Y, Arya G, Ke Y, Zhang C, Wang F, Zuo X, Li M, Wang P. A Programmable DNAzyme for the Sensitive Detection of Nucleic Acids. Angew Chem Int Ed Engl 2024; 63:e202320179. [PMID: 38288561 DOI: 10.1002/anie.202320179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Indexed: 02/17/2024]
Abstract
Nucleic acids in biofluids are emerging biomarkers for the molecular diagnostics of diseases, but their clinical use has been hindered by the lack of sensitive detection assays. Herein, we report the development of a sensitive nucleic acid detection assay named SPOT (sensitive loop-initiated DNAzyme biosensor for nucleic acid detection) by rationally designing a catalytic DNAzyme of endonuclease capability into a unified one-stranded allosteric biosensor. SPOT is activated once a nucleic acid target of a specific sequence binds to its allosteric module to enable continuous cleavage of molecular reporters. SPOT provides a highly robust platform for sensitive, convenient and cost-effective detection of low-abundance nucleic acids. For clinical validation, we demonstrated that SPOT could detect serum miRNAs for the diagnostics of breast cancer, gastric cancer and prostate cancer. Furthermore, SPOT exhibits potent detection performance over SARS-CoV-2 RNA from clinical swabs with high sensitivity and specificity. Finally, SPOT is compatible with point-of-care testing modalities such as lateral flow assays. Hence, we envision that SPOT may serve as a robust assay for the sensitive detection of a variety of nucleic acid targets enabling molecular diagnostics in clinics.
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Affiliation(s)
- Chenzhi Shi
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Donglei Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xiaowei Ma
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Li Pan
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yuanchuan Shao
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina, 27708, USA
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, 30322, USA
| | - Chuan Zhang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Min Li
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
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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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5
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Alkhamis O, Canoura J, Willis C, Wang L, Perry J, Xiao Y. Comparison of Aptamer Signaling Mechanisms Reveals Disparities in Sensor Response and Strategies to Eliminate False Signals. J Am Chem Soc 2023. [PMID: 37217444 DOI: 10.1021/jacs.3c03640] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Aptamers are nucleic acid-based affinity reagents that have been incorporated into a variety of molecular sensor formats. However, many aptamer sensors exhibit insufficient sensitivity and specificity for real-world applications, and although considerable effort has been dedicated to improving sensitivity, sensor specificity has remained largely neglected and understudied. In this work, we have developed a series of sensors using aptamers for the small-molecule drugs flunixin, fentanyl, and furanyl fentanyl and compare their performance─in particular, focusing on their specificity. Contrary to expectations, we observe that sensors using the same aptamer operating under the same physicochemical conditions produce divergent responses to interferents depending on their signal transduction mechanism. For instance, aptamer beacon sensors are susceptible to false-positives from interferents that weakly associate with DNA, while strand-displacement sensors suffer from false-negatives due to interferent-associated signal suppression when both the target and interferent are present. Biophysical analyses suggest that these effects arise from aptamer-interferent interactions that are either nonspecific or induce aptamer conformational changes that are distinct from those induced by true target-binding events. We also demonstrate strategies for improving the sensitivity and specificity of aptamer sensors with the development of a "hybrid beacon," wherein the incorporation of a complementary DNA competitor into an aptamer beacon selectively hinders interferent─but not target─binding and signaling, while simultaneously overcoming signal suppression by interferents. Our results highlight the need for systematic and thorough testing of aptamer sensor response and new aptamer selection methods that optimize specificity more effectively than traditional counter-SELEX.
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Affiliation(s)
- Obtin Alkhamis
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States
| | - Juan Canoura
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States
| | - Connor Willis
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States
| | - Linlin Wang
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States
| | - Jacob Perry
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States
| | - Yi Xiao
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States
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6
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Calabria D, Zangheri M, Pour SRS, Trozzi I, Pace A, Lazzarini E, Calabretta MM, Mirasoli M, Guardigli M. Luminescent Aptamer-Based Bioassays for Sensitive Detection of Food Allergens. BIOSENSORS 2022; 12:644. [PMID: 36005040 PMCID: PMC9405952 DOI: 10.3390/bios12080644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 02/06/2023]
Abstract
The presence of hidden allergens in food products, often due to unintended contamination along the food supply chain (production, transformation, processing, and transport), has raised the urgent need for rapid and reliable analytical methods for detecting trace levels of such species in food products. Indeed, food allergens represent a high-risk factor for allergic subjects due to potentially life-threatening adverse reactions. Portable biosensors based on immunoassays have already been developed as rapid, sensitive, selective, and low-cost analytical platforms that can replace analyses with traditional bench-top instrumentation. Recently, aptamers have attracted great interest as alternative biorecognition molecules for bioassays, since they can bind a variety of targets with high specificity and selectivity, and they enable the development of assays exploiting a variety of transduction and detection technologies. In particular, aptasensors based on luminescence detection have been proposed, taking advantage of the development of ultrasensitive tracers and enhancers. This review aims to summarize and discuss recent efforts in the field of food allergen analysis using aptamer-based bioassays with luminescence detection.
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Affiliation(s)
- Donato Calabria
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
- Interdepartmental Centre for Industrial Aerospace Research (CIRI AEROSPACE), Alma Mater Studiorum, University of Bologna, Via Baldassarre Canaccini 12, I-47121 Forlì, Italy
| | - Martina Zangheri
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
- Interdepartmental Centre for Industrial Agrofood Research (CIRI AGRO), Alma Mater Studiorum, University of Bologna, Via Quinto Bucci 336, I-47521 Cesena, Italy
- Interdepartmental Centre for Industrial Research in Advanced Mechanical Engineering Applications and Materials Technology (CIRI MAM), Alma Mater Studiorum, University of Bologna, Viale Risorgimento 2, I-40136 Bologna, Italy
| | - Seyedeh Rojin Shariati Pour
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
| | - Ilaria Trozzi
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
| | - Andrea Pace
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
| | - Elisa Lazzarini
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
| | - Maria Maddalena Calabretta
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
| | - Mara Mirasoli
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
- Interdepartmental Centre for Industrial Aerospace Research (CIRI AEROSPACE), Alma Mater Studiorum, University of Bologna, Via Baldassarre Canaccini 12, I-47121 Forlì, Italy
- Interdepartmental Centre for Industrial Research in Renewable Resources, Environment, Sea, and Energy (CIRI FRAME), Alma Mater Studiorum, University of Bologna, Via Sant’Alberto 163, I-48123 Ravenna, Italy
| | - Massimo Guardigli
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
- Interdepartmental Centre for Industrial Aerospace Research (CIRI AEROSPACE), Alma Mater Studiorum, University of Bologna, Via Baldassarre Canaccini 12, I-47121 Forlì, Italy
- Interdepartmental Centre for Industrial Research in Renewable Resources, Environment, Sea, and Energy (CIRI FRAME), Alma Mater Studiorum, University of Bologna, Via Sant’Alberto 163, I-48123 Ravenna, Italy
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7
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A sensitive visual DNAzyme-based strategy for Cronobacter sakazakii in PIF by aRPA. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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8
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Chen Y, Qiu D, Zhang X, Liu Y, Cheng M, Lei J, Mergny JL, Ju H, Zhou J. Highly Sensitive Biosensing Applications of a Magnetically Immobilizable Covalent G-Quadruplex-Hemin DNAzyme Catalytic System. Anal Chem 2022; 94:2212-2219. [PMID: 35050586 DOI: 10.1021/acs.analchem.1c04842] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
G-quadruplex/hemin (G4/hemin) DNAzymes are biosensing systems, but their application remains limited by an overall low activity and a rather high level of unwarranted background reactions. Here, these issues were addressed through the rational design of F3T-azaC-hemin, a G4-based construct in which the hemin is covalently linked to the G4 core and its binding site flanked with a nucleotide activator, here d(T-azaC). This design led to a G4-DNAzyme whose performances have been ca. 150-fold increased compared to the parent G4-based system. The utility of F3T-azaC-hemin was demonstrated here through the ultrasensitive chemiluminescent detection of miRNA-221. The limit of detection (LOD) has been decreased to the femtomolar range, making it a new and highly efficient molecular tool in the biosensing technology field.
