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Wang C, Chen L, Tan R, Li Y, Zhao Y, Liao L, Ge Z, Ding C, Xing Z, Zhou P. Carbon dots and composite materials with excellent performances in cancer-targeted bioimaging and killing: a review. Nanomedicine (Lond) 2023. [PMID: 37965983 DOI: 10.2217/nnm-2023-0216] [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] [Indexed: 11/16/2023] Open
Abstract
Carbon dots (CDs) are nanomaterials with excellent properties, including good biocompatibility, small size, ideal photoluminescence and surface modification, and are becoming one of the most attractive nanomaterials for the imaging, detection and treatment of tumors. Based on these advantages, CDs can be combined other materials to obtain composite particles with improved, even new, performance, mainly in photothermal and photodynamic therapies. This paper reviews the research progress of CDs and their composites in targeted tumor imaging, detection, diagnosis, drug delivery and tumor killing. It also discusses and proposes the challenges and perspectives of their future applications in these fields. This review provides ideas for future applications of novel CD-based materials in the diagnosis and treatment of cancer.
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Affiliation(s)
- Chenggang Wang
- School & Hospital of Stomatology, Lanzhou University, Lanzhou, 730000, PR China
- Key Laboratory of Dental Maxillofacial Reconstruction & Biological Intelligence Manufacturing of Gansu Province, Lanzhou University, Lanzhou, 730000, PR China
| | - Lixin Chen
- School & Hospital of Stomatology, Lanzhou University, Lanzhou, 730000, PR China
| | - Rongshuang Tan
- School & Hospital of Stomatology, Lanzhou University, Lanzhou, 730000, PR China
| | - Yuchen Li
- School & Hospital of Stomatology, Lanzhou University, Lanzhou, 730000, PR China
| | - Yiqing Zhao
- School & Hospital of Stomatology, Lanzhou University, Lanzhou, 730000, PR China
| | - Lingzi Liao
- School & Hospital of Stomatology, Lanzhou University, Lanzhou, 730000, PR China
| | - Zhangjie Ge
- School & Hospital of Stomatology, Lanzhou University, Lanzhou, 730000, PR China
| | - Chuanyang Ding
- School & Hospital of Stomatology, Lanzhou University, Lanzhou, 730000, PR China
| | - Zhankui Xing
- The Second Hospital of Lanzhou University, Lanzhou, 730030, PR China
| | - Ping Zhou
- School & Hospital of Stomatology, Lanzhou University, Lanzhou, 730000, PR China
- Key Laboratory of Dental Maxillofacial Reconstruction & Biological Intelligence Manufacturing of Gansu Province, Lanzhou University, Lanzhou, 730000, PR China
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2
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Zhang Y, Zhou W, Xu N, Wang G, Li J, An K, Jiang W, Zhou X, Qiao Q, Jiang X, Xu Z. Aniline as a TICT rotor to derive methine fluorogens for biomolecules: A curcuminoid-BF2 compound for lighting up HSA/BSA. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.04.070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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3
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Vincent S, Mallick S, Barnoin G, Le HN, Michel BY, Burger A. An Expeditious Approach towards the Synthesis and Application of Water-Soluble and Photostable Fluorogenic Chromones for DNA Detection. Molecules 2022; 27:molecules27072267. [PMID: 35408665 PMCID: PMC9000371 DOI: 10.3390/molecules27072267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/25/2022] [Accepted: 03/27/2022] [Indexed: 12/29/2022] Open
Abstract
The intensive research for hybridization probes based on organic molecules with fluorogenic properties is currently attracting particular attention due to their potential to efficiently recognize different DNA conformations and the local environment. However, most established organic chromophores do not meet the requirements of this task, as they do not exhibit good brightness in aqueous buffer media, develop aggregation and/or are not easily conjugated to oligodeoxynucleotides (ODNs) while keeping their photophysics intact. Herein, an important modification strategy was employed for a well-known fluorophore, 2-(4-(diethylamino)phenyl)-3-hydroxychromone (dEAF). Although this push–pull dye absorbs intensively in the visible range and shows emission with large Stokes shifts in all organic solvents, it is strongly quenched in water. This Achilles’ heel prompted us to implement a new strategy to obtain a series of dyes that retain all the photophysical features of dEAF in water, conjugate readily with oligonucleotides, and furthermore demonstrate sensitivity to hydration, thus paving the way for a high-performance fluorogenic DNA hybridization probe.
