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Munzar JD, Ng A, Corrado M, Juncker D. Complementary oligonucleotides regulate induced fit ligand binding in duplexed aptamers. Chem Sci 2017; 8:2251-2256. [PMID: 28507681 PMCID: PMC5408566 DOI: 10.1039/c6sc03993f] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/07/2016] [Indexed: 12/20/2022] Open
Abstract
Duplexed aptamers (DAs) are engineered by hybridizing an aptamer-complementary element (ACE, e.g. a DNA oligonucleotide) to an aptamer; to date, ACEs have been presumed to sequester the aptamer into a non-binding duplex state, in line with a conformational selection-based model of ligand binding. Here, we uncover that DAs can actively bind a ligand from the duplex state through an ACE-regulated induced fit mechanism. Using a widely-studied ATP DNA aptamer and a solution-based equilibrium assay, DAs were found to exhibit affinities up to 1 000 000-fold higher than predicted by conformational selection alone, with different ACEs regulating the level of induced fit binding, as well as the cooperative allostery of the DA (Hill slope of 1.8 to 0.7). To validate these unexpected findings, we developed a non-equilibrium surface-based assay that only signals induced fit binding, and corroborated the results from the solution-based assay. Our findings indicate that ACEs regulate ATP DA ligand binding dynamics, opening new avenues for the study and design of ligand-responsive nucleic acids.
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Affiliation(s)
- Jeffrey D Munzar
- McGill University and Genome Quebec Innovation Centre , 740 Dr. Penfield Avenue , Montreal , Quebec H3A 0G1 , Canada .
- Department of Biomedical Engineering , McGill University , 3775 Rue University , Montreal , Quebec H3A 2B4 , Canada
| | - Andy Ng
- McGill University and Genome Quebec Innovation Centre , 740 Dr. Penfield Avenue , Montreal , Quebec H3A 0G1 , Canada .
- Department of Biomedical Engineering , McGill University , 3775 Rue University , Montreal , Quebec H3A 2B4 , Canada
| | - Mario Corrado
- McGill University and Genome Quebec Innovation Centre , 740 Dr. Penfield Avenue , Montreal , Quebec H3A 0G1 , Canada .
- Department of Biomedical Engineering , McGill University , 3775 Rue University , Montreal , Quebec H3A 2B4 , Canada
| | - David Juncker
- McGill University and Genome Quebec Innovation Centre , 740 Dr. Penfield Avenue , Montreal , Quebec H3A 0G1 , Canada .
- Department of Biomedical Engineering , McGill University , 3775 Rue University , Montreal , Quebec H3A 2B4 , Canada
- Department of Neurology and Neurosurgery , McGill University , 3801 Rue University , Montreal , Quebec H3A 2B4 , Canada
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53
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Zoppe JO, Ataman NC, Mocny P, Wang J, Moraes J, Klok HA. Surface-Initiated Controlled Radical Polymerization: State-of-the-Art, Opportunities, and Challenges in Surface and Interface Engineering with Polymer Brushes. Chem Rev 2017; 117:1105-1318. [PMID: 28135076 DOI: 10.1021/acs.chemrev.6b00314] [Citation(s) in RCA: 603] [Impact Index Per Article: 86.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The generation of polymer brushes by surface-initiated controlled radical polymerization (SI-CRP) techniques has become a powerful approach to tailor the chemical and physical properties of interfaces and has given rise to great advances in surface and interface engineering. Polymer brushes are defined as thin polymer films in which the individual polymer chains are tethered by one chain end to a solid interface. Significant advances have been made over the past years in the field of polymer brushes. This includes novel developments in SI-CRP, as well as the emergence of novel applications such as catalysis, electronics, nanomaterial synthesis and biosensing. Additionally, polymer brushes prepared via SI-CRP have been utilized to modify the surface of novel substrates such as natural fibers, polymer nanofibers, mesoporous materials, graphene, viruses and protein nanoparticles. The last years have also seen exciting advances in the chemical and physical characterization of polymer brushes, as well as an ever increasing set of computational and simulation tools that allow understanding and predictions of these surface-grafted polymer architectures. The aim of this contribution is to provide a comprehensive review that critically assesses recent advances in the field and highlights the opportunities and challenges for future work.
