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Basu S, Hendler-Neumark A, Bisker G. Monitoring Enzyme Activity Using Near-Infrared Fluorescent Single-Walled Carbon Nanotubes. ACS Sens 2024; 9:2237-2253. [PMID: 38669585 PMCID: PMC11129355 DOI: 10.1021/acssensors.4c00377] [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: 02/18/2024] [Revised: 04/03/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024]
Abstract
Enzymes serve as pivotal biological catalysts that accelerate essential chemical reactions, thereby influencing a variety of physiological processes. Consequently, the monitoring of enzyme activity and inhibition not only yields crucial insights into health and disease conditions but also forms the basis of research in drug discovery, toxicology, and the understanding of disease mechanisms. In this context, near-infrared (NIR) fluorescent single-walled carbon nanotubes (SWCNTs) have emerged as effective tools for tracking enzyme activity and inhibition through diverse strategies. This perspective explores the physicochemical attributes of SWCNTs that render them well-suited for such monitoring. Additionally, we delve into the various strategies developed so far for successfully monitoring enzyme activity and inhibition, emphasizing the distinctive features of each principle. Furthermore, we contrast the benefits of SWCNT-based NIR probes with conventional gold standards in monitoring enzyme activity. Lastly, we highlight the current challenges faced in this field and suggest potential solutions to propel it forward. This perspective aims to contribute to the ongoing progress in biodiagnostics and seeks to engage the wider community in developing and applying enzymatic assays using SWCNTs.
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Affiliation(s)
- Srestha Basu
- Department
of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Adi Hendler-Neumark
- Department
of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Gili Bisker
- Department
of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
- Center
for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- Center
for Nanoscience and Nanotechnology, Tel
Aviv University, Tel Aviv 6997801, Israel
- Center
for Light-Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
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2
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Zhra M, Qasem RJ, Aldossari F, Saleem R, Aljada A. A Comprehensive Exploration of Caspase Detection Methods: From Classical Approaches to Cutting-Edge Innovations. Int J Mol Sci 2024; 25:5460. [PMID: 38791499 PMCID: PMC11121653 DOI: 10.3390/ijms25105460] [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: 03/30/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
The activation of caspases is a crucial event and an indicator of programmed cell death, also known as apoptosis. These enzymes play a central role in cancer biology and are considered one promising target for current and future advancements in therapeutic interventions. Traditional methods of measuring caspase activity such as antibody-based methods provide fundamental insights into their biological functions, and are considered essential tools in the fields of cell and cancer biology, pharmacology and toxicology, and drug discovery. However, traditional methods, though extensively used, are now recognized as having various shortcomings. In addition, these methods fall short of providing solutions to and matching the needs of the rapid and expansive progress achieved in studying caspases. For these reasons, there has been a continuous improvement in detection methods for caspases and the network of pathways involved in their activation and downstream signaling. Over the past decade, newer methods based on cutting-edge state-of-the-art technologies have been introduced to the biomedical community. These methods enable both the temporal and spatial monitoring of the activity of caspases and their downstream substrates, and with enhanced accuracy and precision. These include fluorescent-labeled inhibitors (FLIs) for live imaging, single-cell live imaging, fluorescence resonance energy transfer (FRET) sensors, and activatable multifunctional probes for in vivo imaging. Recently, the recruitment of mass spectrometry (MS) techniques in the investigation of these enzymes expanded the repertoire of tools available for the identification and quantification of caspase substrates, cleavage products, and post-translational modifications in addition to unveiling the complex regulatory networks implicated. Collectively, these methods are enabling researchers to unravel much of the complex cellular processes involved in apoptosis, and are helping generate a clearer and comprehensive understanding of caspase-mediated proteolysis during apoptosis. Herein, we provide a comprehensive review of various assays and detection methods as they have evolved over the years, so to encourage further exploration of these enzymes, which should have direct implications for the advancement of therapeutics for cancer and other diseases.
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Affiliation(s)
- Mahmoud Zhra
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Rani J. Qasem
- Department of Pharmacology and Pharmacy Practice, College of Pharmacy, Middle East University, Amman 11831, Jordan
| | - Fai Aldossari
- Zoology Department, College of Science, King Saud University, Riyadh 12372, Saudi Arabia
| | - Rimah Saleem
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Ahmad Aljada
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
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3
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Hennig A, Nau WM. Interaction of Cucurbit[7]uril With Protease Substrates: Application to Nanosecond Time-Resolved Fluorescence Assays. Front Chem 2020; 8:806. [PMID: 33134264 PMCID: PMC7511663 DOI: 10.3389/fchem.2020.00806] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 07/31/2020] [Indexed: 01/04/2023] Open
Abstract
We report the use of the macrocyclic host cucurbit[7]uril (CB7) as a supramolecular additive in nanosecond time-resolved fluorescence (Nano-TRF) assays for proteases to enhance the discrimination of substrates and products and, thereby, the sensitivity. A peptide substrate was labeled with 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) as a long-lived (>300 ns) fluorescent probe and 3-nitrotyrosine was established as a non-fluorescent fluorescence resonance energy transfer (FRET) acceptor that acts as a “dark quencher.” The substrate was cleaved by the model proteases trypsin and chymotrypsin and the effects of the addition of CB7 to the enzyme assay mixture were investigated in detail using UV/VIS absorption as well as steady-state and time-resolved fluorescence spectroscopy. This also allowed us to identify the DBO and nitrotyrosine residues as preferential binding sites for CB7 and suggested a hairpin conformation of the peptide, in which the guanidinium side chain of an arginine residue is additionally bound to a vacant ureido rim of one of the CB7 hosts.
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Affiliation(s)
- Andreas Hennig
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Bremen, Germany.,Institute of Chemistry of New Materials, School of Biology/Chemistry, Universität Osnabrück, Osnabrück, Germany.,Center of Cellular Nanoanalytics (CellNanOs), Universität Osnabrück, Osnabrück, Germany
| | - Werner M Nau
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Bremen, Germany
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4
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Liu Y, Peng S, Angelova L, Nau WM, Hennig A. Label-Free Fluorescent Kinase and Phosphatase Enzyme Assays with Supramolecular Host-Dye Pairs. ChemistryOpen 2019; 8:1350-1354. [PMID: 31741820 PMCID: PMC6848908 DOI: 10.1002/open.201900299] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Indexed: 12/21/2022] Open
Abstract
The combination of the macrocyclic hosts p-sulfonatocalix[4]arene and cucurbit[7]uril with the fluorescent dyes lucigenin and berberine affords two label-free enzyme assays for the detection of kinase and phosphatase activity by fluorescence monitoring. In contrast to established assays, no substrate labeling is required. Since phosphorylation is one of the most important regulatory mechanisms in biological signal transduction, the assays should be useful for identification of inhibitors and activators in high-throughput screening (HTS) format for drug discovery.