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4
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Recent Advancements in Tracking Bacterial Effector Protein Translocation. Microorganisms 2022; 10:microorganisms10020260. [PMID: 35208715 PMCID: PMC8876096 DOI: 10.3390/microorganisms10020260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 11/17/2022] Open
Abstract
Bacteria-host interactions are characterized by the delivery of bacterial virulence factors, i.e., effectors, into host cells where they counteract host immunity and exploit host responses allowing bacterial survival and spreading. These effectors are translocated into host cells by means of dedicated secretion systems such as the type 3 secretion system (T3SS). A comprehensive understanding of effector translocation in a spatio-temporal manner is of critical importance to gain insights into an effector’s mode of action. Various approaches have been developed to understand timing and order of effector translocation, quantities of translocated effectors and their subcellular localization upon translocation into host cells. Recently, the existing toolset has been expanded by newly developed state-of-the art methods to monitor bacterial effector translocation and dynamics. In this review, we elaborate on reported methods and discuss recent advances and shortcomings in this area of tracking bacterial effector translocation.
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5
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Shen D, Bai Y, Liu Y. Chemical Biology Toolbox to Visualize Protein Aggregation in Live Cells. Chembiochem 2021; 23:e202100443. [PMID: 34613660 DOI: 10.1002/cbic.202100443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/05/2021] [Indexed: 11/09/2022]
Abstract
Protein misfolding and aggregation is a complex biochemical process and has been associated with numerous human degenerative diseases. Developing novel chemical and biological tools and approaches to visualize aggregated proteins in live cells is in high demand for mechanistic studies, diagnostics, and therapeutics. In this review, we summarize the recent developments in the chemical biology toolbox applied to protein aggregation studies in live cells. These methods exploited fluorescent protein tags, fluorescent chemical tags, and small-molecule probes to visualize the protein-aggregation process, detect proteome stresses, and quantify the protein homeostasis network capacity. Inspired by these seminal works, we have generalized design principles for the development of new detection methods and probes in the future that will illuminate this important biological process.
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Affiliation(s)
- Di Shen
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China
| | - Yulong Bai
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China
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6
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Chen C, Tachibana SR, Baleeva NS, Myasnyanko IN, Bogdanov AM, Gavrikov AS, Mishin AS, Malyshevskaya KK, Baranov MS, Fang C. Developing Bright Green Fluorescent Protein (GFP)-like Fluorogens for Live-Cell Imaging with Nonpolar Protein-Chromophore Interactions. Chemistry 2021; 27:8946-8950. [PMID: 33938061 DOI: 10.1002/chem.202101250] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Indexed: 11/09/2022]
Abstract
Fluorescence-activating proteins (FAPs) that bind a chromophore and activate its fluorescence have gained popularity in bioimaging. The fluorescence-activating and absorption-shifting tag (FAST) is a light-weight FAP that enables fast reversible fluorogen binding, thus advancing multiplex and super-resolution imaging. However, the rational design of FAST-specific fluorogens with large fluorescence enhancement (FE) remains challenging. Herein, a new fluorogen directly engineered from green fluorescent protein (GFP) chromophore by a unique double-donor-one-acceptor strategy, which exhibits an over 550-fold FE upon FAST binding and a high extinction coefficient of approximately 100,000 M-1 cm-1 , is reported. Correlation analysis of the excited state nonradiative decay rates and environmental factors reveal that the large FE is caused by nonpolar protein-fluorogen interactions. Our deep insights into structure-function relationships could guide the rational design of bright fluorogens for live-cell imaging with extended spectral properties such as redder emissions.