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Affiliation(s)
- Justin O Zoppe
- Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères Bâtiment MXD, Ecole Polytechnique Fédérale de Lausanne (EPFL) , Station 12 CH-1015 Lausanne, Switzerland
| | - Nariye Cavusoglu Ataman
- Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères Bâtiment MXD, Ecole Polytechnique Fédérale de Lausanne (EPFL) , Station 12 CH-1015 Lausanne, Switzerland
| | - Piotr Mocny
- Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères Bâtiment MXD, Ecole Polytechnique Fédérale de Lausanne (EPFL) , Station 12 CH-1015 Lausanne, Switzerland
| | - Jian Wang
- Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères Bâtiment MXD, Ecole Polytechnique Fédérale de Lausanne (EPFL) , Station 12 CH-1015 Lausanne, Switzerland
| | - John Moraes
- Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères Bâtiment MXD, Ecole Polytechnique Fédérale de Lausanne (EPFL) , Station 12 CH-1015 Lausanne, Switzerland
| | - Harm-Anton Klok
- Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères Bâtiment MXD, Ecole Polytechnique Fédérale de Lausanne (EPFL) , Station 12 CH-1015 Lausanne, Switzerland
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54
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Yan H, Zhang L, Yu P, Mao L. Sensitive and Fast Humidity Sensor Based on A Redox Conducting Supramolecular Ionic Material for Respiration Monitoring. Anal Chem 2016; 89:996-1001. [DOI: 10.1021/acs.analchem.6b04350] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Hailong Yan
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Analytical
Chemistry for Living Biosystems, Institute of Chemistry, The Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Zhang
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Analytical
Chemistry for Living Biosystems, Institute of Chemistry, The Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Yu
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Analytical
Chemistry for Living Biosystems, Institute of Chemistry, The Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lanqun Mao
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Analytical
Chemistry for Living Biosystems, Institute of Chemistry, The Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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55
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Ding S, Cao S, Zhu A, Shi G. Wettability Switching of Electrode for Signal Amplification: Conversion of Conformational Change of Stimuli-Responsive Polymer into Enhanced Electrochemical Chiral Analysis. Anal Chem 2016; 88:12219-12226. [DOI: 10.1021/acs.analchem.6b03278] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Shushu Ding
- School of Chemistry and Molecular
Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, People’s Republic of China
| | - Sumei Cao
- School of Chemistry and Molecular
Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, People’s Republic of China
| | - Anwei Zhu
- School of Chemistry and Molecular
Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, People’s Republic of China
| | - Guoyue Shi
- School of Chemistry and Molecular
Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, People’s Republic of China
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56
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Xiao T, Wu F, Hao J, Zhang M, Yu P, Mao L. In Vivo Analysis with Electrochemical Sensors and Biosensors. Anal Chem 2016; 89:300-313. [DOI: 10.1021/acs.analchem.6b04308] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Tongfang Xiao
- Beijing
National Laboratory for Molecular Sciences, CAS Key Laboratory of
Analytical Chemistry for Living Biosystems and Photochemistry, Institute
of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Wu
- Beijing
National Laboratory for Molecular Sciences, CAS Key Laboratory of
Analytical Chemistry for Living Biosystems and Photochemistry, Institute
of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Hao
- Beijing
National Laboratory for Molecular Sciences, CAS Key Laboratory of
Analytical Chemistry for Living Biosystems and Photochemistry, Institute
of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meining Zhang
- Beijing
National Laboratory for Molecular Sciences, CAS Key Laboratory of
Analytical Chemistry for Living Biosystems and Photochemistry, Institute
of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Yu
- Beijing
National Laboratory for Molecular Sciences, CAS Key Laboratory of
Analytical Chemistry for Living Biosystems and Photochemistry, Institute
of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lanqun Mao
- Beijing
National Laboratory for Molecular Sciences, CAS Key Laboratory of
Analytical Chemistry for Living Biosystems and Photochemistry, Institute
of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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57
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Ren H, Long Z, Cui M, Shao K, Zhou K, Ouyang J, Na N. Dual-Functional Nanoparticles for In Situ Sequential Detection and Imaging of ATP and H2 O2. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:3920-3924. [PMID: 27337683 DOI: 10.1002/smll.201601571] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Indexed: 06/06/2023]
Abstract
Within a complex biological sample, the in situ sequential detection of multiple molecules without any interference is greatly desirable. Dual-functional nanoparticles are constructed, with the enzyme-based core-shell structures, for the in situ sequential detection of ATP and H2 O2 within the same biological system.
