1
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Netaev A, Schierbaum N, Seidl K. Artificial Neural Network (ANN)-Based Determination of Fractional Contributions from Mixed Fluorophores using Fluorescence Lifetime Measurements. J Fluoresc 2024; 34:305-311. [PMID: 37212979 PMCID: PMC10808714 DOI: 10.1007/s10895-023-03261-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/04/2023] [Indexed: 05/23/2023]
Abstract
Here we present an artificial neural network (ANN)-approach to determine the fractional contributions Pi from fluorophores to a multi-exponential fluorescence decay in time-resolved lifetime measurements. Conventionally, Pi are determined by extracting two parameters (amplitude and lifetime) for each underlying mono-exponential decay using non-linear fitting. However, in this case parameter estimation is highly sensitive to initial guesses and weighting. In contrast, the ANN-based approach robustly gives the Pi without knowledge of amplitudes and lifetimes. By experimental measurements and Monte-Carlo simulations, we comprehensively show that accuracy and precision of Pi determination with ANNs and hence the number of distinguishable fluorophores depend on the fluorescence lifetimes' differences. For mixtures of up to five fluorophores, we determined the minimum uniform spacing Δτmin between lifetimes to obtain fractional contributions with a standard deviation of 5%. In example, five lifetimes can be distinguished with a respective minimum uniform spacing of approx. 10 ns even when the fluorophores' emission spectra are overlapping. This study underlines the enormous potential of ANN-based analysis for multi-fluorophore applications in fluorescence lifetime measurements.
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Affiliation(s)
- Alexander Netaev
- Fraunhofer Institute for Microelectronic Circuits and Systems, Finkenstr. 61, 47057, Duisburg, Germany.
| | - Nicolas Schierbaum
- Fraunhofer Institute for Microelectronic Circuits and Systems, Finkenstr. 61, 47057, Duisburg, Germany
| | - Karsten Seidl
- Fraunhofer Institute for Microelectronic Circuits and Systems, Finkenstr. 61, 47057, Duisburg, Germany
- Department of Electronic Components and Circuits and Center for Nanointegration Duisburg-Essen (CENIDE), University Duisburg-Essen, 47057, Duisburg, Germany
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2
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Chen Y, Pang S, Li J, Lu Y, Gao C, Xiao Y, Chen M, Wang M, Ren X. Genetically encoded protein sensors for metal ion detection in biological systems: a review and bibliometric analysis. Analyst 2023; 148:5564-5581. [PMID: 37872814 DOI: 10.1039/d3an01412f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Metal ions are indispensable elements in living organisms and are associated with regulating various biological processes. An imbalance in metal ion content can lead to disorders in normal physiological functions of the human body and cause various diseases. Genetically encoded fluorescent protein sensors have the advantages of low biotoxicity, high specificity, and a long imaging time in vivo and have become a powerful tool to visualize or quantify the concentration level of biomolecules in vivo and in vitro, temporal and spatial distribution, and life activity process. This review analyzes the development status and current research hotspots in the field of genetically encoded fluorescent protein sensors by bibliometric analysis. Based on the results of bibliometric analysis, the research progress of genetically encoded fluorescent protein sensors for metal ion detection is reviewed, and the construction strategies, physicochemical properties, and applications of such sensors in biological imaging are summarized.
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Affiliation(s)
- Yuxueyuan Chen
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin 300381, China
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - ShuChao Pang
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin 300381, China
| | - Jingya Li
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yun Lu
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Chenxia Gao
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yanyu Xiao
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Meiling Chen
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Tianjin Key Laboratory of Therapeutic Substance of Traditional Chinese Medicine, Tianjin 301617, China.
| | - Meng Wang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin 301617, China
| | - Xiaoliang Ren
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Tianjin Key Laboratory of Therapeutic Substance of Traditional Chinese Medicine, Tianjin 301617, China.