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Affiliation(s)
- Yun Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Dehui Qiu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Xiaobo Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yuan Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Mingpan Cheng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Jianping Lei
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.,Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex 91128, France
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
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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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10
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Ahmadi Y, Soldo R, Rathammer K, Eibler L, Barišić I. Analyzing Criteria Affecting the Functionality of G-Quadruplex-Based DNA Aptazymes as Colorimetric Biosensors and Development of Quinine-Binding Aptazymes. Anal Chem 2021; 93:5161-5169. [PMID: 33724777 DOI: 10.1021/acs.analchem.0c05052] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A DNA aptazyme consists of an aptamer domain and a DNAzyme module, in which the DNAzyme activity can be regulated by the aptamer-target interaction. The complex of G-quadruplex (GQ) and hemin is a peroxidase-mimicking DNAzyme and has become increasingly popular as a reporter system for biosensing applications. The development of GQ-based aptazymes is of high interest as they can be used as label-free biosensors for the real-time detection of pathogens. Herein, we rationally designed ca. 200 GQ-based aptazyme candidates and evaluated the suitability of 14 aptamers targeting quinine, Protein A, Staphylococcus enterotoxin B, and ATP for this detection concept. As a result, six novel aptazymes were developed for the specific detection of quinine based on two quinine-binding aptamers. The rest of designed probes, however, hardly showed significant functionality. To uncover the reasons, we performed enzyme-linked oligonucleotide assays to find how the affinity of aptamers is affected once conjugated to the DNAzyme sequence or upon integration into the aptazyme probe. Furthermore, we investigated the impact of the structure-switching functionality in the parent aptamer and the effect of the reaction matrix on the efficiency of probes.
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Affiliation(s)
- Yasaman Ahmadi
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Regina Soldo
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Krista Rathammer
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Laura Eibler
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Ivan Barišić
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
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11
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Liu LS, Wang F, Ge Y, Lo PK. Recent Developments in Aptasensors for Diagnostic Applications. ACS APPLIED MATERIALS & INTERFACES 2021; 13:9329-9358. [PMID: 33155468 DOI: 10.1021/acsami.0c14788] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Aptamers are exciting smart molecular probes for specific recognition of disease biomarkers. A number of strategies have been developed to convert target-aptamer binding into physically detectable signals. Since the aptamer sequence was first discovered, a large variety of aptamer-based biosensors have been developed, with considerable attention paid to their potential applications in clinical diagnostics. So far, a variety of techniques in combination with a wide range of functional nanomaterials have been used for the design of aptasensors to further improve the sensitivity and detection limit of target determination. In this paper, the advantages of aptamers over traditional antibodies as the molecular recognition components in biosensors for high-throughput screening target molecules are highlighted. Aptamer-target pairing configurations are predominantly single- or dual-site binding; the design of recognition modes of each aptamer-target pairing configuration is described. Furthermore, signal transduction strategies including optical, electrical, mechanical, and mass-sensitive modes are clearly explained together with examples. Finally, we summarize the recent progress in the development of aptamer-based biosensors for clinical diagnosis, including detection of cancer and disease biomarkers and in vivo molecular imaging. We then conclude with a discussion on the advanced development and challenges of aptasensors.
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Affiliation(s)
- Ling Sum Liu
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Fei Wang
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Yonghe Ge
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Pik Kwan Lo
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
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12
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Nakama T, Takezawa Y, Shionoya M. Site-specific polymerase incorporation of consecutive ligand-containing nucleotides for multiple metal-mediated base pairing. Chem Commun (Camb) 2021; 57:1392-1395. [PMID: 33438690 DOI: 10.1039/d0cc07771b] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An enzymatic method has been developed for the synthesis of DNA oligomers containing consecutive artificial ligand-type nucleotides. Three hydroxypyridone ligand-containing nucleotides forming CuII-mediated unnatural base pairs were continuously incorporated at a pre-specified position by a lesion-bypass Dpo4 polymerase. This enzymatic synthesis was applied to the development of a CuII-responsive DNAzyme. Accordingly, this research will open new routes for the construction of metal-responsive DNA architectures that are manipulated by multiple metal-mediated base pairing.
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Affiliation(s)
- Takahiro Nakama
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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13
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Washing-free Electrochemical Strategy to Detect Target DNA Utilizing Peroxidase Mimicking DNAzyme. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-020-0272-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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14
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Takezawa Y, Hu L, Nakama T, Shionoya M. Sharp Switching of DNAzyme Activity through the Formation of a Cu
II
‐Mediated Carboxyimidazole Base Pair. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009579] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry Graduate School of Science The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Lingyun Hu
- Department of Chemistry Graduate School of Science The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Takahiro Nakama
- Department of Chemistry Graduate School of Science The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry Graduate School of Science The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
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15
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Takezawa Y, Hu L, Nakama T, Shionoya M. Sharp Switching of DNAzyme Activity through the Formation of a Cu
II
‐Mediated Carboxyimidazole Base Pair. Angew Chem Int Ed Engl 2020; 59:21488-21492. [DOI: 10.1002/anie.202009579] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry Graduate School of Science The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Lingyun Hu
- Department of Chemistry Graduate School of Science The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Takahiro Nakama
- Department of Chemistry Graduate School of Science The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry Graduate School of Science The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
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16
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Zhang C, Zhang H, Wu P, Zhang X, Liu J. Suppressing the background activity of hemin for boosting the sensitivity of DNAzyme-based biosensors by SYBR Green I. Biosens Bioelectron 2020; 169:112603. [PMID: 32947082 DOI: 10.1016/j.bios.2020.112603] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/04/2020] [Accepted: 09/06/2020] [Indexed: 02/08/2023]
Abstract
Peroxidase-like DNAzymes have been extensively used to replace horseradish peroxidase (HRP) for developing biosensors for signal amplification. However, the background activity from the cofactor (i.e., free hemin) has limited the sensitivity of such sensors. Herein, we aim to find an inhibitor for hemin to suppress the background signal, and a classic split DNAzyme-based sensor was used to detect a complementary DNA oligonucleotide. After screening a series of dyes, SYBR Green I (SG, one of the DNA stanning dyes) was selected for suppressing the background. Simply by adding 0.84 μM SG, the background from 50 nM hemin was suppressed over 30-fold. The suppression was caused by the interaction between SG and hemin. In the presence of the target DNA, the formed duplex region and G-quadruplex structure can better bind SG and hemin respectively, thus preventing the interaction between them and showing a high activity of the DNAzyme. The optimized sensor showed a detection limit of 3.8 pM for the target DNA (p53 gene). In addition, the backgrounds from chemiluminescence, colorimetric and fluorescence sensing modes can all be reduced by adding SG to the split DNAzyme system. The suppression of the background of peroxidase DNAzymes is a critical step towards practical use of related biosensors.