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Affiliation(s)
- Hong Ren
- Key Laboratory of Theoretical and Computational Photochemistry, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Zi Long
- Key Laboratory of Theoretical and Computational Photochemistry, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Mengchao Cui
- Key Laboratory of Theoretical and Computational Photochemistry, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Kang Shao
- Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences, Beijing, 10021, China
| | - Kaixiang Zhou
- Key Laboratory of Theoretical and Computational Photochemistry, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Jin Ouyang
- Key Laboratory of Theoretical and Computational Photochemistry, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Na Na
- Key Laboratory of Theoretical and Computational Photochemistry, College of Chemistry, Beijing Normal University, Beijing, 100875, China
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58
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Xu M, Gao Z, Zhou Q, Lin Y, Lu M, Tang D. Terbium ion-coordinated carbon dots for fluorescent aptasensing of adenosine 5'-triphosphate with unmodified gold nanoparticles. Biosens Bioelectron 2016; 86:978-984. [PMID: 27498324 DOI: 10.1016/j.bios.2016.07.105] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 07/28/2016] [Accepted: 07/29/2016] [Indexed: 01/11/2023]
Abstract
This work reports on a novel time-resolved fluorescent aptasensing platform for the quantitative monitoring of adenosine 5'-triphosphate (ATP) by interaction of dispersive/agglomerate gold nanoparticles (AuNPs) with terbium ion-coordinated carbon dots (Tb-CDs). To construct such a fluorescent nanoprobe, Tb-CDs with high-efficient fluorescent intensity are first synthesized by the microwave method with terbium ions (Tb(3+)). The aptasensing system consists of ATP aptamer, AuNP and Tb-CD. The dispersive/agglomerate gold nanoparticles are acquired through the reaction of the aptamer with target ATP. Upon target ATP introduction, the aptamers bind with the analytes to form new aptamer-ATP complexes and coat on the surface of AuNPs to inhibit their aggregation in the high salt solution. In this case, the fluorescent signal of Tb-CDs is quenched by the dispersive AuNPs on the basis of the fluorescence resonance energy transfer (FRET). At the absence of target analyte, gold nanoparticles tend to aggregate in the high salt state even if the aptamers are present. Thus, the added Tb-CDs maintain their intrinsic fluorescent intensity. Experimental results indicated that the aptasensing system exhibited good fluorescent responses toward ATP in the dynamic range from 40nM to 4.0μM with a detection limit of 8.5nM at 3sblank criterion. The repeatability and intermediate precision is less than 9.5% at three concentrations including 0.04, 0.4 and 2.0μM ATP. The selectivity was acceptable toward guanosine 5'-triphosphate, uridine 5'-triphosphate and cytidine 5'-triphosphate. The methodology was applied to evaluate the blank human serum spiked with target ATP, and the recoveries (at 3 concentration levels) ranged between 97.0% and 103.7%. Importantly, this detection scheme is rapid, simple, cost-effective, and does not require extensive sample preparation or separation.
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Affiliation(s)
- Mingdi Xu
- Key Laboratory of Analysis and Detection for Food Safety (MOE&Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou, 350108 PR China
| | - Zhuangqiang Gao
- Key Laboratory of Analysis and Detection for Food Safety (MOE&Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou, 350108 PR China
| | - Qian Zhou
- Key Laboratory of Analysis and Detection for Food Safety (MOE&Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou, 350108 PR China
| | - Youxiu Lin
- Key Laboratory of Analysis and Detection for Food Safety (MOE&Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou, 350108 PR China
| | - Minghua Lu
- Institute of Environmental and Analytical Science, School of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan, 475004 PR China.
| | - Dianping Tang
- Key Laboratory of Analysis and Detection for Food Safety (MOE&Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou, 350108 PR China.