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3
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Mo Y, Zhou H, Xu J, Chen X, Li L, Zhang S. Genetically encoded fluorescence lifetime biosensors: overview, advances, and opportunities. Analyst 2023; 148:4939-4953. [PMID: 37721109 DOI: 10.1039/d3an01201h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Genetically encoded biosensors based on fluorescent proteins (FPs) are powerful tools for tracking analytes and cellular events with high spatial and temporal resolution in living cells and organisms. Compared with intensiometric readout and ratiometric readout, fluorescence lifetime readout provides absolute measurements, independent of the biosensor expression level and instruments. Thus, genetically encoded fluorescence lifetime biosensors play a vital role in facilitating accurate quantitative assessments within intricate biological systems. In this review, we first provide a concise description of the categorization and working mechanism of genetically encoded fluorescence lifetime biosensors. Subsequently, we elaborate on the combination of the fluorescence lifetime imaging technique and lifetime analysis methods with fluorescence lifetime biosensors, followed by their application in monitoring the dynamics of environment parameters, analytes and cellular events. Finally, we discuss worthwhile considerations for the design, optimization and development of fluorescence lifetime-based biosensors from three representative cases.
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Affiliation(s)
- Yidan Mo
- State Key Laboratory of Precision Spectroscopy, East China Normal University, No. 500, Dongchuan Rd, Shanghai 200241, China
| | - Huangmei Zhou
- State Key Laboratory of Precision Spectroscopy, East China Normal University, No. 500, Dongchuan Rd, Shanghai 200241, China
| | - Jinming Xu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, No. 500, Dongchuan Rd, Shanghai 200241, China
| | - Xihang Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, No. 500, Dongchuan Rd, Shanghai 200241, China
| | - Lei Li
- School of Science, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, China.
| | - Sanjun Zhang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, No. 500, Dongchuan Rd, Shanghai 200241, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
- NYU-ECNU Institute of Physics at NYU Shanghai, No. 3663, North Zhongshan Rd, Shanghai 200062, China.
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4
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Molinari PE, Krapp AR, Zurbriggen MD, Carrillo N. Lighting the light reactions of photosynthesis by means of redox-responsive genetically encoded biosensors for photosynthetic intermediates. Photochem Photobiol Sci 2023; 22:2005-2018. [PMID: 37195389 DOI: 10.1007/s43630-023-00425-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 04/17/2023] [Indexed: 05/18/2023]
Abstract
Oxygenic photosynthesis involves light and dark phases. In the light phase, photosynthetic electron transport provides reducing power and energy to support the carbon assimilation process. It also contributes signals to defensive, repair, and metabolic pathways critical for plant growth and survival. The redox state of components of the photosynthetic machinery and associated routes determines the extent and direction of plant responses to environmental and developmental stimuli, and therefore, their space- and time-resolved detection in planta becomes critical to understand and engineer plant metabolism. Until recently, studies in living systems have been hampered by the inadequacy of disruptive analytical methods. Genetically encoded indicators based on fluorescent proteins provide new opportunities to illuminate these important issues. We summarize here information about available biosensors designed to monitor the levels and redox state of various components of the light reactions, including NADP(H), glutathione, thioredoxin, and reactive oxygen species. Comparatively few probes have been used in plants, and their application to chloroplasts poses still additional challenges. We discuss advantages and limitations of biosensors based on different principles and propose rationales for the design of novel probes to estimate the NADP(H) and ferredoxin/flavodoxin redox poise, as examples of the exciting questions that could be addressed by further development of these tools. Genetically encoded fluorescent biosensors are remarkable tools to monitor the levels and/or redox state of components of the photosynthetic light reactions and accessory pathways. Reducing equivalents generated at the photosynthetic electron transport chain in the form of NADPH and reduced ferredoxin (FD) are used in central metabolism, regulation, and detoxification of reactive oxygen species (ROS). Redox components of these pathways whose levels and/or redox status have been imaged in plants using biosensors are highlighted in green (NADPH, glutathione, H2O2, thioredoxins). Analytes with available biosensors not tried in plants are shown in pink (NADP+). Finally, redox shuttles with no existing biosensors are circled in light blue. APX, ASC peroxidase; ASC, ascorbate; DHA, dehydroascorbate; DHAR, DHA reductase; FNR, FD-NADP+ reductase; FTR, FD-TRX reductase; GPX, glutathione peroxidase; GR, glutathione reductase; GSH, reduced glutathione; GSSG, oxidized glutathione; MDA, monodehydroascorbate; MDAR, MDA reductase; NTRC, NADPH-TRX reductase C; OAA, oxaloacetate; PRX, peroxiredoxin; PSI, photosystem I; PSII: photosystem II; SOD, superoxide dismutase; TRX, thioredoxin.