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Affiliation(s)
- Chi Zhang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu, 610059, China
| | - Houchun Zhang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu, 610059, China
| | - Peng Wu
- Key Laboratory of Green Chemistry and Technology, Analytical & Testing Center, Sichuan University, 29 Wangjiang Road, Chengdu, 610064, China
| | - Xinfeng Zhang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu, 610059, China; Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Ontario N2L 3G1, Canada.
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Ontario N2L 3G1, Canada.
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17
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Effect of Distance from Catalytic Synergy Group to Iron Porphyrin Center on Activity of G-Quadruplex/Hemin DNAzyme. Molecules 2020; 25:molecules25153425. [PMID: 32731553 PMCID: PMC7435396 DOI: 10.3390/molecules25153425] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/16/2020] [Accepted: 07/27/2020] [Indexed: 11/17/2022] Open
Abstract
G-quadruplex/Hemin (G4/Hemin) complex has been widely used in biocatalysis and analytical applications. Meanwhile, compared with natural proteinous enzyme, its low catalytic activity is still limiting its applications. Even though several methods have been developed to enhance the peroxidation efficiency, the important core of the G4 design based enhancement mechanism is still indistinct. Here, we focus the mechanism study on the two most important microdomains: the iron porphyrin center and the catalytic synergy group within the 3' flanking. These microdomains not only provide the pocket for the combination of substrate, but also offer the axial coordination for the accelerated formation of Compound I (catalytic intermediate). In order to obtain a more suitable space layout to further accelerate the catalytic process, we have used the bases within the 3' flanking to precisely regulate the distance between microdomains. Finally, the position-dependent effect on catalytic enhancement is observed. When dC is positioned at the second-position of 3' flanking, the newly obtained DNAzyme achieves an order of magnitude improvement compared to parent G4/Hemin in catalytic activity. The results highlight the influence of the distance between the catalytic synergy group and iron porphyrin center on the activity of DNAzyme, and provide insightful information for the design of highly active DNAzymes.
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18
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LIU Z, LIU T, TAO CA, CHEN X, HUANG J, WANG F, WANG J. Amplified Analysis of DNA or Proteins by TdT-generated DNAzyme. ANAL SCI 2020; 36:835-840. [DOI: 10.2116/analsci.19p387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Zhuoliang LIU
- College of Liberal Arts and Sciences, National University of Defense Technology
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University
| | - Tianxiong LIU
- College of Liberal Arts and Sciences, National University of Defense Technology
| | - Cheng-an TAO
- College of Liberal Arts and Sciences, National University of Defense Technology
| | - Xianzhe CHEN
- College of Liberal Arts and Sciences, National University of Defense Technology
| | - Jian HUANG
- College of Liberal Arts and Sciences, National University of Defense Technology
| | - Fang WANG
- College of Liberal Arts and Sciences, National University of Defense Technology
| | - Jianfang WANG
- College of Liberal Arts and Sciences, National University of Defense Technology
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19
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Nakama T, Takezawa Y, Sasaki D, Shionoya M. Allosteric Regulation of DNAzyme Activities through Intrastrand Transformation Induced by Cu(II)-Mediated Artificial Base Pairing. J Am Chem Soc 2020; 142:10153-10162. [PMID: 32396728 DOI: 10.1021/jacs.0c03129] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Allosteric regulation is gaining increasing attention as a basis for the production of stimuli-responsive materials in many research areas including DNA nanotechnology. We expected that metal-mediated artificial base pairs, consisting of ligand-type nucleotides and a bridging metal ion, could serve as allosteric units that regulate the function of DNA molecules. In this study, we established a rational design strategy for developing CuII-responsive allosteric DNAzymes by incorporating artificial hydroxypyridone ligand-type nucleotides (H) that form a CuII-mediated base pair (H-CuII-H). We devised a new enzymatic method using a standard DNA polymerase and a ligase to prepare DNA strands containing H nucleotides. Previously reported DNAzymes were modified by introducing a H-H pair into the stem region, and the stem-loop sequences were altered so that the structure becomes catalytically inactive in the absence of CuII ions. The formation of a H-CuII-H base pair triggers intrastrand transformation from the inactive to the active structure, enabling allosteric regulation of the DNAzyme activity in response to CuII ions. The activity of the H-modified DNAzyme was reversibly switched by the addition and removal of CuII ions under isothermal conditions. Similarly, by incorporating a H-CuII-H pair into an in vitro-selected AgI-dependent DNAzyme, we have developed a DNAzyme that exhibits an AND logic-gate response to CuII and AgI ions. The rational design strategy and the easy enzymatic synthetic method presented here provide a versatile way to develop a variety of metal-responsive allosteric DNA materials, including molecular machines and logic circuits, based on metal-mediated artificial base pairing.
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Affiliation(s)
- Takahiro Nakama
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Daisuke Sasaki
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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20
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Mi L, Sun Y, Shi L, Li T. Hemin-Bridged MOF Interface with Double Amplification of G-Quadruplex Payload and DNAzyme Catalysis: Ultrasensitive Lasting Chemiluminescence MicroRNA Imaging. ACS APPLIED MATERIALS & INTERFACES 2020; 12:7879-7887. [PMID: 31983198 DOI: 10.1021/acsami.9b18053] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Here, we report a double-amplified sensing platform for ultrasensitive chemiluminescence (CL) miRNA detection in real patients' blood in which a hemin-bridged metal-organic framework (MOF) is employed as a functional interface to boost the payload and catalysis of G-quadruplex (G4) DNAzymes. Hemin is here used as the organic ligand for the MOF synthesis, which endows the MOF with an intrinsic peroxidase-like catalytic activity. Most importantly, the MOF surface provides a large amount of binding sites for polymeric G4 DNAzymes that are produced by miRNA-triggered rolling circle amplification reactions, and meanwhile, the interfaced G4 DNAzymes on MOFs (G4/MOFzymes) display an about 100-fold higher catalytic activity than those in solution. By using the G4/MOFzyme catalysts in the luminol/H2O2 CL system, the amplification detection of two acute myocardial infarction (AMI)-related miRNAs (low to 1 fM seen with naked eyes) is achieved in human serum with a smartphone as a portable imaging detector, which provides a facile methodology for point-of-care (POC) diagnosis of AMI. Compared with previous smartphone-based counterparts not requiring sophisticated equipment, this new facile methodology shows both 6 orders of magnitude higher sensitivity and an ∼50-fold longer duration for CL miRNA imaging. These unique features allow our developed G4/MOFzymes to be further employed as a novel luminescent ink for printing commonly used patterns.