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59
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Babu E, Muthu Mareeswaran P, Ramdass A, Ramesh P, Rajagopal S. Label free luminescence strategy for sensitive detection of ATP using aptamer-Ru(II) complexes. JOURNAL OF LUMINESCENCE 2016; 175:267-273. [DOI: 10.1016/j.jlumin.2016.02.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/09/2024]
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60
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Ng S, Lim HS, Ma Q, Gao Z. Optical Aptasensors for Adenosine Triphosphate. Theranostics 2016; 6:1683-702. [PMID: 27446501 PMCID: PMC4955066 DOI: 10.7150/thno.15850] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 05/09/2016] [Indexed: 12/16/2022] Open
Abstract
Nucleic acids are among the most researched and applied biomolecules. Their diverse two- and three-dimensional structures in conjunction with their robust chemistry and ease of manipulation provide a rare opportunity for sensor applications. Moreover, their high biocompatibility has seen them being used in the construction of in vivo assays. Various nucleic acid-based devices have been extensively studied as either the principal element in discrete molecule-like sensors or as the main component in the fabrication of sensing devices. The use of aptamers in sensors - aptasensors, in particular, has led to improvements in sensitivity, selectivity, and multiplexing capacity for a wide verity of analytes like proteins, nucleic acids, as well as small biomolecules such as glucose and adenosine triphosphate (ATP). This article reviews the progress in the use of aptamers as the principal component in sensors for optical detection of ATP with an emphasis on sensing mechanism, performance, and applications with some discussion on challenges and perspectives.
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Affiliation(s)
| | | | | | - Zhiqiang Gao
- Department of Chemistry, National University of Singapore, Singapore 117543
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61
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Pfeiffer F, Mayer G. Selection and Biosensor Application of Aptamers for Small Molecules. Front Chem 2016; 4:25. [PMID: 27379229 PMCID: PMC4908669 DOI: 10.3389/fchem.2016.00025] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 05/30/2016] [Indexed: 12/12/2022] Open
Abstract
Small molecules play a major role in the human body and as drugs, toxins, and chemicals. Tools to detect and quantify them are therefore in high demand. This review will give an overview about aptamers interacting with small molecules and their selection. We discuss the current state of the field, including advantages as well as problems associated with their use and possible solutions to tackle these. We then discuss different kinds of small molecule aptamer-based sensors described in literature and their applications, ranging from detecting drinking water contaminations to RNA imaging.
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Affiliation(s)
- Franziska Pfeiffer
- Department of Chemical Biology, Life and Medical Sciences Institute, University of Bonn Bonn, Germany
| | - Günter Mayer
- Department of Chemical Biology, Life and Medical Sciences Institute, University of Bonn Bonn, Germany
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62
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Yu P, He X, Mao L. Tuning interionic interaction for highly selective in vivo analysis. Chem Soc Rev 2016; 44:5959-68. [PMID: 26505054 DOI: 10.1039/c5cs00082c] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The development of highly selective methodologies to enable in vivo recording of chemical signals is of great importance for studying brain functions and brain activity mapping. However, the complexity of cerebral systems presents a great challenge in the development of chem/(bio)sensors that are capable of directly and selectively recording bioactive molecules involved in brain functions. As one of the most important and popular interactions in nature, interionic interaction constitutes the chemical essence of high specificity in natural systems, which inspires us to develop highly selective chem/(bio)sensors for in vivo analysis by precisely engineering interionic interaction in the in vivo sensing system. In this tutorial review, we focus on the recent progress in the tuning of interionic interaction to improve the selectivity of biosensors for in vivo analysis. The type and property of the interionic interaction is first introduced and several strategies to improve the selectivity of the biosensors, including enzyme-based electrochemical biosensors, aptamer-based electrochemical biosensors, and the strategies to recruit recognition molecules are reviewed. We also present an overview of the potential applications of the biosensors for in vivo analysis and thereby for physiological investigations. Finally, we present the major challenges and opportunities regarding the high selectivity of in vivo analysis based on tuning interionic interaction. We believe that this tutorial review provides critical insights for highly selective in vivo analysis and offers new concepts and strategies to understand brain chemistry.