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Affiliation(s)
- Yan‐Cen Liu
- Department of Life Sciences and ChemistryJacobs University Bremen gGmbHCampus Ring 128759BremenGermany
| | - Shu Peng
- Department of Life Sciences and ChemistryJacobs University Bremen gGmbHCampus Ring 128759BremenGermany
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials, Ministry of EducationNankai UniversityTianjin300071 TianjinChina
| | - Lora Angelova
- Department of Life Sciences and ChemistryJacobs University Bremen gGmbHCampus Ring 128759BremenGermany
| | - Werner M. Nau
- Department of Life Sciences and ChemistryJacobs University Bremen gGmbHCampus Ring 128759BremenGermany
| | - Andreas Hennig
- Department of Life Sciences and ChemistryJacobs University Bremen gGmbHCampus Ring 128759BremenGermany
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5
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Rojo-Arreola L, Navarrete del Toro M, Cordova-Murueta J, García-Carreño F. Techniques for protein digestion research in Decapoda: A review. Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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6
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Glucovanillin: A potent inhibitor of lipase from Acinetobacter radioresistens. INFORMATICS IN MEDICINE UNLOCKED 2018. [DOI: 10.1016/j.imu.2018.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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7
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Scale-up and inhibitory studies on productivity of lipase from Acinetobacter radioresistens PR8. J Biosci Bioeng 2017; 124:150-155. [DOI: 10.1016/j.jbiosc.2017.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 03/09/2017] [Indexed: 11/21/2022]
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8
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Sun Z, Chen X, Wang G, Li L, Fu G, Kuruc M, Wang X. Identification of functional metabolic biomarkers from lung cancer patient serum using PEP technology. Biomark Res 2016; 4:11. [PMID: 27252855 PMCID: PMC4888258 DOI: 10.1186/s40364-016-0065-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 05/12/2016] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Reprogrammed metabolism is a new hallmark of cancer. In many types of cancer, most of the genes in the glycolytic pathway are overexpressed, reflecting an essential shift of metabolism during cancer development. The reprogrammed metabolism contributes to cancer development in multiple ways, from supplying the elevated energy requirement to creating a microenvironment suitable for tumor growth and suppressing the human immune surveillance system. METHOD In this study, a functional proteomics top-down approach was used to systematically monitor metabolic enzyme activities in resolved serum proteins produced by a modified 2-D gel separation and subsequent Protein Elution Plate, a method collectively called PEP. RESULTS We found that the enrichment of low abundance proteins with a bead based product called AlbuVoid™(,) is important to increase the number of observable features and to increase the level of signal achievable from the assay used. From our methods, significant metabolic enzyme activities were detected in both normal and lung cancer patient sera in many fractions after the elution of the 2-D gel separated proteins to the Protein Elution Plate (PEP). Eighteen fractions with the most dramatic metabolic enzyme activity difference between the normal and lung cancer patient sera were submitted for mass spectrometry protein identification. Proteins from the glycolytic metabolic pathway, such as GAPDH along with other proteins not previously annotated to the glycolytic pathway were identified. Further verification with commercially purified GAPDH showed that the addition of purified GAPDH to the metabolic enzyme assay system employed enhanced the enzyme activity, demonstrating that proteins identified from the PEP technology and mass spectrometry could be further verified with biological assay. CONCLUSION This study identified several potential functional enzyme biomarkers from lung cancer patient serum, it provides an alternative and complementary approach to sequence annotation for the discovery of biomarkers in human diseases.
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Affiliation(s)
- Zhenyu Sun
- />The Third Hospital Affiliated to Nantong University School of Medicine, Wuxi, China
| | - Xiaofeng Chen
- />Shanghai Huashan Hospital, Fudan University School of Medicine, Shanghai, China
| | - Gan. Wang
- />Institute of Environmental Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201 USA
| | - Liang Li
- />Zibo Central Hospital, Zibo, China
| | | | - Matthew Kuruc
- />Biotech Support Group, LLC, Monmouth Junction, NJ USA
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9
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Yin J, Miao P. Apoptosis Evaluation by Electrochemical Techniques. Chem Asian J 2015; 11:632-41. [DOI: 10.1002/asia.201501045] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Indexed: 01/22/2023]
Affiliation(s)
- Jian Yin
- CAS Key Lab of Bio-Medical Diagnostics; Suzhou Institute of Biomedical Engineering and Technology; Chinese Academy of Sciences; Suzhou 215163 P.R. China
| | - Peng Miao
- CAS Key Lab of Bio-Medical Diagnostics; Suzhou Institute of Biomedical Engineering and Technology; Chinese Academy of Sciences; Suzhou 215163 P.R. China
- University of Chinese Academy of Sciences; Beijing 100049 P.R. China
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10
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Zhang L, Lei J, Liu J, Ma F, Ju H. Persistent luminescence nanoprobe for biosensing and lifetime imaging of cell apoptosis via time-resolved fluorescence resonance energy transfer. Biomaterials 2015; 67:323-34. [PMID: 26232881 DOI: 10.1016/j.biomaterials.2015.07.037] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 07/17/2015] [Accepted: 07/20/2015] [Indexed: 10/23/2022]
Abstract
Time-resolved fluorescence technique can reduce the short-lived background luminescence and auto-fluorescence interference from cells and tissues by exerting the delay time between pulsed excitation light and signal acquisition. Here, we prepared persistent luminescence nanoparticles (PLNPs) to design a universal time-resolved fluorescence resonance energy transfer (TR-FRET) platform for biosensing, lifetime imaging of cell apoptosis and in situ lifetime quantification of intracellular caspase-3. Three kinds of PLNPs-based nanoprobes are assembled by covalently binding dye-labeled peptides or DNA to carboxyl-functionalized PLNPs for the efficient detection of caspase-3, microRNA and protein. The peptides-functionalized nanoprobe is also employed for fluorescence lifetime imaging to monitor cell apoptosis, which shows a dependence of cellular fluorescence lifetime on caspase-3 activity and thus leads to an in situ quantification method. This work provides a proof-of-concept for PLNPs-based TR-FRET analysis and demonstrates its potential in exploring dynamical information of life process.