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Affiliation(s)
- Lan Mi
- Department of Chemistry , University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Yudie Sun
- Department of Chemistry , University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Lin Shi
- Department of Chemistry , University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Tao Li
- Department of Chemistry , University of Science and Technology of China , Hefei , Anhui 230026 , China
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21
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LIU ZL, TAO CA, WANG JF. Progress on Applications of G-quadruplex in Biochemical Analysis. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(19)61212-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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22
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Zhang Y, Gambardella A, Üçüncü M, Geng J, Clavadetscher J, Bradley M, Lilienkampf A. Multifunctional, histidine-tagged polymers: antibody conjugation and signal amplification. Chem Commun (Camb) 2020; 56:13856-13859. [DOI: 10.1039/d0cc04591h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A polymer scaffold, with multiple reactive centres, was synthesised by RAFT polymerisation and conjugated to the antibody herceptin. A hexahistidine RAFT agent enabled simple purification of polymer–protein conjugates.
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Affiliation(s)
- Yichuan Zhang
- EaStCHEM School of Chemistry
- University of Edinburgh
- Edinburgh
- UK
- Shenzhen Institutes of Advanced Technology
| | | | - Muhammed Üçüncü
- EaStCHEM School of Chemistry
- University of Edinburgh
- Edinburgh
- UK
- Department of Analytical Chemistry, Faculty of Pharmacy
| | - Jin Geng
- EaStCHEM School of Chemistry
- University of Edinburgh
- Edinburgh
- UK
- Shenzhen Institutes of Advanced Technology
| | | | - Mark Bradley
- EaStCHEM School of Chemistry
- University of Edinburgh
- Edinburgh
- UK
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23
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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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24
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Wang H, Wang H, Zhang M, Jia Y, Li Z. A label-free aptamer-based biosensor for microRNA detection by the RNA-regulated fluorescence of malachite green. RSC Adv 2019; 9:32906-32910. [PMID: 35529731 PMCID: PMC9073149 DOI: 10.1039/c9ra07552f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 10/02/2019] [Indexed: 12/24/2022] Open
Abstract
MicroRNAs (miRNAs) have been considered as promising molecular biomarkers for disease diagnosis, prognosis, as well as drug development. Herein, we wish to report a low background and label-free aptamer-based biosensor for miRNA assay by RNA-regulated fluorescence of malachite green (MG). In this biosensor-based strategy, target miRNA can specifically hybridize with the DNA extension template to form the T7 in vitro transcription system. Then the following transcription amplification produces a large number of MG RNA aptamers (MGAs) which light up the fluorescence of the MG, achieving significant fluorescence enhancement for miRNA quantitative analysis. The aptamer-based biosensor exhibits high sensitivity with a quite low detection limit of 10 amol target miRNA and high specificity to clearly discriminate very similar miRNA family members, even only one base difference. Furthermore, we have demonstrated that the biosensor is practical and reliable for the quantitative detection of miRNA in complex real samples.
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Affiliation(s)
- Honghong Wang
- School of Chemistry and Biology Engineering, University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Hui Wang
- School of Chemistry and Biology Engineering, University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Mai Zhang
- School of Chemistry and Biology Engineering, University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Yuting Jia
- School of Chemistry and Biology Engineering, University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Zhengping Li
- School of Chemistry and Biology Engineering, University of Science and Technology Beijing Beijing 100083 P. R. China
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25
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Man T, Lai W, Xiao M, Wang X, Chandrasekaran AR, Pei H, Li L. A versatile biomolecular detection platform based on photo-induced enhanced Raman spectroscopy. Biosens Bioelectron 2019; 147:111742. [PMID: 31672389 DOI: 10.1016/j.bios.2019.111742] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/19/2019] [Accepted: 09/28/2019] [Indexed: 12/25/2022]
Abstract
Surface-enhanced Raman spectroscopy (SERS) as one of the effective tools for sensitive and selective detection of biomolecules has attracted tremendous attention. Here, we construct a versatile biomolecular detection platform based on photo-induced enhanced Raman spectroscopy (PIERS) effect for ultrasensitive detection of multiple analytes. In our PIERS sensor, we exploit the molecular recognition capacity of aptamers and the high affinity of aptamers with analyte to trigger TiO2@AgNP substrates binding with Raman tag-labeled gold nanoparticles probes via analyte, thus forming sandwich complexes. Additionally, combining plasmonic nanoparticles with photo-activated substrates allows PIERS sensor to achieve increased sensitivity beyond the normal SERS effect upon ultraviolet irradiation. Accordingly, the PIERS can be implemented for analysis of multiple analytes by designing different analyte aptamers, and we further demonstrate that the constructed PIERS sensor can serve as a versatile detection platform for sensitively analyzing various biomolecules including small molecules (adenosine triphosphate (ATP), limit of detection (LOD) of 0.1 nM), a biomarker (thrombin, LOD of 50 pM), and a drug (cocaine, LOD of 5 nM). Therefore, this versatile biomolecular detection platform based on PIERS effect for ultrasensitive detection of multiple analytes holds great promise to be a practical tool.
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Affiliation(s)
- Tiantian Man
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, PR China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, PR China
| | - Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, PR China
| | - Xiwei Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, PR China
| | | | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, PR China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, PR China.