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63
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Ultrasensitive electrochemical detection of protein tyrosine kinase-7 by gold nanoparticles and methylene blue assisted signal amplification. Biosens Bioelectron 2016; 83:39-44. [PMID: 27101533 DOI: 10.1016/j.bios.2016.04.032] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 04/09/2016] [Accepted: 04/12/2016] [Indexed: 01/08/2023]
Abstract
We present here an ultrasensitive and simple strategy for protein tyrosine kinase-7 (PTK7) detection based on the recognition-induced structure change of sgc8 aptamer, and the signal change of methylene blue (MB) that interacted with sandwiched DNA complex. To construct such a sensor, an homogeneous nano-surface was formed firstly on the glass carbon electrode (GCE) by using negatively charged Nafion (Nf) as the inner layer and positively charged gold nanoparticles ((+)AuNPs) as the outer layer, followed by the immobilization of sgc8 aptamer based on Au-S bond. In the presence of helper probe (HP), sandwiched DNA complex was formed between the sgc8 aptamer and the DNA modified gold nanoparticle probe (DNA-AuNPs). Then, a strong current signal was produced due to the capture of abundant MB molecules by both the sandwiched DNA complex and the multiple DNAs that modified on AuNPs surface. However, the specific binding of sgc8 aptamer with PNK7 would trigger a structure transition of it, and directly prevented the following formation of sandwiched structure and the capture of MB. Thus, PTK7 detection could be realized based on monitoring the signal reduction of MB upon incubation of sgc8 aptamer with PTK7. Under optimal conditions, a low detection limit of 372 fM was obtained for PNK7 detection. Due to the employment of sgc8 aptamer, the proposed biosensor exhibited high selectivity to PNK7. Moreover, satisfactory results were obtained when the proposed method was applied for PNK7 detection in cellular debris.
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65
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Wang L, Fang L, Liu S. Responsive hairpin DNA aptamer switch to program the strand displacement reaction for the enhanced electrochemical assay of ATP. Analyst 2016. [PMID: 26215159 DOI: 10.1039/c5an00725a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A responsive hairpin DNA aptamer switch was ingeniously designed for enzyme-free, sensitive and selective electrochemical detection of ATP. It takes full advantage of the target-triggered liberation effect of the toehold region and the concomitant proximity effect with the branch-migration region to execute the toehold-mediated strand displacement reaction on the electrode surface.
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Affiliation(s)
- Li Wang
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53, Zhengzhou Rd., Qingdao, Shandong 266042, China.
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66
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Zhang Y, Liu J, Zhang CY. Real-time monitoring of small biological molecules by ligation-mediated polymerase chain reaction. Chem Commun (Camb) 2016; 51:12270-3. [PMID: 26139082 DOI: 10.1039/c5cc04269k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We develop a ligation-mediated polymerase chain reaction (PCR) for real-time detection of small biological molecules in a high-throughput format. This method is extremely sensitive with a detection limit of as low as 18.8 fM for ATP and 17.3 fM for NAD(+), and it can discriminate target molecules from their analogues as well.
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Affiliation(s)
- Yan Zhang
- Single-Molecule Detection and Imaging Laboratory, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
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67
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Qian Q, Hao J, Ma W, Yu P, Mao L. Tuning interionic interaction by rationally controlling solution pH for highly selective colorimetric sensing of arginine. Anal Bioanal Chem 2016; 408:3005-12. [DOI: 10.1007/s00216-016-9323-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Revised: 12/26/2015] [Accepted: 01/11/2016] [Indexed: 10/22/2022]
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68
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Chen F, Cai C, Chen X, Chen C. "Click on the bidirectional switch": the aptasensor for simultaneous detection of lysozyme and ATP with high sensitivity and high selectivity. Sci Rep 2016; 6:18814. [PMID: 26742854 PMCID: PMC4705532 DOI: 10.1038/srep18814] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 11/25/2015] [Indexed: 12/21/2022] Open
Abstract
A bifunctional and simple aptasensor was designed to one-spot simultaneously detect two analytes, lysozyme and ATP. The aptasensor was obtained by the electronic interaction between methyl violet (MV) and dsDNA. The dsDNA was obtained by hybridization of ATP aptamer and lysozyme aptamer. And we used the resonance light scattering (RLS) technique to detect the concentration of lysozyme and ATP. During the procedure of detection, the aptasensor works like a bidirectional switch, the corresponding side of the dsDNA will open when the target (lysozyme or ATP) "click" the aptamer, which results in corresponding RLS signal change. By the combination of the RLS technique, it is found that the changed RLS intensity was proportional to the concentration of lysozyme and ATP. The mixtures of ATP and lysozyme also met two binary function relations. The results indicated that the aptasensor could achieve simultaneous detection of ATP and lysozyme, the detection limits of ATP and lysozyme could reach 10(-11) M and 10(-12) M, respectively. The aptasensor shows potential application for small molecule and protein detection by RLS, it could extend the application of RLS technique.
