1
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Yu J, Zhang Y, Zhao Y, Zhang X, Ren H. Highly Sensitive and Selective Detection of Inorganic Phosphates in the Water Environment by Biosensors Based on Bioluminescence Resonance Energy Transfer. Anal Chem 2023; 95:4904-4913. [PMID: 36942460 DOI: 10.1021/acs.analchem.2c04748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
The accurate detection of phosphate in water is very important to prevent water eutrophication and ensure the health of water quality. However, traditional phosphomolybdenum blue spectrophotometry is not sensitive, is time-consuming, and demands large amounts of chemical reagents. Therefore, highly sensitive, rapid, and environmentally friendly Pi detection methods are urgently needed. Here, we developed a bioluminescence resonance energy transfer (BRET)-based biosensor, which can detect Pi in water quickly, highly sensitively, and highly selectively. The NanoLuc and the Venus fluorescent protein were selected as the bioluminescence donor and energy acceptor, respectively. The best-performing BRET sensor variant, VenusΔC10-PΔC12-ΔN4Nluc, was identified by Pi-specific binding protein (PiBP) screening and systematic truncation. Single-factor experiments optimized the key parameters affecting the detection performance of the sensor. Under the optimal detection conditions, the detection limit of this method was 1.3 μg·L-1, the detection range was 3.3-434 μg·L-1, and it had excellent selectivity, repeatability, and stability. This low-cost and environment-friendly BRET sensor showed a good application prospect in real water quality detection.
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Affiliation(s)
- Jie Yu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yan Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yanping Zhao
- School of Environment, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Xuxiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
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2
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Deng H, Yan S, Huang Y, Lei C, Nie Z. Design strategies for fluorescent proteins/mimics and their applications in biosensing and bioimaging. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115757] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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3
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Chung CI, Sato Y, Ohmuro-Matsuyama Y, Machida S, Kurumizaka H, Kimura H, Ueda H. Intrabody-based FRET probe to visualize endogenous histone acetylation. Sci Rep 2019; 9:10188. [PMID: 31308423 PMCID: PMC6629662 DOI: 10.1038/s41598-019-46573-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 07/02/2019] [Indexed: 01/07/2023] Open
Abstract
Post-translational histone modifications are major regulators of gene expression. However, conventional immunoassays do not provide sufficient information regarding their spatial and temporal dynamic changes. Fluorescence/Förster resonance energy transfer (FRET)-based probes are capable of monitoring the dynamic changes associated with histone modifications in real-time by measuring the balance between histone-modifying enzyme activities. Recently, a genetically encoded histone-modification fluorescent probe using a single-chain variable region (scFv) fragment of a specific antibody was developed. The probe, modification-specific intracellular antibody, is capable of monitoring histone-acetylation levels in both cultured cells and living organisms based on the ratio of fluorescence intensities between the cell nucleus and cytoplasm. In this study, we constructed a FRET probe composed of yellow fluorescent protein attached at the N-terminus of an acetyl H3K9-specific scFv, tethered to a cyan fluorescent protein. When the FRET probe was expressed in human cells, both FRET efficiency and fluorescence intensity in the nucleus increased following histone-deacetylase inhibitor treatment. Using these two parameters, endogenous histone-acetylation levels were quantified over a high dynamic range. This probe provides a simple approach to quantify spatial and temporal dynamic changes in histone acetylation.
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Affiliation(s)
- Chan-I Chung
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan.,Department of Pharmaceutical Chemistry, University of California San Francisco, 555 Mission Bay Blvd South, San Francisco, 94158, California, USA
| | - Yuko Sato
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
| | - Yuki Ohmuro-Matsuyama
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
| | - Shinichi Machida
- Laboratory of Structural Biology, Graduate School of Advanced Science & Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science & Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.,Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
| | - Hiroshi Ueda
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan.