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Affiliation(s)
- Lei Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, PR China
| | - Jianping Lei
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, PR China.
| | - Jintong Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, PR China
| | - Fengjiao Ma
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, PR China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, PR China.
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11
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Sista P, Ghosh K, Martinez JS, Rocha RC. Metallo-Biopolymers: Conjugation Strategies and Applications. POLYM REV 2014. [DOI: 10.1080/15583724.2014.913063] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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12
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Borisova NE, Kostin AA, Eroshkina EA, Reshetova MD, Lyssenko KA, Spodine EN, Puntus LN. Lanthanide Complexes with Tetradentate
N
,
N′
,
O
,
O′
‐Dipyridyl‐Based Ligands: Structure, Stability, and Photophysical Properties. Eur J Inorg Chem 2014. [DOI: 10.1002/ejic.201301271] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Nataliya E. Borisova
- Chemistry Department, M. V. Lomonosov Moscow State University, 1 Leninskie Gory, 119991 Moscow, Russian Federation, http://fhmas.chem.msu.ru
| | - Andrey A. Kostin
- Chemistry Department, M. V. Lomonosov Moscow State University, 1 Leninskie Gory, 119991 Moscow, Russian Federation, http://fhmas.chem.msu.ru
| | - Elizaveta A. Eroshkina
- Chemistry Department, M. V. Lomonosov Moscow State University, 1 Leninskie Gory, 119991 Moscow, Russian Federation, http://fhmas.chem.msu.ru
| | - Marina D. Reshetova
- Chemistry Department, M. V. Lomonosov Moscow State University, 1 Leninskie Gory, 119991 Moscow, Russian Federation, http://fhmas.chem.msu.ru
| | - Konstantin A. Lyssenko
- N. A. Nesmeyanov Institute of Organoelement Compounds, Vavilova st. 28, 119334 Moscow, Russia
| | - Evgenia N. Spodine
- Faculty of Chemical and Pharmaceutical Sciences, University of Chile, Center for the Development of Nanoscience and Nanotechnology (CEDENNA), Sergio Livingstone P. 1007, Independencia, Santiago, Chile
| | - Lada N. Puntus
- N. A. Nesmeyanov Institute of Organoelement Compounds, Vavilova st. 28, 119334 Moscow, Russia
- Kotel'nikov Institute of Radio Engineering and Electronics of Russian Academy of Sciences, Mokhovaya st. 11‐7, 125009 Moscow, Russia
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13
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Wang Y, Liu X, Zhang J, Aili D, Liedberg B. Time-resolved botulinum neurotoxin A activity monitored using peptide-functionalized Au nanoparticle energy transfer sensors. Chem Sci 2014. [DOI: 10.1039/c3sc53305k] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
A peptide mimicking SNAP-25 was immobilized on Au nanoparticles for the monitoring of botulinum neurotoxin light chain A activity.
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Affiliation(s)
- Yi Wang
- Centre for Biomimetic Sensor Science
- Nanyang Technological University
- , 637553 Singapore
- School of Materials Science and Engineering
- Nanyang Technological University
| | - Xiaohu Liu
- Centre for Biomimetic Sensor Science
- Nanyang Technological University
- , 637553 Singapore
| | - Jinling Zhang
- Centre for Biomimetic Sensor Science
- Nanyang Technological University
- , 637553 Singapore
- School of Materials Science and Engineering
- Nanyang Technological University
| | - Daniel Aili
- Centre for Biomimetic Sensor Science
- Nanyang Technological University
- , 637553 Singapore
- Division of Molecular Physics
- Department of Physics, Chemistry and Biology
| | - Bo Liedberg
- Centre for Biomimetic Sensor Science
- Nanyang Technological University
- , 637553 Singapore
- School of Materials Science and Engineering
- Nanyang Technological University
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14
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Liu Y, Tu D, Zhu H, Ma E, Chen X. Lanthanide-doped luminescent nano-bioprobes: from fundamentals to biodetection. NANOSCALE 2013; 5:1369-84. [PMID: 23223801 DOI: 10.1039/c2nr33239f] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Trivalent lanthanide (Ln(3+))-doped luminescent inorganic nanoparticles (NPs), characterized by long-lived luminescence, large Stokes and/or anti-Stokes shifts, narrow emission bands and high photochemical stability, are considered to be promising candidates as luminescent bioprobes in biomedicine and biotechnology. In this feature article, we provide a brief overview of the most recent advances in Ln(3+)-doped luminescent inorganic NPs as sensors, which covers from their chemical and physical fundamentals to biodetection, such as controlled synthesis methodology, surface modification chemistry, optical physics, and their promising applications in diverse bioassays, with an emphasis on heterogeneous and homogeneous in vitro biodetection. Finally, some of the most important emerging trends and future efforts toward this active research field are also proposed.
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Affiliation(s)
- Yongsheng Liu
- Key Laboratory of Optoelectronic Materials Chemistry and Physics, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
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15
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Vuojola J, Syrjänpää M, Lamminmäki U, Soukka T. Genetically Encoded Protease Substrate Based on Lanthanide-Binding Peptide for Time-Gated Fluorescence Detection. Anal Chem 2013; 85:1367-73. [DOI: 10.1021/ac302030q] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Johanna Vuojola
- Department of Biotechnology, University of Turku, Tykistökatu 6A, FI-20520 Turku, Finland
| | - Markku Syrjänpää
- Department of Biotechnology, University of Turku, Tykistökatu 6A, FI-20520 Turku, Finland
| | - Urpo Lamminmäki
- Department of Biotechnology, University of Turku, Tykistökatu 6A, FI-20520 Turku, Finland
| | - Tero Soukka
- Department of Biotechnology, University of Turku, Tykistökatu 6A, FI-20520 Turku, Finland
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Liu J, Lu Y, Liang J. A novel fluorescence derivatization method combined with HPLC for determining the activities of endogenous caspase. Analyst 2012; 137:5097-104. [PMID: 22970428 DOI: 10.1039/c2an35822k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A novel fluorescence derivatization method combined with HPLC was developed to detect the activity of caspase-3 and -8 in two cell lines (Hela cells and A549 cells) which were activated by low temperature-assisted ultraviolet irradiation (LT-UV), mitomycin C (MMC) and camptothecin during the apoptosis, respectively. Two peptide substrates for either caspase-3 or -8 were designed, of which peptide fragments were obtained by enzymatic modification, followed by fluorescence derivatization. A single fluorescent product was formed when a peptide was heated at 120 °C for 10 min in a neutral aqueous medium (pH 7.0) containing catechol, sodium periodate and sodium borate. Commercial kits for detecting the activity of caspase-3 and -8 were used as a control. The relative activity of the caspases detected by fluorescence derivatization was similar to that obtained by commercial kits, which indicated that the novel method is reliable. The activity assays of recombinant human caspases showed that the novel method provided higher selectivity than that of commercial kits, which proved it to be more accurate for determining the activity of caspases in apoptosis.