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Affiliation(s)
- Pamela E Molinari
- Instituto de Biología Molecular y Celular de Rosario (UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Adriana R Krapp
- Instituto de Biología Molecular y Celular de Rosario (UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Düsseldorf, Germany
| | - Néstor Carrillo
- Instituto de Biología Molecular y Celular de Rosario (UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.
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5
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San Martín A, Arce-Molina R, Aburto C, Baeza-Lehnert F, Barros LF, Contreras-Baeza Y, Pinilla A, Ruminot I, Rauseo D, Sandoval PY. Visualizing physiological parameters in cells and tissues using genetically encoded indicators for metabolites. Free Radic Biol Med 2022; 182:34-58. [PMID: 35183660 DOI: 10.1016/j.freeradbiomed.2022.02.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 02/07/2023]
Abstract
The study of metabolism is undergoing a renaissance. Since the year 2002, over 50 genetically-encoded fluorescent indicators (GEFIs) have been introduced, capable of monitoring metabolites with high spatial/temporal resolution using fluorescence microscopy. Indicators are fusion proteins that change their fluorescence upon binding a specific metabolite. There are indicators for sugars, monocarboxylates, Krebs cycle intermediates, amino acids, cofactors, and energy nucleotides. They permit monitoring relative levels, concentrations, and fluxes in living systems. At a minimum they report relative levels and, in some cases, absolute concentrations may be obtained by performing ad hoc calibration protocols. Proper data collection, processing, and interpretation are critical to take full advantage of these new tools. This review offers a survey of the metabolic indicators that have been validated in mammalian systems. Minimally invasive, these indicators have been instrumental for the purposes of confirmation, rebuttal and discovery. We envision that this powerful technology will foster metabolic physiology.
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Affiliation(s)
- A San Martín
- Centro de Estudios Científicos (CECs), Valdivia, Chile.
| | - R Arce-Molina
- Centro de Estudios Científicos (CECs), Valdivia, Chile
| | - C Aburto
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Universidad Austral de Chile, Valdivia, Chile
| | | | - L F Barros
- Centro de Estudios Científicos (CECs), Valdivia, Chile
| | - Y Contreras-Baeza
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Universidad Austral de Chile, Valdivia, Chile
| | - A Pinilla
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Universidad Austral de Chile, Valdivia, Chile
| | - I Ruminot
- Centro de Estudios Científicos (CECs), Valdivia, Chile
| | - D Rauseo
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Universidad Austral de Chile, Valdivia, Chile
| | - P Y Sandoval
- Centro de Estudios Científicos (CECs), Valdivia, Chile
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6
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Smith EN, Schwarzländer M, Ratcliffe RG, Kruger NJ. Shining a light on NAD- and NADP-based metabolism in plants. TRENDS IN PLANT SCIENCE 2021; 26:1072-1086. [PMID: 34281784 DOI: 10.1016/j.tplants.2021.06.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 05/20/2023]
Abstract
The pyridine nucleotides nicotinamide adenine dinucleotide [NAD(H)] and nicotinamide adenine dinucleotide phosphate [NADP(H)] simultaneously act as energy transducers, signalling molecules, and redox couples. Recent research into photosynthetic optimisation, photorespiration, immunity, hypoxia/oxygen signalling, development, and post-harvest metabolism have all identified pyridine nucleotides as key metabolites. Further understanding will require accurate description of NAD(P)(H) metabolism, and genetically encoded fluorescent biosensors have recently become available for this purpose. Although these biosensors have begun to provide novel biological insights, their limitations must be considered and the information they provide appropriately interpreted. We provide a framework for understanding NAD(P)(H) metabolism and explore what fluorescent biosensors can, and cannot, tell us about plant biology, looking ahead to the pressing questions that could be answered with further development of these tools.