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4
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Islam J, Riley BT, Fercher C, Jones ML, Buckle AM, Howard CB, Cox RP, Bell TDM, Mahler S, Corrie SR. Wavelength-Dependent Fluorescent Immunosensors via Incorporation of Polarity Indicators near the Binding Interface of Antibody Fragments. Anal Chem 2019; 91:7631-7638. [DOI: 10.1021/acs.analchem.9b00445] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jiaul Islam
- Department of Chemical Engineering, ARC Centre of Excellence in Convergent BioNano Science and Technology, Monash University, Clayton VIC 3800, Australia
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia QLD 4072, Australia
| | - Blake T. Riley
- Dept. of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton VIC 3800, Australia
| | - Christian Fercher
- Department of Chemical Engineering, ARC Centre of Excellence in Convergent BioNano Science and Technology, Monash University, Clayton VIC 3800, Australia
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia QLD 4072, Australia
| | - Martina L. Jones
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia QLD 4072, Australia
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia QLD 4072, Australia
| | - Ashley M. Buckle
- Dept. of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton VIC 3800, Australia
| | - Christopher B. Howard
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia QLD 4072, Australia
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia QLD 4072, Australia
| | - Rosalind P. Cox
- School of Chemistry, Monash University, Clayton VIC 3800, Australia
| | - Toby D. M. Bell
- School of Chemistry, Monash University, Clayton VIC 3800, Australia
| | - Stephen Mahler
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia QLD 4072, Australia
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia QLD 4072, Australia
| | - Simon R. Corrie
- Department of Chemical Engineering, ARC Centre of Excellence in Convergent BioNano Science and Technology, Monash University, Clayton VIC 3800, Australia
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia QLD 4072, Australia
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5
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Shu M, Xu Y, Dong JX, Zhong C, Hammock BD, Wang WJ, Wu GP. Development of a noncompetitive idiometric nanobodies phage immumoassay for the determination of fumonisin B1. FOOD AGR IMMUNOL 2019. [DOI: 10.1080/09540105.2019.1604637] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Mei Shu
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Yang Xu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, People’s Republic of China
| | - Jie-xian Dong
- Departments of Neurobiology, Physiology and Behavior, and of Physiology and Membrane Biology, University of California, Davis, CA, USA
| | - Chan Zhong
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Bruce D. Hammock
- Department of Entomology and UCD Comprehensive Cancer Center, University of California, Davis, CA, USA
| | - Wen-jun Wang
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Guo-ping Wu
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, People’s Republic of China
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6
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Shu M, Xu Y, Dong JX, Zhong C, Hammock BD, Wang WJ, Wu GP. Development of a noncompetitive idiometric nanobodies phage immumoassay for the determination of fumonisin B1. FOOD AGR IMMUNOL 2019. [DOI: https://doi.org/10.1080/09540105.2019.1604637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Mei Shu
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Yang Xu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, People’s Republic of China
| | - Jie-xian Dong
- Departments of Neurobiology, Physiology and Behavior, and of Physiology and Membrane Biology, University of California, Davis, CA, USA
| | - Chan Zhong
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Bruce D. Hammock
- Department of Entomology and UCD Comprehensive Cancer Center, University of California, Davis, CA, USA
| | - Wen-jun Wang
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Guo-ping Wu
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, People’s Republic of China
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7
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Zhou X, Cui Z, Liu L, Sun Z, Lin M, Hu Q, Wang H, Xiao X. Small molecule-protein interactions in branch migration thermodynamics: modelling and application in the homogeneous detection of proteins and small molecules. Analyst 2018; 143:2755-2759. [PMID: 29850719 DOI: 10.1039/c8an00555a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We have disclosed the unique inhibition effect of small molecule-protein interactions toward the DNA branch migration process and constructed a complete thermodynamic model for it. The disclosed effect was further coupled with the steric hindrance effect to establish a homogeneous assay for proteins and small molecules with ultra-high inhibition factors and sensitivity.
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Affiliation(s)
- Xing Zhou
- Centre of Reproductive Medicine/Family Planning Research Institute, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, PR China.