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Affiliation(s)
- Jiachi Liu
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
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17
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Deng W, Goldys EM. Plasmonic approach to enhanced fluorescence for applications in biotechnology and the life sciences. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:10152-10163. [PMID: 22568517 DOI: 10.1021/la300332x] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
One of the most rapidly growing areas of physics and nanotechnology is concerned with plasmonic effects on the nanometer scale; these have applications in sensing and imaging technologies. Nanoplasmonic colloids such as Ag and Au have been attracting active interest, and there has been a recent explosion in the use of these metallic nanostructures to modify the spectral properties of fluorophores favorably and to enhance the fluorescence emission intensity. In this feature article, we summarize our work over a range of nanoplasmonics-assisted biological applications such as flow cytometry, immunoassays, cell imaging and bioassays where we use custom-designed plasmonic nanostructures (Ag and Au) to enhance fluorescence signatures. This fluorophore-metal effect offers unique advantages in providing improved photostability and enhanced fluorescence signals. We discuss the plasmonic enhancement of lanthanide fluorophores whose long and microsecond lifetimes offer the advantage of background-free fluorescence detection, but low photon cycling rates lead to poor brightness. We also show that plasmonic colloids are capable of enhancing the emission of fluorescent nanoparticles, including upconverting nanocrystals and lanthanide nanocomposites.
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Affiliation(s)
- Wei Deng
- MQ BioFocus Research Centre, Macquarie University, North Ryde 2113 NSW, Australia
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18
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Vuojola J, Riuttamäki T, Kulta E, Arppe R, Soukka T. Fluorescence-quenching-based homogeneous caspase-3 activity assay using photon upconversion. Anal Chim Acta 2012; 725:67-73. [PMID: 22502613 DOI: 10.1016/j.aca.2012.03.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 03/05/2012] [Accepted: 03/07/2012] [Indexed: 12/28/2022]
Abstract
Caspase proteases are key mediators in apoptosis and thus of great interest in pharmaceutical industry. Enzyme-activity assays are commonly employed in the screening of protease inhibitors that are potential drug candidates. Conventional homogeneous fluorescence-based assays are susceptible to autofluorescence originating from biological material. This background autofluorescence can be eliminated by using upconverting phosphors (UCPs) that emit visible light upon excitation at near-infrared. In the assay energy was transferred from a UCP-donor to a conventional fluorophore acceptor that resided at one end of a caspase-3-specific substrate peptide. Attached to the other end was a quencher molecule that was used to attenuate the acceptor emission through intramolecular energy transfer in an intact peptide. In non-inhibitory conditions the enzyme reaction separated the fluorophore from the quencher and the emission of the fluorophore was recovered. The method was applied for the detection and characterization of a known caspase-3 inhibitor Z-DEVD-FMK, and the assay gave IC(50) values of approximately 13 nM for this inhibitor. We have demonstrated the applicability of UCPs on a fluorescence-quenching-based homogeneous enzyme-activity assay for the detection of caspase-3 inhibitors. The use of near-infrared excitable UCPs enables inexpensive instrumentation and total elimination of autofluorescence, while the use of an internally quenched substrate molecule diminishes the background resulting from radiatively excited acceptor molecules. The reduction of autofluorescence and radiative background result in high signal-to-background ratios (ratios of approximately 100 were obtained). By further utilizing assay miniaturization and signal enhancement in a white microtitration plate, a significant reduction in the reagent consumption can be achieved rendering the assay applicable for high-throughput screening.
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Affiliation(s)
- Johanna Vuojola
- Department of Biotechnology, University of Turku, Turku, Finland.
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Zauner T, Berger-Hoffmann R, Müller K, Hoffmann R, Zuchner T. Highly adaptable and sensitive protease assay based on fluorescence resonance energy transfer. Anal Chem 2011; 83:7356-63. [PMID: 21892820 DOI: 10.1021/ac201274f] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Proteases are widely used in analytical sciences and play a central role in several widespread diseases. Thus, there is an immense need for highly adaptable and sensitive assays for the detection and monitoring of various proteolytic enzymes. We established a simple protease fluorescence resonance energy transfer (pro-FRET) assay for the determination of protease activities, which could in principle be adapted for the detection of all proteases. As proof of principle, we demonstrated the potential of our method using trypsin and enteropeptidase in complex biological mixtures. Briefly, the assay is based on the cleavage of a FRET peptide substrate, which results in a dramatic increase of the donor fluorescence. The assay was highly sensitive and fast for both proteases. The detection limits for trypsin and enteropeptidase in Escherichia coli lysate were 100 and 10 amol, respectively. The improved sensitivity for enteropeptidase was due to the application of an enzyme cascade, which leads to signal amplification. The pro-FRET assay is highly specific as even high concentrations of other proteases did not result in significant background signals. In conclusion, this sensitive and simple assay can be performed in complex biological mixtures and can be easily adapted to act as a versatile tool for the sensitive detection of proteases.