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Affiliation(s)
- Feng Chen
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, Hunan 411105, China
| | - Changqun Cai
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, Hunan 411105, China
| | - Xiaoming Chen
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, Hunan 411105, China
| | - Chunyan Chen
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, Hunan 411105, China
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69
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Direct and simultaneous quantification of ATP, ADP and AMP by (1)H and (31)P Nuclear Magnetic Resonance spectroscopy. Talanta 2015; 150:485-92. [PMID: 26838434 DOI: 10.1016/j.talanta.2015.12.051] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 12/13/2015] [Accepted: 12/19/2015] [Indexed: 01/06/2023]
Abstract
ATP, ADP and AMP are energy substances with vital biological significance. Based on the structural differences, a simple, rapid and comprehensive method has been established by (1)H and (31)P Nuclear Magnetic Resonance ((1)H-NMR and (31)P-NMR) spectroscopies. Sodium 3-(trimethylsilyl) propionate-2,2,3,3-d4 (TMSP) and anhydrous disodium hydrogen phosphate (Na2HPO4) were selected as internal standards for (1)H-NMR and (31)P-NMR, respectively. Those three compounds and corresponding internal standards can be easily distinguished both by (1)H-NMR and (31)P-NMR. In addition, they all have perfect linearity in a certain range: 0.1-100mM for (1)H-NMR and 1-75 mM for (31)P-NMR. To validate the precision of this method, mixed samples of different concentrations were measured. Recovery experiments were conducted in serum (91-113% by (1)H-NMR and 89-113% by (31)P-NMR).
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70
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Wang L, Yuan L, Zeng X, Peng J, Ni Y, Er JC, Xu W, Agrawalla BK, Su D, Kim B, Chang YT. A Multisite-Binding Switchable Fluorescent Probe for Monitoring Mitochondrial ATP Level Fluctuation in Live Cells. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201510003] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Lu Wang
- Department of Chemistry and Medicinal Chemistry Programme; National University of Singapore; Singapore 117543 Singapore
| | - Lin Yuan
- Department of Chemistry and Medicinal Chemistry Programme; National University of Singapore; Singapore 117543 Singapore
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 (PR China
| | - Xian Zeng
- Department of Pharmacy, National; University of Singapore; Singapore 117543 Singapore
| | - Juanjuan Peng
- Laboratory of Bioimaging Probe Development; Singapore Bioimaging Consortium; Singapore 138667 Singapore
| | - Yong Ni
- Laboratory of Bioimaging Probe Development; Singapore Bioimaging Consortium; Singapore 138667 Singapore
| | - Jun Cheng Er
- Department of Chemistry and Medicinal Chemistry Programme; National University of Singapore; Singapore 117543 Singapore
| | - Wang Xu
- Department of Chemistry and Medicinal Chemistry Programme; National University of Singapore; Singapore 117543 Singapore
| | - Bikram Keshari Agrawalla
- Department of Chemistry and Medicinal Chemistry Programme; National University of Singapore; Singapore 117543 Singapore
| | - Dongdong Su
- Laboratory of Bioimaging Probe Development; Singapore Bioimaging Consortium; Singapore 138667 Singapore
| | - Beomsue Kim
- Laboratory of Bioimaging Probe Development; Singapore Bioimaging Consortium; Singapore 138667 Singapore
| | - Young-Tae Chang
- Department of Chemistry and Medicinal Chemistry Programme; National University of Singapore; Singapore 117543 Singapore
- Laboratory of Bioimaging Probe Development; Singapore Bioimaging Consortium; Singapore 138667 Singapore
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Wang L, Yuan L, Zeng X, Peng J, Ni Y, Er JC, Xu W, Agrawalla BK, Su D, Kim B, Chang YT. A Multisite-Binding Switchable Fluorescent Probe for Monitoring Mitochondrial ATP Level Fluctuation in Live Cells. Angew Chem Int Ed Engl 2015; 55:1773-6. [PMID: 26676712 DOI: 10.1002/anie.201510003] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 11/25/2015] [Indexed: 11/09/2022]
Abstract
Adenosine triphosphate (ATP), commonly produced in mitochondria, is required by almost all the living organisms; thus fluorescent probes for monitoring mitochondrial ATP levels fluctuation are essential and highly desired. Herein, we report a multisite-binding switchable fluorescent probe, ATP-Red 1, which selectively and rapidly responds to intracellular concentrations of ATP. Live-cell imaging indicated that ATP-Red 1 mainly localized to mitochondria with good biocompatibility and membrane penetration. In particular, with the help of ATP-Red 1, we successfully observed not only the decreased mitochondrial ATP levels in the presence of KCN and starvation state, but also the increased mitochondrial ATP levels in the early stage of cell apoptosis. These results indicate that ATP-Red 1 is a useful tool for investigating ATP-relevant biological processes.