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26
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Label-free Pb2+ detection on the layer-by-layer platform using real-time dual polarization interferometry. Talanta 2019; 202:336-341. [DOI: 10.1016/j.talanta.2019.05.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/20/2019] [Accepted: 05/02/2019] [Indexed: 11/17/2022]
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27
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Heiat M, Negahdary M. Sensitive diagnosis of alpha-fetoprotein by a label free nanoaptasensor designed by modified Au electrode with spindle-shaped gold nanostructure. Microchem J 2019. [DOI: 10.1016/j.microc.2019.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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28
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Munzar JD, Ng A, Juncker D. Duplexed aptamers: history, design, theory, and application to biosensing. Chem Soc Rev 2019; 48:1390-1419. [PMID: 30707214 DOI: 10.1039/c8cs00880a] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nucleic acid aptamers are single stranded DNA or RNA sequences that specifically bind a cognate ligand. In addition to their widespread use as stand-alone affinity binding reagents in analytical chemistry, aptamers have been engineered into a variety of ligand-specific biosensors, termed aptasensors. One of the most common aptasensor formats is the duplexed aptamer (DA). As defined herein, DAs are aptasensors containing two nucleic acid elements coupled via Watson-Crick base pairing: (i) an aptamer sequence, which serves as a ligand-specific receptor, and (ii) an aptamer-complementary element (ACE), such as a short DNA oligonucleotide, which is designed to hybridize to the aptamer. The ACE competes with ligand binding, such that DAs generate a signal upon ligand-dependent ACE-aptamer dehybridization. DAs possess intrinsic advantages over other aptasensor designs. For example, DA biosensing designs generalize across DNA and RNA aptamers, DAs are compatible with many readout methods, and DAs are inherently tunable on the basis of nucleic acid hybridization. However, despite their utility and popularity, DAs have not been well defined in the literature, leading to confusion over the differences between DAs and other aptasensor formats. In this review, we introduce a framework for DAs based on ACEs, and use this framework to distinguish DAs from other aptasensor formats and to categorize cis- and trans-DA designs. We then explore the ligand binding dynamics and chemical properties that underpin DA systems, which fall under conformational selection and induced fit models, and which mirror classical SN1 and SN2 models of nucleophilic substitution reactions. We further review a variety of in vitro and in vivo applications of DAs in the chemical and biological sciences, including riboswitches and riboregulators. Finally, we present future directions of DAs as ligand-responsive nucleic acids. Owing to their tractability, versatility and ease of engineering, DA biosensors bear a great potential for the development of new applications and technologies in fields ranging from analytical chemistry and mechanistic modeling to medicine and synthetic biology.
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Affiliation(s)
- Jeffrey D Munzar
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
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29
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Sun Y, Shi L, Wang Q, Mi L, Li T. Spherical Nucleic Acid Enzyme (SNAzyme) Boosted Chemiluminescence miRNA Imaging Using a Smartphone. Anal Chem 2019; 91:3652-3658. [DOI: 10.1021/acs.analchem.8b05696] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Yudie Sun
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
| | - Lin Shi
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
| | - Qiwei Wang
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
| | - Lan Mi
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
| | - Tao Li
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
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30
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Yang L, Wu Q, Chen Y, Liu X, Wang F, Zhou X. Amplified MicroRNA Detection and Intracellular Imaging Based on an Autonomous and Catalytic Assembly of DNAzyme. ACS Sens 2019; 4:110-117. [PMID: 30562005 DOI: 10.1021/acssensors.8b01000] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Abnormal microRNAs (miRNAs) expression is demonstrated to associate with various important biological processes, including tumorigenesis, metastasis, and progression. Given the low miRNA expression at the earlier stage of diseases, its amplified detection still requires more efforts. Inspired by the two-stage arithmetic amplifier of electric devices, we reported an autonomous and catalytic assembly of DNAzyme strategy by integrating a DNAzyme biocatalyst and catalytic hairpin assembly (CHA) circuit. Here the catalytically inactive DNAzyme subunits were respectively grafted into these metastable CHA hairpin reactants that were kinetically impeded without false cross-hybridizations. The target catalyzed the nonenzymatic CHA-mediated successive assembly of dumbbell-like bis-DNAzyme nanostructures, leading to the efficient DNAzyme-mediated cleavage of fluorophore/quencher-modified substrate and to the generation of an amplified fluorescence signal. The present CHA-DNAzyme amplifier can be employed as a versatile and general sensing platform for analyzing other analytes (e.g., miRNA) by introducing a sensing module into the present system. Moreover, the homogeneous CHA-DNAzyme method could realize the sensitive intracellular miRNA imaging in living cells, which is attributed to the inherently synergistic amplification property between DNAzyme and CHA reactions. Given the attractive analytical features of the autonomous CHA-DNAzyme system, the present strategy shows great promise for analyzing additional different analytes in clinical research fields.
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Affiliation(s)
- Lei Yang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Qiong Wu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yuqi Chen
- Key Laboratory of Biomedical Polymers (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Xiaoqing Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Fuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Xiang Zhou
- Key Laboratory of Biomedical Polymers (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
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Taheri RA, Eskandari K, Negahdary M. An electrochemical dopamine aptasensor using the modified Au electrode with spindle-shaped gold nanostructure. Microchem J 2018. [DOI: 10.1016/j.microc.2018.08.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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32
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Kurapati R, Bianco A. Peroxidase mimicking DNAzymes degrade graphene oxide. NANOSCALE 2018; 10:19316-19321. [PMID: 30306169 DOI: 10.1039/c8nr06535g] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
DNAzymes made of supramolecular guanine-rich G-quadruplexes and hemin are attracting a lot of interest due to their peroxidase activity mimicking the natural enzyme horseradish peroxidase (HRP). Herein, we demonstrate that DNAzyme consisting of a PS2.M-hemin complex can be an alternative to natural HRP for the oxidation and degradation of graphene oxide (GO). The degradation of GO sheets was carried out by incubating the PS2.M-hemin complex in the presence of hydrogen peroxide for 30 days. The degradation of GO has been confirmed using transmission electron microscopy and 2d Raman mapping. The current study suggests that the peroxidase activity of DNAzymes is similar to HRP and DNAzymes are able to degrade carbon-based nanomaterials.
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Affiliation(s)
- Rajendra Kurapati
- University of Strasbourg, CNRS, Immunology, Immunopathology and Therapeutic Chemistry, UPR 3572, 67000 Strasbourg, France.
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33
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Song J, Xu C, Huang S, Lei W, Ruan Y, Lu H, Zhao W, Xu J, Chen H. Ultrasmall Nanopipette: Toward Continuous Monitoring of Redox Metabolism at Subcellular Level. Angew Chem Int Ed Engl 2018; 57:13226-13230. [DOI: 10.1002/anie.201808537] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Juan Song
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Cong‐Hui Xu
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Shi‐Zhen Huang
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Wen Lei
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Yi‐Fan Ruan
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Hai‐Jie Lu
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Wei Zhao
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Jing‐Juan Xu
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Hong‐Yuan Chen
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
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34
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Song J, Xu C, Huang S, Lei W, Ruan Y, Lu H, Zhao W, Xu J, Chen H. Ultrasmall Nanopipette: Toward Continuous Monitoring of Redox Metabolism at Subcellular Level. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201808537] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Juan Song
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Cong‐Hui Xu
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Shi‐Zhen Huang
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Wen Lei
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Yi‐Fan Ruan
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Hai‐Jie Lu
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Wei Zhao
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Jing‐Juan Xu
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Hong‐Yuan Chen
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
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35
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Zhang H, Li X, He F, Zhao M, Ling L. Turn-off colorimetric sensor for sequence-specific recognition of single-stranded DNA based upon Y-shaped DNA structure. Sci Rep 2018; 8:12021. [PMID: 30104740 PMCID: PMC6089895 DOI: 10.1038/s41598-018-30529-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/31/2018] [Indexed: 12/19/2022] Open
Abstract
A novel turn-off colorimetric sensor for sequence-specific recognition of single-stranded DNA (ssDNA) was established by combining Y-shaped DNA duplex and G-quadruplex-hemin DNAzyme. A G-rich single-stranded DNA (Oligo-1) displays peroxidase mimicking catalytic activity due to the specific binding with hemin in the presence of K+, which was able to catalyze the oxidation of colorless 2,2'-azinobis(3-ethylbenzothiazoline)-6-sulfonic acid (ABTS2-) by H2O2 to generate green ABTS•- radical for colorimetric assay. Oligonucleotide 2 (Oligo-2) was partly complementary with Oligo-1 and the target DNA. Upon addition of target DNA, Oligo-1, Oligo-2 and target DNA can hybridize with each other to form Y-shaped DNA duplex. The DNAzyme sequence of Oligo-1 was partly caged into Y-shaped DNA duplex, resulting in the inactivation of the DNAzyme and a sharp decrease of the absorbance of the oxidation product of ABTS2-. Under the optimum condition, the absorbance decreased linearly with the concentration of target DNA over the range of 1.0-250 nM and the detection limit was 0.95 nM (3σ/slope) Moreover, satisfied result was obtained for the discrimination of single-base or two-base mismatched DNA.