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Affiliation(s)
- Thomas Zauner
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, 04103 Leipzig, Germany
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Mizukami S, Yamamoto T, Yoshimura A, Watanabe S, Kikuchi K. Covalent protein labeling with a lanthanide complex and its application to photoluminescence lifetime-based multicolor bioimaging. Angew Chem Int Ed Engl 2011; 50:8750-2. [PMID: 21793145 DOI: 10.1002/anie.201103775] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Indexed: 11/07/2022]
Affiliation(s)
- Shin Mizukami
- Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan
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21
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Mizukami S, Yamamoto T, Yoshimura A, Watanabe S, Kikuchi K. Covalent Protein Labeling with a Lanthanide Complex and Its Application to Photoluminescence Lifetime-Based Multicolor Bioimaging. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103775] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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22
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Kawaguchi M, Okabe T, Terai T, Hanaoka K, Kojima H, Minegishi I, Nagano T. A Time-Resolved Fluorescence Probe for Dipeptidyl Peptidase 4 and Its Application in Inhibitor Screening. Chemistry 2010; 16:13479-86. [DOI: 10.1002/chem.201001077] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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23
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Song C, Ye Z, Wang G, Yuan J, Guan Y. Core-shell nanoarchitectures: a strategy to improve the efficiency of luminescence resonance energy transfer. ACS NANO 2010; 4:5389-5397. [PMID: 20681528 DOI: 10.1021/nn100820u] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The development of core-shell nanoparticles has shown a wide range of new applications in the fields of chemistry, bioscience, and materials science because of their improved physical and chemical properties over their single-component counterparts. In the present work, we took the core-shell nanoarchitectures as an example to research the luminescence resonance energy transfer (LRET) process between a luminescent Tb3+ chelate, N,N,N(1),N(1)-[4'-phenyl-2,2':6',2'-terpyridine-6,6'-diyl]bis(methylenenitrilo)tetrakis(acetate)-Tb3+ (PTTA-Tb3+), and an organic dye, 5-carboxytetramethylrhodamine (CTMR). PTTA-Tb3+ and CTMR were chosen as the donor-acceptor pair of LRET in our model construction because of their effective spectral overlapping. The core-shell nanoparticles featuring a CTMR-SiO2 core surrounded by a concentric PTTA-Tb3+-SiO2 shell were prepared using a reverse microemulsion method. These nanoparticles are spherical, uniform in size, and highly photostable. The results of LRET experiments show that the sensitized emission lifetime of the acceptor in the nanoparticles is significantly prolonged (∼246 μs), which is attributed to the long emission lifetime of the Tb3+ chelate donor. According to the results of the steady-state and time-resolved luminescence spectroscopy, an energy transfer efficiency of ∼80% and a large Förster distance between the donor and the acceptor in the core-shell nanoparticles are calculated, respectively. The new core-shell nanoparticles with a high LRET efficiency and long Förster distance enable them to be promising optical probes for a variety of possible applications such as molecular imaging and multiplex signaling.
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Affiliation(s)
- Cuihong Song
- Department of Instrumentation and Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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24
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Deng W, Jin D, Drozdowicz-Tomsia K, Yuan J, Goldys EM. Europium chelate (BHHCT-Eu3+) and its metal nanostructure enhanced luminescence applied to bioassays and time-gated bioimaging. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:10036-10043. [PMID: 20405866 DOI: 10.1021/la100158g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
We report the use of europium chelate, 4,4'-bis(1'',1'',1'',2'',2'',3'',3''-heptafluoro-4'',6''-hexanedion-6''-yl)chlorosulfo-o-terphenyl-Eu(3+) (BHHCT-Eu(3+)), in silver nanostructure-enhanced luminescence and its application to bioassays and bioimaging. The highest luminescence intensity enhancement factor of BHHCT-Eu(3+) achieved in this study was about 11 times, while the simultaneously measured luminescence lifetime was reduced 2-fold. The luminophore photostability was also improved by a factor of 3. On the basis of these experimental results, we estimated the impact of silver nanostructures on the excitation and emission enhancement factors. Luminescence enhancement was demonstrated in two geometries: on planar glass substrates and on silica beads. In the biotin-modified IgG antibody assay the bead geometry provided slightly higher enhancement factor and greater sensitivity. Subsequently, we applied such bead substrates to time-gated luminescence imaging of Giardia lamblia cells stained by BHHCT-Eu(3+) where we observed improved brightness by a factor of 2. Such improved photostability and brightness of BHHCT-Eu(3+) in the presence of metal nanostructures are highly desirable for ultrasensitive bioassays and bioimaging, especially with time gating.
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Affiliation(s)
- Wei Deng
- Department of Engineering and Physics, Macquarie University, North Ryde 2109 NSW, Australia
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25
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Lathia US, Ornatsky O, Baranov V, Nitz M. Development of inductively coupled plasma-mass spectrometry-based protease assays. Anal Biochem 2010; 398:93-8. [PMID: 19912984 PMCID: PMC2825755 DOI: 10.1016/j.ab.2009.11.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Revised: 10/28/2009] [Accepted: 11/08/2009] [Indexed: 11/26/2022]
Abstract
Rapid, sensitive, and quantitative assays for proteases are important for drug development and in the diagnosis of disease. Here an assay for protease activity that uses inductively coupled plasma-mass spectrometry (ICP-MS) detection is described. Peptidic alpha-chymotrypsin substrates were synthesized containing a lanthanide ion chelate at the N terminus to provide a distinct elemental tag. A biotin label was appended to the C terminus of the peptide, allowing separation of uncleaved peptide from the enzymatic digestion. The enzyme activity was determined by quantifying the lanthanide ion signal of the peptide cleavage products by ICP-MS. Biotinylated substrates synthesized include Lu-DTPA-Asp-Leu-Leu-Val-Tyr approximately Asp-Lys(biotin) and Lu-DTPA-betaAla-betaAla-betaAla-betaAla-Gly-Ser-Ala-Tyr approximately Gly-Lys-Arg-Lys(biotin)-amide. Parallel assays with a commercially available fluorogenic substrate (Suc-AAPF-AMC) for alpha-chymotrypsin were performed for comparison. Using the ICP-MS assay, enzyme concentrations as low as 2pM could be readily detected, superior to the detection limit of an assay using the alpha-chymotrypsin fluorogenic substrate (Suc-AAPF-AMC). Furthermore, we demonstrated the use of this approach to detect chymotrypsin activity in HeLa cell lysates.