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8
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Song X, Nie R, Liu X, Chen Y, Yang L. Multiplex immunoassays using surface modification-mediated porous layer open tubular capillary. Anal Chim Acta 2018; 1043:1-10. [PMID: 30392656 DOI: 10.1016/j.aca.2018.04.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 04/01/2018] [Accepted: 04/04/2018] [Indexed: 12/11/2022]
Abstract
We proposed an innovative surface modification-mediated porous layer open tubular (PLOT) capillary, which was modified via an in situ biphasic reaction. This capillary comprised three-dimensional homogeneous and porous structures, which could increase the surface-area-to-volume ratio for antibody immobilization. The PLOT capillary was shown as an ideal immunoreaction base to enhance the sensitivity of immunoassays and shorten analysis time. By connecting two separate PLOT capillaries using a suitable sleeve tube, we can perform multiplex targets detection in the same sample. We developed a sensitive, rapid, and multiplex PLOT capillary-mediated immunosensor for the simultaneous identification of alpha fetoprotein (AFP) and carcinoembryonic antigen (CEA) in clinical serum samples with good accuracy. The detection sensitivity of the PLOT immunosensor improved by 10-fold compared with that of bare-capillary sensor, and the whole analysis could be completed within 1 h. This work suggest that suitable surface modification strategy is an effective tool to improve the analytical performance of conventional immunoassay and our study provided a feasible, sensitive, and multi-target assay for the detection of cancer biomarkers, which would be of valuable application in clinical diagnosis.
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Affiliation(s)
- Xingda Song
- Key Laboratory of Nanobiosensing and Nanobioanalysis at Universities of Jilin Province, Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province, 130024, China
| | - Rongbin Nie
- Key Laboratory of Nanobiosensing and Nanobioanalysis at Universities of Jilin Province, Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province, 130024, China
| | - Xiaoxia Liu
- College of Arts and Sciences, Shanxi Agricultural University, Jinzhong, Shanxi Province, 030801, China
| | - Yiping Chen
- Beijing Engineering Research Center for BioNanotechnology & CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing, 100190, China.
| | - Li Yang
- Key Laboratory of Nanobiosensing and Nanobioanalysis at Universities of Jilin Province, Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province, 130024, China.
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9
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Obeng EM, Dullah EC, Razak NSA, Danquah MK, Budiman C, Ongkudon CM. Elucidating endotoxin-biomolecule interactions with FRET: extending the frontiers of their supramolecular complexation. J Biol Methods 2017; 4:e71. [PMID: 31453229 PMCID: PMC6706125 DOI: 10.14440/jbm.2017.172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/24/2017] [Accepted: 02/28/2017] [Indexed: 01/22/2023] Open
Abstract
Endotoxin has been one of the topical chemical contaminants of major concern to researchers, especially in the field of bioprocessing. This major concern of researchers stems from the fact that the presence of Gram-negative bacterial endotoxin in intracellular products is unavoidable and requires complex downstream purification steps. For instance, endotoxin interacts with recombinant proteins, peptides, antibodies and aptamers and these interactions have formed the foundation for most biosensors for endotoxin detection. It has become imperative for researchers to engineer reliable means/techniques to detect, separate and remove endotoxin, without compromising the quality and quantity of the end-product. However, the underlying mechanism involved during endotoxin-biomolecule interaction is still a gray area. The use of quantitative molecular microscopy that provides high resolution of biomolecules is highly promising, hence, may lead to the development of improved endotoxin detection strategies in biomolecule preparation. Förster resonance energy transfer (FRET) spectroscopy is one of the emerging most powerful tools compatible with most super-resolution techniques for the analysis of molecular interactions. However, the scope of FRET has not been well-exploited in the analysis of endotoxin-biomolecule interaction. This article reviews endotoxin, its pathophysiological consequences and the interaction with biomolecules. Herein, we outline the common potential ways of using FRET to extend the current understanding of endotoxin-biomolecule interaction with the inference that a detailed understanding of the interaction is a prerequisite for the design of strategies for endotoxin identification and removal from protein milieus.