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Affiliation(s)
- Hong Zhang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, P. R. China
| | - Xintong Li
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, P. R. China
| | - Fan He
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, P. R. China
| | - Mingqin Zhao
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, P. R. China.
| | - Liansheng Ling
- School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P. R. China.
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36
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Zhou Z, Luo G, Wulf V, Willner I. Application of DNA Machineries for the Barcode Patterned Detection of Genes or Proteins. Anal Chem 2018; 90:6468-6476. [PMID: 29737162 DOI: 10.1021/acs.analchem.7b04916] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The study introduces an analytical platform for the detection of genes or aptamer-ligand complexes by nucleic acid barcode patterns generated by DNA machineries. The DNA machineries consist of nucleic acid scaffolds that include specific recognition sites for the different genes or aptamer-ligand analytes. The binding of the analytes to the scaffolds initiate, in the presence of the nucleotide mixture, a cyclic polymerization/nicking machinery that yields displaced strands of variable lengths. The electrophoretic separation of the resulting strands provides barcode patterns for the specific detection of the different analytes. Mixtures of DNA machineries that yield, upon sensing of different genes (or aptamer ligands), one-, two-, or three-band barcode patterns are described. The combination of nucleic acid scaffolds acting, in the presence of polymerase/nicking enzyme and nucleotide mixture, as DNA machineries, that generate multiband barcode patterns provide an analytical platform for the detection of an individual gene out of many possible genes. The diversity of genes (or other analytes) that can be analyzed by the DNA machineries and the barcode patterned imaging is given by the Pascal's triangle. As a proof-of-concept, the detection of one of six genes, that is, TP53, Werner syndrome, Tay-Sachs normal gene, BRCA1, Tay-Sachs mutant gene, and cystic fibrosis disorder gene by six two-band barcode patterns is demonstrated. The advantages and limitations of the detection of analytes by polymerase/nicking DNA machineries that yield barcode patterns as imaging readout signals are discussed.
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Affiliation(s)
- Zhixin Zhou
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Guofeng Luo
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Verena Wulf
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Itamar Willner
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
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37
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Wang LJ, Ren M, Liang L, Zhang CY. Controllable fabrication of bio-bar codes for dendritically amplified sensing of human T-lymphotropic viruses. Chem Sci 2018; 9:4942-4949. [PMID: 29938021 PMCID: PMC5994793 DOI: 10.1039/c8sc01641k] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 05/09/2018] [Indexed: 01/10/2023] Open
Abstract
We demonstrate for the first time the controllable fabrication of bio-bar codes for dendritically amplified sensing of low-abundant HTLV-II DNA.
Human T-lymphotropic virus type II (HTLV-II) is an important type-C retrovirus, closely related to a variety of human diseases. Here, we demonstrate for the first time the controllable fabrication of bio-bar codes for dendritically amplified sensing of low-abundant HTLV-II DNA by the integration of terminal deoxynucleotidyl transferase (TdT)-catalyzed template-free polymerization extension with bio-bar-code amplification (BCA). HTLV-II DNA hybridizes with magnetic microparticle (MMP)-modified capture probe 1, forming a stable DNA duplex with a protruding 3′-hydroxylated sequence which may function as a primer to initiate the TdT-catalyzed first-step polymerization extension for the generation of a poly-thymidine (T) sequence. The resultant poly-T products may hybridize with poly-adenine (A) capture probe 2, inducing the self-assembly of multiple capture probe 2-/reporter probe-functionalized Au nanoparticles (AuNPs) onto the MMP. Subsequently, the reporter probes may act as the primers to initiate the TdT-catalyzed second-step polymerization extension, producing large numbers of G-rich DNAzymes for the generation of an enhanced chemiluminescence signal. Taking advantage of the efficient polymerization extension reaction catalyzed by TdT, the high amplification efficiency of BCA, and the intrinsically high sensitivity of G-rich DNAzyme-driven chemiluminescence, this method exhibits ultrahigh sensitivity with a limit of detection of as low as 0.50 aM and a large dynamic range of 9 orders of magnitude from 1 aM to 1 nM. Moreover, this method can be applied for the discrimination of a single-base mismatch and the measurement of HTLV-II DNA in both human serum and human T-lymphocytic leukemia cells, holding great potential in biomedical research and clinical diagnosis.
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Affiliation(s)
- Li-Juan Wang
- College of Chemistry, Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86 0531 86186033
| | - Ming Ren
- College of Chemistry, Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86 0531 86186033
| | - Li Liang
- Department of Tumor Chemotherapy and Radiation Sickness , Peking University Third Hospital , Beijing 100191 , China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86 0531 86186033
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38
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Wang Y, Shan D, Wu G, Wang H, Ru F, Zhang X, Li L, Qian Y, Lu X. A novel “dual-potential” ratiometric electrochemiluminescence DNA sensor based on enhancing and quenching effect by G-quadruplex / hemin and Au-Luminol bifunctional nanoparticles. Biosens Bioelectron 2018; 106:64-70. [DOI: 10.1016/j.bios.2018.01.052] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/22/2018] [Accepted: 01/23/2018] [Indexed: 11/26/2022]
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39
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Wang S, Sun J, Zhao J, Lu S, Yang X. Photo-Induced Electron Transfer-Based Versatile Platform with G-Quadruplex/Hemin Complex as Quencher for Construction of DNA Logic Circuits. Anal Chem 2018; 90:3437-3442. [PMID: 29425022 DOI: 10.1021/acs.analchem.7b05145] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
G-quadruplex has been developed as an innovator for analytical chemistry and biomedicine due to its vibrant binding activity, structural polymorphism, and critical roles in biological regulation. Herein, a simple but versatile platform was obtained by integrating split G-quadruplex and fluorophore into a molecular beacon, where the photoinduced electron transfer could occur when the fluorophore approached the preformed G-quadruplex/hemin complexes. Such design subtly combined the G4 disruption-induced fluorescent turn-on strategy and the photoinduced electron transfer property into one platform for constructing the logic circuits. On the basis of such a universal platform, a series of binary logic gates (OR, INHIBIT, AND, and XOR), a combinatorial gate (INHIBIT-OR), and even a complex logic operation for discrimination of multiples of three from natural numbers less than ten have been successfully achieved only by employing such platform as work unit and single-strand DNAs as inputs. The set-reset function of this platform could be realized by alternatively introducing blocking and releasing strands. In addition, this platform could operate in a biological matrix stably and precisely. Therefore, such a universal platform lays the foundation for complicating the logic systems, realizing the biocomputing and also points out a new direction for target detection.