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Affiliation(s)
- Urja S. Lathia
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6
| | - Olga Ornatsky
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6
| | - Vladimir Baranov
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6
| | - Mark Nitz
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6
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26
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Akiba H, Sumaoka J, Komiyama M. Selective detection of phosphotyrosine in the presence of various phosphate-containing biomolecules with the aid of a terbium(III) complex. Chembiochem 2009; 10:1773-6. [PMID: 19565595 DOI: 10.1002/cbic.200900227] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hiroki Akiba
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-Ku, Tokyo, 153-8904, Japan
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27
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Marguerre AK, Krämer R. Lanthanide-based fluorogenic peptide substrate for the highly sensitive detection of thermolysin. Bioorg Med Chem Lett 2009; 19:5757-9. [DOI: 10.1016/j.bmcl.2009.07.152] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 07/30/2009] [Accepted: 07/31/2009] [Indexed: 10/20/2022]
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28
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Nau WM, Ghale G, Hennig A, Bakirci H, Bailey DM. Substrate-Selective Supramolecular Tandem Assays: Monitoring Enzyme Inhibition of Arginase and Diamine Oxidase by Fluorescent Dye Displacement from Calixarene and Cucurbituril Macrocycles. J Am Chem Soc 2009; 131:11558-70. [DOI: 10.1021/ja904165c] [Citation(s) in RCA: 184] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Werner M. Nau
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Garima Ghale
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Andreas Hennig
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Hüseyin Bakirci
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - David M. Bailey
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
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29
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Li YT, Li CW, Sung WC, Chen SH. Heme Protein Assisted Dispersion of Gold Nanoparticle Multilayers on Chips: From Stabilization to High-Density Double-Stranded DNAs Fabricated in Situ for Protein/DNA Binding. Anal Chem 2009; 81:4076-81. [DOI: 10.1021/ac900295j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yu-Ting Li
- Department of Chemistry, National Cheng Kung University, No. 1 College Road, Tainan, 701, Taiwan, and Department of Medical Imaging and Radiological Sciences, College of Health Science, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chun-Wei Li
- Department of Chemistry, National Cheng Kung University, No. 1 College Road, Tainan, 701, Taiwan, and Department of Medical Imaging and Radiological Sciences, College of Health Science, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wang-Chou Sung
- Department of Chemistry, National Cheng Kung University, No. 1 College Road, Tainan, 701, Taiwan, and Department of Medical Imaging and Radiological Sciences, College of Health Science, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shu-Hui Chen
- Department of Chemistry, National Cheng Kung University, No. 1 College Road, Tainan, 701, Taiwan, and Department of Medical Imaging and Radiological Sciences, College of Health Science, Kaohsiung Medical University, Kaohsiung, Taiwan
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30
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Mizukami S, Tonai K, Kaneko M, Kikuchi K. Lanthanide-Based Protease Activity Sensors for Time-Resolved Fluorescence Measurements. J Am Chem Soc 2008; 130:14376-7. [DOI: 10.1021/ja800322b] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shin Mizukami
- Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kazuhiro Tonai
- Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masahiro Kaneko
- Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kazuya Kikuchi
- Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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31
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Motré A, Li Y, Kong H. Enhancing helicase-dependent amplification by fusing the helicase with the DNA polymerase. Gene 2008; 420:17-22. [DOI: 10.1016/j.gene.2008.04.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2007] [Revised: 04/16/2008] [Accepted: 04/25/2008] [Indexed: 10/22/2022]
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32
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Henares TG, Mizutani F, Sekizawa R, Hisamoto H. Single-drop analysis of various proteases in a cancer cell lysate using a capillary-assembled microchip. Anal Bioanal Chem 2008; 391:2507-12. [DOI: 10.1007/s00216-008-2105-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Revised: 03/25/2008] [Accepted: 03/27/2008] [Indexed: 11/29/2022]
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33
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A dual-step fluorescence resonance energy transfer-based quenching assay for screening of caspase-3 inhibitors. Anal Biochem 2008; 375:71-81. [DOI: 10.1016/j.ab.2007.12.032] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2007] [Revised: 12/20/2007] [Accepted: 12/22/2007] [Indexed: 11/24/2022]
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34
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Fluorescence detection techniques for protein kinase assay. Anal Bioanal Chem 2008; 390:2049-57. [DOI: 10.1007/s00216-008-1986-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2007] [Revised: 02/12/2008] [Accepted: 02/14/2008] [Indexed: 12/25/2022]
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35
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Hanaoka K, Kikuchi K, Terai T, Komatsu T, Nagano T. A Gd3+-Based Magnetic Resonance Imaging Contrast Agent Sensitive to β-Galactosidase Activity Utilizing a Receptor-Induced Magnetization Enhancement (RIME) Phenomenon. Chemistry 2008; 14:987-95. [DOI: 10.1002/chem.200700785] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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36
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Dirscherl G, König B. The Use of Solid‐Phase Synthesis Techniques for the Preparation of Peptide–Metal Complex Conjugates. European J Org Chem 2008. [DOI: 10.1002/ejoc.200700787] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Georg Dirscherl
- Institut für Organische Chemie, Universität Regensburg, 9340 Regensburg, Germany, Fax: +49‐941‐943‐1717
| | - Burkhard König
- Institut für Organische Chemie, Universität Regensburg, 9340 Regensburg, Germany, Fax: +49‐941‐943‐1717
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37
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Sahoo H, Hennig A, Florea M, Roth D, Enderle T, Nau WM. Single-label kinase and phosphatase assays for tyrosine phosphorylation using nanosecond time-resolved fluorescence detection. J Am Chem Soc 2007; 129:15927-34. [PMID: 18044894 DOI: 10.1021/ja074975w] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The collision-induced fluorescence quenching of a 2,3-diazabicyclo[2.2.2]oct-2-ene-labeled asparagine (Dbo) by hydrogen atom abstraction from the tyrosine residue in peptide substrates was introduced as a single-labeling strategy to assay the activity of tyrosine kinases and phosphatases. The assays were tested for 12 different combinations of Dbo-labeled substrates and with the enzymes p60c-Src Src kinase, EGFR kinase, YOP protein tyrosine phosphatase, as well as acid and alkaline phosphatases, thereby demonstrating a broad application potential. The steady-state fluorescence changed by a factor of up to 7 in the course of the enzymatic reaction, which allowed for a sufficient sensitivity of continuous monitoring in steady-state experiments. The fluorescence lifetimes (and intensities) were found to be rather constant for the phosphotyrosine peptides (ca. 300 ns in aerated water), while those of the unphosphorylated peptides were as short as 40 ns (at pH 7) and 7 ns (at pH 13) as a result of intramolecular quenching. Owing to the exceptionally long fluorescence lifetime of Dbo, the assays were alternatively performed by using nanosecond time-resolved fluorescence (Nano-TRF) detection, which leads to an improved discrimination of background fluorescence and an increased sensitivity. The potential for inhibitor screening was demonstrated through the inhibition of acid and alkaline phosphatases by molybdate.
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Affiliation(s)
- Harekrushna Sahoo
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
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38
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Nau WM, Hennig A, Koner AL. Squeezing Fluorescent Dyes into Nanoscale Containers—The Supramolecular Approach to Radiative Decay Engineering. ACTA ACUST UNITED AC 2007. [DOI: 10.1007/4243_2007_007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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39
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Dubaele S, Martin C, Bohn J, Chène P. Biochemical study of recombinant PcrA from Staphylococcus aureus for the development of screening assays. BMB Rep 2007; 40:7-14. [PMID: 17244476 DOI: 10.5483/bmbrep.2007.40.1.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Helicases are ubiquitous enzymes, which utilize the energy liberated during nucleotide triphosphate hydrolysis to separate double-stranded nucleic acids into single strands. These enzymes are very attractive targets for the development of new antibacterial compounds. The PcrA DNA helicase from Staphylococcus aureus is a good candidate for drug discovery. This enzyme is unique in the genome of S. aureus and essential for this bacterium. Furthermore, it has recently been published that it is possible to identify inhibitors of DNA helicases such as PcrA. In this report, we study the properties of recombinant PcrA from S. aureus purified from Escherichia coli to develop ATPase and helicase assays to screen for inhibitors.