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Affiliation(s)
- Edward N Smith
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK; Current address: Department of Molecular Systems Biology, University of Groningen, 9747 AG Groningen, The Netherlands.
| | - Markus Schwarzländer
- Institute of Plant Biology and Biotechnology (IBBP), Westfälische Wilhelms-Universität Münster, D-48143 Münster, Germany
| | | | - Nicholas J Kruger
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
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7
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Wu CS, Wu SC, Yang BT, Wu ZY, Chou YH, Chen P, Hsu HC. Hemispherical Cesium Lead Bromide Perovskite Single-Mode Microlasers with High-Quality Factors and Strong Purcell Enhancement. ACS APPLIED MATERIALS & INTERFACES 2021; 13:13556-13564. [PMID: 33689258 DOI: 10.1021/acsami.0c21738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We realized a single-mode laser with an ultra-high quality factor in individual cesium lead bromide (CsPbBr3) perovskite micro-hemispheres fabricated by chemical vapor deposition. A series of lasing property analysis based on cavity size was reported under this material system. Due to good optical confinement capability of the whispering gallery resonant cavity and high optical gain of CsPbBr3 perovskite micro-hemispheres, single-mode lasing behavior was achieved with an ultra-high quality factor as large as 11,460 at room temperature. To study in detail the physical effects between lasing threshold and cavity, a set of cavity size dependence photoluminescence analyses were performed. We found that the lasing threshold increases while the cavity size decreases. Time-resolved PL analysis was conducted to confirm the relation between cavity size and lasing threshold. The larger cavity stands for longer PL lifetime and indicates easier-to-achieve carrier population inversion. Strong Purcell enhancement could be further investigated by the spontaneous emission coupling factor β and internal quantum efficiency as a function of cavity size. A high β-factor of 0.37 could be obtained from a 2.2 μm diameter hemisphere microcavity and a high Purcell factor of 14 in a 1.9 μm diameter hemisphere microcavity showing strong Purcell enhancement effect in our system.
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Affiliation(s)
- Chun-Sheng Wu
- Department of Photonics, National Cheng Kung University, No. 1, University Road, East District, Tainan 70101, Taiwan
| | - Sheng-Chan Wu
- Department of Photonics, National Cheng Kung University, No. 1, University Road, East District, Tainan 70101, Taiwan
| | - Bo-Ting Yang
- Department of Photonics, National Cheng Kung University, No. 1, University Road, East District, Tainan 70101, Taiwan
| | - Zong Yu Wu
- Department of Photonics, National Cheng Kung University, No. 1, University Road, East District, Tainan 70101, Taiwan
| | - Yu Hsun Chou
- Department of Photonics, National Cheng Kung University, No. 1, University Road, East District, Tainan 70101, Taiwan
| | - Peter Chen
- Department of Photonics, National Cheng Kung University, No. 1, University Road, East District, Tainan 70101, Taiwan
- Hierarchical Green-Energy Materials (Hi-GEM) Research Center, National Cheng Kung University, No. 1, University Road, East District, Tainan 70101, Taiwan
| | - Hsu-Cheng Hsu
- Department of Photonics, National Cheng Kung University, No. 1, University Road, East District, Tainan 70101, Taiwan
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8
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Ultra-Stable Polycrystalline CsPbBr 3 Perovskite-Polymer Composite Thin Disk for Light-Emitting Applications. NANOMATERIALS 2020; 10:nano10122382. [PMID: 33260437 PMCID: PMC7759973 DOI: 10.3390/nano10122382] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 11/24/2020] [Accepted: 11/27/2020] [Indexed: 02/06/2023]
Abstract
Organic–inorganic halide organometal perovskites have demonstrated very promising performance in optoelectronic applications, but their relatively poor chemical and colloidal stability hampers the further improvement of devices based on these materials. Perovskite material engineering is crucial for achieving high photoluminescence quantum yields (PLQYs) and long stability. Herein, these goals are attained by incorporating bulk-structure CsPbBr3, which prevents colloidal degradation, into polymethyl methacrylate (PMMA) polymer in thin-disk form. This technology can potentially realize future disk lasers with no optical and structural contributions from the polymer. The polycrystalline CsPbBr3 perovskite particles were simply obtained by using a mechanical processing technique. The CsPbBr3 was then incorporated into the PMMA polymer using a solution blending method. The polymer enhanced the PLQYs by removing the surface trap states and increasing the water resistance and stability under ambient conditions. In our experimental investigation, the CsPbBr3/PMMA composites were extraordinarily stable and remained strongly luminescent after water immersion for three months and air exposure for over one year, maintaining 80% of their initial photoluminescence intensity. The CsPbBr3/PMMA thin disk produced amplified spontaneous emission for a long time in air and for more than two weeks in water.