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Affiliation(s)
- Shuang Wang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Changchun , Jilin 130022 , China.,University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Jian Sun
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Changchun , Jilin 130022 , China
| | - Jiahui Zhao
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Changchun , Jilin 130022 , China.,University of Chinese Academy of Sciences , Beijing 100039 , China
| | - Shasha Lu
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Changchun , Jilin 130022 , China.,University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Xiurong Yang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Changchun , Jilin 130022 , China
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40
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Shahbazi N, Hosseinkhani S, Khajeh K, Ranjbar B. Structural and functional study of a simple, rapid, and label-free DNAzyme-based DNA biosensor for optimization activity. Biopolymers 2017; 107. [DOI: 10.1002/bip.23028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 03/23/2017] [Accepted: 04/26/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Narges Shahbazi
- Department of Nanobiotechnology, Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
| | - Saman Hosseinkhani
- Department of Nanobiotechnology, Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
- Department of Biochemistry, Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
| | - Khosro Khajeh
- Department of Nanobiotechnology, Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
- Department of Biochemistry, Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
| | - Bijan Ranjbar
- Department of Nanobiotechnology, Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
- Department of Biophysics, Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
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41
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Yu Y, Su G, Zhu H, Zhu Q, Chen Y, Xu B, Li Y, Zhang W. Proximity hybridization-mediated isothermal exponential amplification for ultrasensitive electrochemical protein detection. Int J Nanomedicine 2017; 12:5903-5914. [PMID: 28860756 PMCID: PMC5566414 DOI: 10.2147/ijn.s142015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In this study, we fabricated a novel electrochemical biosensing platform on the basis of target-triggered proximity hybridization-mediated isothermal exponential amplification reaction (EXPAR) for ultrasensitive protein analysis. Through rational design, the aptamers for protein recognition were integrated within two DNA probes. Via proximity hybridization principle, the affinity protein-binding event was converted into DNA assembly process. The recognition of protein by aptamers can trigger the strand displacement through the increase of the local concentrations of the involved probes. As a consequence, the output DNA was displaced, which can hybridize with the duplex probes immobilized on the electrode surface subsequently, leading to the initiation of the EXPAR as well as the cleavage of duplex probes. Each cleavage will release the gold nanoparticles (AuNPs) binding sequence. With the modification of G-quadruplex sequence, electrochemical signals were yielded by the AuNPs through oxidizing 3,3',5,5'-tetramethylbenzidine in the presence of H2O2. The study we proposed exhibited high sensitivity toward platelet-derived growth factor BB (PDGF-BB) with the detection limit of 52 fM. And, this method also showed great selectivity among the PDGF isoforms and performed well in spiked human serum samples.
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Affiliation(s)
- Yanyan Yu
- School of Pharmacy, Nantong University, Nantong, People's Republic of China
| | - Gaoxing Su
- School of Pharmacy, Nantong University, Nantong, People's Republic of China
| | - Hongyan Zhu
- School of Pharmacy, Nantong University, Nantong, People's Republic of China
| | - Qing Zhu
- School of Pharmacy, Nantong University, Nantong, People's Republic of China
| | - Yong Chen
- School of Pharmacy, Nantong University, Nantong, People's Republic of China
| | - Bohui Xu
- School of Pharmacy, Nantong University, Nantong, People's Republic of China
| | - Yuqin Li
- School of Pharmacy, Nantong University, Nantong, People's Republic of China
| | - Wei Zhang
- School of Pharmacy, Nantong University, Nantong, People's Republic of China
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42
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Li X, Zhang H, Tang Y, Wu P, Xu S, Zhang X. A Both-End Blocked Peroxidase-Mimicking DNAzyme for Low-Background Chemiluminescent Sensing of miRNA. ACS Sens 2017; 2:810-816. [PMID: 28723123 DOI: 10.1021/acssensors.7b00178] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
G-quadruplex DNAzymes that exhibited peroxidase-like activity have been shown to be appealing reporters for amplified readout of biosensing events simply by their formation or dissociation in the presence of analytes. For low background signaling, the efficient preblock of DNAzymes is critically important. Herein, we report a both-end blocked DNAzyme beacon strategy for chemiluminescent biosensing. The catalytic activity of peroxidase-mimicking DNAzyme can be inactivated fully by fixing both ends of the DNAzyme sequence, and easily recovered via a strand displace reaction between the miRNA and the block DNA. The efficient block and recovery of DNAzymes provide the both-end blocked beacon the highest signal-to-background ratio (over 25) among the reported DNAzymes for amplification-free detection of miRNA. As a result, the beacon allowed detection of subpicomolar miRNA without any labeling and amplification procedures, which is about 40-fold more sensitive than the traditional hairpin fluorescence beacon. Also, it exhibited excellent discrimination ability that can distinguish single-base mismatch miRNA. The simplicity, high sensitivity, and selectivity provided by the beacon make it a promising alternative tool for nucleic acid detection.