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Affiliation(s)
- Sandy Dubaele
- Novartis Institutes for BioMedical Research, Oncology Research, CH-4002 Basel, Switzerland
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40
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O'Shea DJ, O'Riordan TC, O'Sullivan PJ, Papkovsky DB. Homogeneous time-resolved fluorescence assays for the detection of activity and inhibition of phosphatase enzymes employing phosphorescently labeled peptide substrates. Anal Chim Acta 2007; 583:349-56. [PMID: 17386566 DOI: 10.1016/j.aca.2006.10.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2006] [Revised: 10/10/2006] [Accepted: 10/11/2006] [Indexed: 10/24/2022]
Abstract
A rapid, homogenous, antibody-free assay for phosphatase enzymes was developed using the phosphorescent platinum (II)-coproporphyrin label (PtCP) and time-resolved fluorescent detection. An internally quenched decameric peptide substrate containing a phospho-tyrosine residue, labeled with PtCP-maleimide and dabcyl-NHS at its termini was designed. Phosphatase catalysed dephosphorylation of the substrate resulted in a minor increase in PtCP signal, while subsequent cleavage by chymotrypsin at the dephosphorylated Tyr-Leu site provided a 3.5 fold enhancement of PtCP phosphorescence. This phosphorescence phosphatase enhancement assay was optimized to a 96 well plate format with detection on a commercial TR-F plate reader, and applied to measure the activity and inhibition of alkaline phosphatase, recombinant human CD45, and tyrosine phosphatases in Jurkat cell lysates within 40 min. Parameters of these enzymatic reactions such as Km's, limits of detection (L.O.D's) and IC50 values for the non-specific inhibitor sodium orthovanadate were also determined.
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Affiliation(s)
- Desmond J O'Shea
- Biochemistry Department, University College Cork, Cavanagh Pharmacy Building, College Road, Cork, Ireland
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41
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Laitala V, Hemmilä I. Homogeneous assay based on anti-Stokes' shift time-resolved fluorescence resonance energy-transfer measurement. Anal Chem 2007; 77:1483-7. [PMID: 15732934 DOI: 10.1021/ac048414o] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report here a novel, time-resolved, lanthanide-based energy-transfer assay utilizing nonoverlapping acceptor fluorophores, which have their absorption energetically at a higher level than the emittive transitions of the donor. The technique was studied by comparing a series of nonoverlapping acceptors in a homogeneous DNA model assay utilizing Eu3+ chelate as a donor. The assay provides strong energy-transfer enhanced acceptor emission and enables the anti-Stokes' shift FRET measurement, in which the induced acceptor emission is at shorter wavelength than the donor emission. This results in high sensitivity, and 0.8 pM detection limit was measured for the DNA target. The acceptor signal of the assay is characterized by exceptional lifetime properties and is not strictly following the Forster's theory. The mechanism of nonoverlapping energy transfer is considered, and we propose that when nonoverlapping acceptors are utilized, the energy transfer arises from the upper 5D2 and 5D1 excited states of europium. The assumption was studied using a simplified energy level scheme of the Eu3+ donor and the acceptors, and a correlation between the acceptor emission behavior and the energy level scheme was found.
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Affiliation(s)
- Ville Laitala
- PerkinElmer Life and Analytical Sciences, Wallac, P.O. Box 10, Fin-20101 Turku, Finland.
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42
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Hennig A, Florea M, Roth D, Enderle T, Nau WM. Design of peptide substrates for nanosecond time-resolved fluorescence assays of proteases: 2,3-Diazabicyclo[2.2.2]oct-2-ene as a noninvasive fluorophore. Anal Biochem 2007; 360:255-65. [PMID: 17134673 DOI: 10.1016/j.ab.2006.09.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2006] [Revised: 09/15/2006] [Accepted: 09/17/2006] [Indexed: 11/26/2022]
Abstract
Fluorescence protease assays were investigated with peptide substrates containing a 2,3-diazabicyclo[2.2.2]oct-2-ene-labeled asparagine (Dbo) as a fluorescent amino acid. The special characteristic of the fluorophore Dbo is its exceedingly long fluorescence lifetime (ca. 300 ns in water under air), which allows the use of nanosecond time-resolved fluorescence (Nano-TRF) detection to efficiently suppress shorter-lived background emission. In addition, the natural amino acids tryptophan and tyrosine can be employed as intramolecular fluorescence quenchers, which facilitates substrate design. Fourteen synthetic peptide substrates (composed of 2-19 amino acids) and five enzymes (trypsin, pepsin, carboxypeptidase A, leucine aminopeptidase, and chymotrypsin) were investigated and, in all 28 examined combinations, enzymatic activity was detected by monitoring the increase in steady state fluorescence with time and determining the reaction rates as kcat/Km values, which ranged from 0.2 to 80x10(6) M-1 min-1. The results suggest an excellent compatibility of the very small and hydrophilic fluorescent probe Dbo with solid-phase peptide synthesis and the investigated proteases. For all 14 peptides the fluorescence lifetimes before and after enzymatic cleavage were measured and Nano-TRF measurements were performed in 384-well microplates. The fluorescence lifetimes of the different peptides provide the basis for the rational design of Dbo-based fluorescent substrates for protease assays. Measurements in Nano-TRF mode revealed, in addition to efficient suppression of background fluorescence, an increased differentiation between cleaved and uncleaved substrate. The Dbo-based assays can be adapted for high-throughput screening.