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9
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Cao S, Li H, Liu Y, Zhang M, Wang M, Zhou Z, Chen J, Zhang S, Xu J, Knutson JR. Femtosecond Fluorescence Spectra of NADH in Solution: Ultrafast Solvation Dynamics. J Phys Chem B 2020; 124:771-776. [PMID: 31941277 PMCID: PMC7477843 DOI: 10.1021/acs.jpcb.9b10656] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ultrafast solvation dynamics of reduced nicotinamide adenine dinucleotide (NADH) free in solution has been investigated, using both a femtosecond upconversion spectrophotofluorometer and a picosecond time-correlated single-photon counting (TCSPC) apparatus. The familiar time constant of solvent relaxation originating in "bulk water" was found to be ∼1.4 ps, revealing ultrafast solvent reorientation upon excitation. We also found a slower spectral relaxation process with an apparent time of 27 ps, suggesting there could either be dissociable "biological water" hydration sites on the surface of NADH or internal dielectric rearrangements of the flexible solvated molecule on that timescale. In contrast, the femtosecond fluorescence anisotropy measurement revealed that rotational diffusion happened on two different timescales (3.6 ps (local) and 141 ps (tumbling)); thus, any dielectric rearrangement scenario for the 27 ps relaxation must occur without significant chromophore oscillator rotation. The coexistence of quasi-static self quenching (QSSQ) with the slower relaxation is also discussed.
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Affiliation(s)
- Simin Cao
- State Key Laboratory of Precision Spectroscopy , East China Normal University , Shanghai 200062 , China
| | - Haoyang Li
- State Key Laboratory of Precision Spectroscopy , East China Normal University , Shanghai 200062 , China
| | - Yangyi Liu
- State Key Laboratory of Precision Spectroscopy , East China Normal University , Shanghai 200062 , China
| | - Mengjie Zhang
- State Key Laboratory of Precision Spectroscopy , East China Normal University , Shanghai 200062 , China
| | - Mengyu Wang
- State Key Laboratory of Precision Spectroscopy , East China Normal University , Shanghai 200062 , China
| | - Zhongneng Zhou
- State Key Laboratory of Precision Spectroscopy , East China Normal University , Shanghai 200062 , China
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy , East China Normal University , Shanghai 200062 , China
| | - Sanjun Zhang
- State Key Laboratory of Precision Spectroscopy , East China Normal University , Shanghai 200062 , China
| | - Jianhua Xu
- State Key Laboratory of Precision Spectroscopy , East China Normal University , Shanghai 200062 , China
| | - Jay R Knutson
- Laboratory for Advanced Microscopy and Biophotonics, National Heart, Lung and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
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10
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Morten MJ, Lopez SG, Steinmark IE, Rafferty A, Magennis SW. Stacking-induced fluorescence increase reveals allosteric interactions through DNA. Nucleic Acids Res 2019; 46:11618-11626. [PMID: 30277520 PMCID: PMC6265455 DOI: 10.1093/nar/gky887] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 09/19/2018] [Indexed: 12/14/2022] Open
Abstract
From gene expression to nanotechnology, understanding and controlling DNA requires a detailed knowledge of its higher order structure and dynamics. Here we take advantage of the environment-sensitive photoisomerization of cyanine dyes to probe local and global changes in DNA structure. We report that a covalently attached Cy3 dye undergoes strong enhancement of fluorescence intensity and lifetime when stacked in a nick, gap or overhang region in duplex DNA. This is used to probe hybridization dynamics of a DNA hairpin down to the single-molecule level. We also show that varying the position of a single abasic site up to 20 base pairs away modulates the dye–DNA interaction, indicative of through-backbone allosteric interactions. The phenomenon of stacking-induced fluorescence increase (SIFI) should find widespread use in the study of the structure, dynamics and reactivity of nucleic acids.