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Affiliation(s)
- Eugene M Obeng
- Biotechnology Research Institute, University Malaysia Sabah, Kota Kinabalu, Sabah 88400, Malaysia
| | - Elvina C Dullah
- Biotechnology Research Institute, University Malaysia Sabah, Kota Kinabalu, Sabah 88400, Malaysia
| | | | - Michael K Danquah
- Department of Chemical Engineering, Curtin University Sarawak, Miri, Sarawak 98009, Malaysia
| | - Cahyo Budiman
- Biotechnology Research Institute, University Malaysia Sabah, Kota Kinabalu, Sabah 88400, Malaysia
| | - Clarence M Ongkudon
- Biotechnology Research Institute, University Malaysia Sabah, Kota Kinabalu, Sabah 88400, Malaysia
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10
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Creation of Antigen-Dependent β-Lactamase Fusion Protein Tethered by Circularly Permuted Antibody Variable Domains. Methods Mol Biol 2017. [PMID: 28293886 DOI: 10.1007/978-1-4939-6940-1_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Antibody-based molecular switches that are able to recognize a range of exogenous antigens can be highly useful as a versatile biosensor. However, regulating the catalytic activity of enzymes by antibodies is still hard to achieve. Here, we describe a design method of unique antibody variable region Fv introduced with two circular permutations, called Clampbody. By tethering the Clampbody to a circularly permuted TEM-1 β-lactamase (BLA), we successfully constructed a genetically encoded molecular switch Cbody-cpBLA that shows antigen-dependent catalytic activity.
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11
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Yoshikoshi K, Watanabe T, Hohsaka T. Double-Fluorescent-Labeled Single-Chain Antibodies Showing Antigen-Dependent Fluorescence Ratio Change. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2016. [DOI: 10.1246/bcsj.20150384] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Kensuke Yoshikoshi
- School of Materials Science, Japan Advanced Institute of Science and Technology
| | - Takayoshi Watanabe
- School of Materials Science, Japan Advanced Institute of Science and Technology
| | - Takahiro Hohsaka
- School of Materials Science, Japan Advanced Institute of Science and Technology
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12
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Iwai H, Kojima-Misaizu M, Dong J, Ueda H. Creation of a Ligand-Dependent Enzyme by Fusing Circularly Permuted Antibody Variable Region Domains. Bioconjug Chem 2016; 27:868-73. [DOI: 10.1021/acs.bioconjchem.6b00040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Hiroto Iwai
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Miki Kojima-Misaizu
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Jinhua Dong
- Chemical Resources Laboratory, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan
| | - Hiroshi Ueda
- Chemical Resources Laboratory, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan
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13
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Schulenburg C, Faccio G, Jankowska D, Maniura-Weber K, Richter M. A FRET-based biosensor for the detection of neutrophil elastase. Analyst 2016; 141:1645-8. [DOI: 10.1039/c5an01747e] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The direct and specific detection of biomarkers activity is crucial as it can allow monitoring the state of tissue or wound, as well as the progression of the inflammatory process.
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Affiliation(s)
- C. Schulenburg
- Department of Biointerfaces
- Empa - Swiss Federal Laboratories for Materials Science and Technology
- 9014 St. Gallen (CH)
- Switzerland
| | - G. Faccio
- Department of Biointerfaces
- Empa - Swiss Federal Laboratories for Materials Science and Technology
- 9014 St. Gallen (CH)
- Switzerland
| | - D. Jankowska
- Department of Biointerfaces
- Empa - Swiss Federal Laboratories for Materials Science and Technology
- 9014 St. Gallen (CH)
- Switzerland
| | - K. Maniura-Weber
- Department of Biointerfaces
- Empa - Swiss Federal Laboratories for Materials Science and Technology
- 9014 St. Gallen (CH)
- Switzerland
| | - M. Richter
- Department of Biointerfaces
- Empa - Swiss Federal Laboratories for Materials Science and Technology
- 9014 St. Gallen (CH)
- Switzerland
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