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Affiliation(s)
- Xianming Li
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
| | - Houchun Zhang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
| | - Yurong Tang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
| | - Peng Wu
- Analytical & Testing Center, Sichuan University, Chengdu 610064, China
| | - Shuxia Xu
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
| | - Xinfeng Zhang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
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43
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Zhang H, Peng L, Li M, Ma J, Qi S, Chen H, Zhou L, Chen X. A label-free colorimetric biosensor for sensitive detection of vascular endothelial growth factor-165. Analyst 2017; 142:2419-2425. [PMID: 28561084 DOI: 10.1039/c7an00541e] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sensitive detection of a low abundant protein is essential for biomedical research and clinical diagnostics. Herein, we develop a label-free colorimetric biosensor for the sensitive detection of recombinant human vascular endothelial growth factor-165 (VEGF165). This biosensor consists of an aptamer-based hairpin probe, an assistant DNA-trigger duplex and a linear template. In the presence of VEGF165, the specific binding of VEGF165 with the aptamer-based hairpin probe results in the opening of a hairpin probe and the opened hairpin probe subsequently hybridizes with the single-stranded region of the assistant DNA-trigger duplex to initiate the strand displacement amplification (SDA) to yield abundant triggers. The released triggers can further function as the primers to anneal with the hairpin probe and lead to the opening of the hairpin structure, which subsequently hybridizes with the assistant DNA-trigger duplex to initiate the next round of SDA reaction and generates more triggers. Large amounts of triggers could be generated by the synergistic operation of dual SDA reaction, and the obtained triggers can initiate a new round of SDA reaction to yield numerous G-quadruplex DNAzymes, which subsequently catalyze the conversion of ABTS2- to ABTS˙- by H2O2 to yield a color change with the assistance of a cofactor hemin. In contrast, in the absence of target VEGF165, the hairpin probe, the assistant DNA-trigger duplex and the linear template can stably coexist in solution, and thus no color change is observed because no trigger can initiate SDA to generate the G-quadruplex DNAzyme. This biosensor has a low detection limit of 1.70 pM and a dynamic range over 3 orders of magnitude from 24.00 pM to 11.25 nM. Moreover, the biosensor shows excellent specificity toward the target VEGF165 and the entire reaction can be carried out in an isothermal manner without the involvement of a high precision thermal cycler, making the current assay extremely cost effective.
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Affiliation(s)
- Huige Zhang
- National Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China. and Department of Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Liang Peng
- Facility Center of Life Science Research, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Maoxing Li
- Lanzhou General Hospital of PLA, Lanzhou 730050, China
| | - Ji Ma
- Lanzhou General Hospital of PLA, Lanzhou 730050, China
| | - Shengda Qi
- National Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China. and Department of Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Hongli Chen
- National Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China. and Department of Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Lei Zhou
- National Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China. and Department of Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Xingguo Chen
- National Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China. and Department of Chemistry, Lanzhou University, Lanzhou 730000, China
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44
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Cai N, Tan L, Li Y, Xia T, Hu T, Su X. Biosensing platform for the detection of uric acid based on graphene quantum dots and G-quadruplex/hemin DNAzyme. Anal Chim Acta 2017; 965:96-102. [DOI: 10.1016/j.aca.2017.01.067] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/27/2017] [Accepted: 01/31/2017] [Indexed: 12/22/2022]
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45
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Vázquez-González M, Liao WC, Cazelles R, Wang S, Yu X, Gutkin V, Willner I. Mimicking Horseradish Peroxidase Functions Using Cu 2+-Modified Carbon Nitride Nanoparticles or Cu 2+-Modified Carbon Dots as Heterogeneous Catalysts. ACS NANO 2017; 11:3247-3253. [PMID: 28234445 DOI: 10.1021/acsnano.7b00352] [Citation(s) in RCA: 185] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Cu2+-functionalized carbon nitride nanoparticles (Cu2+-g-C3N4 NPs), ∼200 nm, and Cu2+-carbon dots (Cu2+-C-dots), ∼8 nm, act as horseradish peroxidase-mimicking catalysts. The nanoparticles catalyze the generation of chemiluminescence in the presence of luminol/H2O2 and catalyze the oxidation of dopamine by H2O2 to form aminochrome. The Cu2+-g-C3N4-driven generation of chemiluminescence is used to develop a H2O2 sensor and is implemented to develop a glucose detection platform and a sensor for probing glucose oxidase. Also, the Cu2+-C-dots are functionalized with the β-cyclodextrin (β-CD) receptor units. The concentration of dopamine, at the Cu2+-C-dots' surface, by means of the β-CD receptor sites, leads to a 4-fold enhancement in the oxidation of dopamine by H2O2 to yield aminochrome compared to that of the unmodified C-dots.
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Affiliation(s)
- Margarita Vázquez-González
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Wei-Ching Liao
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Rémi Cazelles
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Shan Wang
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Xu Yu
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Vitaly Gutkin
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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A label-free colorimetric isothermal cascade amplification for the detection of disease-related nucleic acids based on double-hairpin molecular beacon. Anal Chim Acta 2017; 957:55-62. [DOI: 10.1016/j.aca.2016.12.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 12/10/2016] [Accepted: 12/16/2016] [Indexed: 11/20/2022]
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Chen J, Guo Y, Zhou J, Ju H. The Effect of Adenine Repeats on G-quadruplex/hemin Peroxidase Mimicking DNAzyme Activity. Chemistry 2017; 23:4210-4215. [PMID: 28121370 DOI: 10.1002/chem.201700040] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Indexed: 01/19/2023]
Abstract
The catalytic activity of G-quadruplex/hemin is much lower than that of proteinous enzymes, so it is very important to increase its activity. Very recently, flanking sequences, which can be regarded as an external part of G-quadruplexes, were found to enhance the activity of G-quadruplex/hemin DNAzyme. However, little is known about the effect of internal parts, such as loop sequences and linkers, on the activity. In the present study, adenine repeats were incorporated into several designed G-quadruplex structures either in the loops, bulges, or linkers, and the constructed G-quadruplex/hemin DNAzyme exhibit about fivefold improvement in peroxidase-mimicking activity in some cases. The enhancement effect may result from the formation of compound I, protoporphyrin⋅FeIV =O.+ , accelerated by dA repeats, which was demonstrated by H2 O2 decay kinetics and pH dependency analysis. The novel enhancement methods described here may help in the development of high-activity DNAzymes, illustrated by a dimer G-quadruplex with flanking adenine at one end, a relatively long adenine run in one loop, and another adenine run in the linker.
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Affiliation(s)
- Jielin Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yuehua Guo
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
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Zhang Z, Liu B, Liu J. Molecular Imprinting for Substrate Selectivity and Enhanced Activity of Enzyme Mimics. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1602730. [PMID: 27925383 DOI: 10.1002/smll.201602730] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/26/2016] [Indexed: 06/06/2023]
Abstract
Using molecular imprinting, a peroxidase-mimicking DNAzyme has achieved substrate specificity with enhanced activity in a nanoscale gel for three different substrates.
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Affiliation(s)
- Zijie Zhang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Ave W, Waterloo, ON, N2L 3G1, Canada
| | - Biwu Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Ave W, Waterloo, ON, N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Ave W, Waterloo, ON, N2L 3G1, Canada
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Computational Biosensors: Molecules, Algorithms, and Detection Platforms. MODELING, METHODOLOGIES AND TOOLS FOR MOLECULAR AND NANO-SCALE COMMUNICATIONS 2017. [PMCID: PMC7123247 DOI: 10.1007/978-3-319-50688-3_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Advanced nucleic acid-based sensor-applications require computationally intelligent biosensors that are able to concurrently perform complex detection and classification of samples within an in vitro platform. Realization of these cutting-edge computational biosensor systems necessitates innovation and integration of three key technologies: molecular probes with computational capabilities, algorithmic methods to enable in vitro computational post processing and classification, and immobilization and detection approaches that enable the realization of deployable computational biosensor platforms. We provide an overview of current technologies, including our contributions towards the development of computational biosensor systems.
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