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Affiliation(s)
- Michael J Morten
- School of Chemistry, WestCHEM, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, UK
| | - Sergio G Lopez
- School of Chemistry, WestCHEM, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, UK
| | - I Emilie Steinmark
- School of Chemistry, WestCHEM, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, UK
| | - Aidan Rafferty
- School of Chemistry, WestCHEM, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, UK
| | - Steven W Magennis
- School of Chemistry, WestCHEM, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, UK
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11
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Cao S, Zhou Z, Li H, Jia M, Liu Y, Wang M, Zhang M, Zhang S, Chen J, Xu J, Knutson JR. A fraction of NADH in solution is "dark": Implications for metabolic sensing via fluorescence lifetime. Chem Phys Lett 2019; 726:18-21. [PMID: 32921799 PMCID: PMC7486008 DOI: 10.1016/j.cplett.2019.04.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The metabolic cofactor and energy carrier NADH (nicotinamide adenine dinucleotide, reduced) has fluorescence yield and lifetime that depends strongly on conformation, a fact that has enabled metabolic monitoring of cells via FLIM (Fluorescence Lifetime Microscopy). Using femtosecond fluorescence upconversion, we show that this molecule in solution participates in ultrafast self-quenching along with both bulk solvent relaxation and spectral relaxation on 1.4 and 26 ps timescales. This, in effect, means up to a third of NADH is effectively "dark" for FLIM in the 400-500 nm observation window commonly employed. Methods to compensate for, avoid or measure dark species corrections are outlined.
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Affiliation(s)
- Simin Cao
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Zhongneng Zhou
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Haoyang Li
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Menghui Jia
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Yangyi Liu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Mengyu Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Mengjie Zhang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Sanjun Zhang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Jianhua Xu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Jay R. Knutson
- Laboratory for Advanced Microscopy and Biophotonics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, United States
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12
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Li L, Zhang C, Wang P, Wang A, Zhou J, Chen G, Xu J, Yang Y, Zhao Y, Zhang S, Tian Y. Imaging the Redox States of Live Cells with the Time-Resolved Fluorescence of Genetically Encoded Biosensors. Anal Chem 2019; 91:3869-3876. [PMID: 30777423 DOI: 10.1021/acs.analchem.8b04292] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Redox environments in cells influence many important physiological and pathological processes. In this study, the time-resolved fluorescence of a recently reported thiol redox-sensitive sensor based on vertebrate fluorescent protein UnaG, roUnaG, was studied, along with the application of the time-resolved fluorescence of roUnaG to image the redox states of the mitochondria, cytoplasm, and nucleus in live cells. Time-resolved fluorescence images of roUnaG clearly demonstrated that potent anticancer compound KP372-1 induced extreme oxidative stress. A more stressful redox state observed in activated macrophages further demonstrated the validity of roUnaG with time-resolved fluorescence. For comparison, time-resolved fluorescence images of four other frequently used redox biosensors (roGFP1, HyPer, HyPerRed, and rxRFP) were also captured. The time-resolved fluorescence allows an intrinsically ratiometric measurement for biosensors with one excitation wavelength and provides new opportunities for bioimaging.
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Affiliation(s)
- Lei Li
- State Key Laboratory of Precision Spectroscopy , East China Normal University , 3663 North Zhongshan Road , Shanghai 200062 , China.,School of Science , Jiangnan University , Wuxi 214122 , China
| | | | - Peng Wang
- State Key Laboratory of Precision Spectroscopy , East China Normal University , 3663 North Zhongshan Road , Shanghai 200062 , China
| | | | - Jiasheng Zhou
- State Key Laboratory of Precision Spectroscopy , East China Normal University , 3663 North Zhongshan Road , Shanghai 200062 , China
| | - Guoqing Chen
- School of Science , Jiangnan University , Wuxi 214122 , China
| | - Jianhua Xu
- State Key Laboratory of Precision Spectroscopy , East China Normal University , 3663 North Zhongshan Road , Shanghai 200062 , China
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences , Chinese Academy of Sciences , Shanghai 200031 , China
| | | | - Sanjun Zhang
- State Key Laboratory of Precision Spectroscopy , East China Normal University , 3663 North Zhongshan Road , Shanghai 200062 , China.,Collaborative Innovation Center of Extreme Optics , Shanxi University , Taiyuan , Shanxi 030006 , China.,NYU-ECNU Institute of Physics at NYU Shanghai , No. 3663, North Zhongshan Road , Shanghai 200062 , China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering , East China Normal University , Dongchuan Road 500 , Shanghai 200241 , China
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pH Resistant Ratiometric Measurement of Nicotinamide Adenine Dinucleotide Levels by Time-resolved Fluorescence Spectroscopy. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2019. [DOI: 10.1016/s1872-2040(18)61138-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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