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Affiliation(s)
- Lu Wang
- Department of Chemistry and Medicinal Chemistry Programme, National University of Singapore, Singapore, 117543, Singapore
| | - Lin Yuan
- Department of Chemistry and Medicinal Chemistry Programme, National University of Singapore, Singapore, 117543, Singapore. .,State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 (PR, China.
| | - Xian Zeng
- Department of Pharmacy, National, University of Singapore, Singapore, 117543, Singapore
| | - Juanjuan Peng
- Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, Singapore, 138667, Singapore
| | - Yong Ni
- Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, Singapore, 138667, Singapore
| | - Jun Cheng Er
- Department of Chemistry and Medicinal Chemistry Programme, National University of Singapore, Singapore, 117543, Singapore
| | - Wang Xu
- Department of Chemistry and Medicinal Chemistry Programme, National University of Singapore, Singapore, 117543, Singapore
| | - Bikram Keshari Agrawalla
- Department of Chemistry and Medicinal Chemistry Programme, National University of Singapore, Singapore, 117543, Singapore
| | - Dongdong Su
- Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, Singapore, 138667, Singapore
| | - Beomsue Kim
- Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, Singapore, 138667, Singapore
| | - Young-Tae Chang
- Department of Chemistry and Medicinal Chemistry Programme, National University of Singapore, Singapore, 117543, Singapore. .,Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, Singapore, 138667, Singapore.
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72
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Zhou Q, Lin Y, Lin Y, Wei Q, Chen G, Tang D. In situ amplified electrochemical aptasensing for sensitive detection of adenosine triphosphate by coupling target-induced hybridization chain reaction with the assembly of silver nanotags. Talanta 2015; 146:23-8. [PMID: 26695229 DOI: 10.1016/j.talanta.2015.08.035] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 08/13/2015] [Accepted: 08/16/2015] [Indexed: 10/23/2022]
Abstract
Biomolecular immobilization and construction of the sensing platform are usually crucial for the successful development of a high-efficiency detection system. Herein we report on a novel and label-free signal-amplified aptasensing for sensitive electrochemical detection of small molecules (adenosine triphosphate, ATP, used in this case) by coupling with target-induced hybridization chain reaction (HCR) and the assembly of electroactive silver nanotags. The system mainly consisted of two alternating hairpin probes, a partial-pairing trigger-aptamer duplex DNA and a capture probe immobilized on the electrode. Upon target ATP introduction, the analyte attacked the aptamer and released the trigger DNA, which was captured by capture DNA immobilized on the electrode to form a newly partial-pairing double-stranded DNA. Thereafter, the exposed domain at trigger DNA could be utilized as the initator strand to open the hairpin probes in sequence, and propagated a chain reaction of hybridization events between two alternating hairpins to form a long nicked double-helix. The electrochemical signal derived from the assembled silver nanotags on the nicked double-helix. Under optimal conditions, the electrochemical aptasensor could exhibit a high sensitivity and a low detection limit, and allowed the detection of ATP at a concentration as low as 0.03 pM. Our design showed a high selectivity for target ATP against its analogs because of the high-specificity ATP-aptamer reaction, and its applicable for monitoring ATP in the spiking serum samples. Improtantly, the distinct advantages of the developed aptasensor make it hold a great potential for the development of simple and robust sensing strategies for the detection of other small molecules by controlling the apatmer sequence.
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Affiliation(s)
- Qian Zhou
- Key Laboratory of Analysis and Detection for Food Safety (Ministry of Education & Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou 350108, PR China
| | - Youxiu Lin
- Key Laboratory of Analysis and Detection for Food Safety (Ministry of Education & Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou 350108, PR China
| | - Yuping Lin
- Key Laboratory of Analysis and Detection for Food Safety (Ministry of Education & Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou 350108, PR China
| | - Qiaohua Wei
- Key Laboratory of Analysis and Detection for Food Safety (Ministry of Education & Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou 350108, PR China.
| | - Guonan Chen
- Key Laboratory of Analysis and Detection for Food Safety (Ministry of Education & Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou 350108, PR China
| | - Dianping Tang
- Key Laboratory of Analysis and Detection for Food Safety (Ministry of Education & Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou 350108, PR China
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