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Affiliation(s)
- Andreas Hennig
- School of Engineering and Science, International University Bremen, Campus Ring 1, D-28759 Bremen, Germany
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43
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Burke M, O'Sullivan PJ, Ponomarev GV, Yashunsky DV, Papkovsky DB. Analysis of close proximity quenching of phosphorescent metalloporphyrin labels in oligonucleotide structures. Anal Chim Acta 2006; 585:139-46. [PMID: 17386658 DOI: 10.1016/j.aca.2006.12.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2006] [Revised: 12/12/2006] [Accepted: 12/14/2006] [Indexed: 12/16/2022]
Abstract
Quenching of phosphorescent platinum(II) and palladium(II) coproporphyrin (MeCP) labelled oligonucleotides was investigated. Strong hybridization-specific quenching was observed in duplex DNA structures with a variety of quenchers and with two identical porphyrin labels when in close proximity. Classical resonance energy transfer mechanism was ruled out, since quenching did not correlate with spectral overlaps and lifetime changes were insignificant. Quenching of MeCP by the free quenchers in solution revealed that porphyrin-porphyrin quenching is predominantly static while other dyes quench dynamically. The results suggest that the quenching in DNA duplex proceeds via direct contact.
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Affiliation(s)
- M Burke
- Biochemistry Department/ABCRF, Cavanagh Pharmacy Building, University College Cork, Cork, Ireland
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Sapsford KE, Berti L, Medintz IL. Materialien für den resonanten Fluoreszenzenergietransfer (FRET): jenseits klassischer Donor-Acceptor-Kombinationen. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200503873] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Sapsford KE, Berti L, Medintz IL. Materials for Fluorescence Resonance Energy Transfer Analysis: Beyond Traditional Donor–Acceptor Combinations. Angew Chem Int Ed Engl 2006; 45:4562-89. [PMID: 16819760 DOI: 10.1002/anie.200503873] [Citation(s) in RCA: 1017] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The use of Förster or fluorescence resonance energy transfer (FRET) as a spectroscopic technique has been in practice for over 50 years. A search of ISI Web of Science with just the acronym "FRET" returns more than 2300 citations from various areas such as structural elucidation of biological molecules and their interactions, in vitro assays, in vivo monitoring in cellular research, nucleic acid analysis, signal transduction, light harvesting and metallic nanomaterials. The advent of new classes of fluorophores including nanocrystals, nanoparticles, polymers, and genetically encoded proteins, in conjunction with ever more sophisticated equipment, has been vital in this development. This review gives a critical overview of the major classes of fluorophore materials that may act as donor, acceptor, or both in a FRET configuration. We focus in particular on the benefits and limitations of these materials and their combinations, as well as the available methods of bioconjugation.
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Affiliation(s)
- Kim E Sapsford
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6910, 4555 Overlook Avenue SW, Washington, DC 20375, USA
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Sun H, Chattopadhaya S, Wang J, Yao SQ. Recent developments in microarray-based enzyme assays: from functional annotation to substrate/inhibitor fingerprinting. Anal Bioanal Chem 2006; 386:416-26. [PMID: 16791553 DOI: 10.1007/s00216-006-0511-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2006] [Revised: 04/11/2006] [Accepted: 04/25/2006] [Indexed: 01/26/2023]
Abstract
Recent advances in proteomics have provided impetus towards the development of robust technologies for high-throughput studies of enzymes. The term "catalomics" defines an emerging '-omics' field in which high-throughput studies of enzymes are carried out by using advanced chemical proteomics approaches. Of the various available methods, microarrays have emerged as a powerful and versatile platform to accelerate not only the functional annotation but also the substrate and inhibitor specificity (e.g. substrate and inhibitor fingerprinting, respectively) of enzymes. Herein, we review recent developments in the fabrication of various types of microarray technologies (protein-, peptide- and small-molecule-based microarrays) and their applications in high-throughput characterizations of enzymes.
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Affiliation(s)
- Hongyan Sun
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore, Singapore
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Affiliation(s)
- Andreas Hennig
- School of Engineering and Science, International University Bremen, Campus Ring 1, 28759 Bremen, Germany
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Hynes J, O'Riordan TC, Curtin J, Cotter TG, Papkovsky DB. Fluorescence based oxygen uptake analysis in the study of metabolic responses to apoptosis induction. J Immunol Methods 2005; 306:193-201. [PMID: 16212976 DOI: 10.1016/j.jim.2005.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2005] [Revised: 07/18/2005] [Accepted: 09/07/2005] [Indexed: 11/22/2022]
Abstract
Mitochondrial activity has been shown to be centrally involved in the progression of apoptosis. The electron transport chain is a major player in this process and oxygen uptake analysis provides detailed information on its activity. Here we examined the ability of a fluorescence based oxygen uptake assay to inform on cellular responses to apoptosis induction. HL60 cells treated with camptothecin and UV light were used as a model and the ability of the assay to detect dose and time dependent decreases in respiratory activity analysed. The data obtained were compared to more specific markers of apoptosis including annexin V binding, and caspase-3 activity. Reductions in oxygen uptake rates were seen at lower doses than increases in annexin V binding or mitochondrial membrane potential depolarisation. These reductions were observed earlier than detectable caspase-3 activity and were unaffected by pre-treatment with the caspase-3 inhibitor benzyloxycarbonyl-Val-Ala-Asp-fluoro-methylketone (zVADfmk).
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Affiliation(s)
- James Hynes
- Biochemistry Department, University College Cork, Lee Maltings, Cork, Ireland
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Laitala V, Hemmilä I. Homogeneous assay based on low quantum yield Sm(III)-donor and anti-Stokes’ shift time-resolved fluorescence resonance energy-transfer measurement. Anal Chim Acta 2005. [DOI: 10.1016/j.aca.2005.07.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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O'Riordan TC, Hynes J, Yashunski D, Ponomarev GV, Papkovsky DB. Homogeneous assays for cellular proteases employing the platinum(II)–coproporphyrin label and time-resolved phosphorescence. Anal Biochem 2005; 342:111-9. [PMID: 15958187 DOI: 10.1016/j.ab.2005.04.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2005] [Revised: 04/05/2005] [Accepted: 04/12/2005] [Indexed: 11/29/2022]
Abstract
Phosphorescent platinum(II) coproporphyrin label (PtCP) is evaluated for the detection of cellular proteases by time-resolved fluorescence in homogeneous format. An octameric peptide containing the recognition motif for the caspase-3 enzyme was dual labeled with a new maleimide derivative of PtCP and with the dark quencher dabcyl. Following photophysical characterization, the quenched substrate was employed in cleavage assays for caspase-3 using Jurkat and HL60 cell lines treated with proapoptotic stimuli performed on a commercial plate reader. Dose-response and time course assays for the drug camptothecin were obtained for comparison with conventional fluorometric detection.
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Affiliation(s)
- Tomás C O'Riordan
- Laboratory of Biophysics and Bioanalysis, Department of Biochemistry, University College Cork, Lee Maltings, Prospect Row, Cork, Ireland
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