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Affiliation(s)
- Cheng Chen
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR 97331-4003, USA
| | - Sean R Tachibana
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR 97331-4003, USA
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Alexey M Bogdanov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Alexey S Gavrikov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Alexander S Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Kseniya K Malyshevskaya
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia.,Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow, 117997, Russia
| | - Chong Fang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR 97331-4003, USA
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7
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Suss O, Motiei L, Margulies D. Broad Applications of Thiazole Orange in Fluorescent Sensing of Biomolecules and Ions. Molecules 2021; 26:2828. [PMID: 34068759 PMCID: PMC8126248 DOI: 10.3390/molecules26092828] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/13/2022] Open
Abstract
Fluorescent sensing of biomolecules has served as a revolutionary tool for studying and better understanding various biological systems. Therefore, it has become increasingly important to identify fluorescent building blocks that can be easily converted into sensing probes, which can detect specific targets with increasing sensitivity and accuracy. Over the past 30 years, thiazole orange (TO) has garnered great attention due to its low fluorescence background signal and remarkable 'turn-on' fluorescence response, being controlled only by its intramolecular torsional movement. These features have led to the development of numerous molecular probes that apply TO in order to sense a variety of biomolecules and metal ions. Here, we highlight the tremendous progress made in the field of TO-based sensors and demonstrate the different strategies that have enabled TO to evolve into a versatile dye for monitoring a collection of biomolecules.
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Affiliation(s)
| | | | - David Margulies
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel; (O.S.); (L.M.)
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8
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Sokolov AI, Myasnyanko IN, Baleeva NS, Baranov MS. Styrene Derivatives of Indole and Pyranone as Fluorogenic Substrates for FAST Protein. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021010234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Anderson NT, Weyant KB, Mukherjee A. Characterization of flavin binding in oxygen-independent fluorescent reporters. AIChE J 2020; 66. [PMID: 34305141 DOI: 10.1002/aic.17083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Fluorescent proteins based on light, oxygen, and voltage (LOV) sensing photoreceptors are among the few reporter gene technologies available for studying living systems in oxygen-free environments that render reporters based on the green fluorescent protein nonfluorescent. LOV reporters develop fluorescence by binding flavin mononucleotide (FMN), which they endogenously obtain from cells. As FMN is essential to cell physiology as well as for determining fluorescence in LOV proteins, it is important to be able to study and characterize flavin binding in LOV reporters. To this end, we report a method for reversibly separating FMN from two commonly used LOV reporters to prepare stable and soluble apoproteins. Using fluorescence titration, we measured the equilibrium dissociation constant for binding with all three cellular flavins: FMN, flavin adenine dinucleotide, and riboflavin. Finally, we exploit the riboflavin affinity of apo LOV reporters, identified in this work, to develop a fluorescence turn-on biosensor for vitamin B2.
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Affiliation(s)
- Nolan T. Anderson
- Department of Chemical Engineering University of California Santa Barbara California 93106 USA
| | - Kevin B. Weyant
- Smith School of Chemical & Biomolecular Engineering Cornell University Ithaca New York 14853 USA
| | - Arnab Mukherjee
- Department of Chemical Engineering University of California Santa Barbara California 93106 USA
- Department of Chemistry University of California Santa Barbara California 93106 USA
- Neuroscience Research Institute University of California Santa Barbara California 93106 USA
- Center for Bioengineering University of California Santa Barbara California 93106 USA
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10
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Cambré A, Aertsen A. Bacterial Vivisection: How Fluorescence-Based Imaging Techniques Shed a Light on the Inner Workings of Bacteria. Microbiol Mol Biol Rev 2020; 84:e00008-20. [PMID: 33115939 PMCID: PMC7599038 DOI: 10.1128/mmbr.00008-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The rise in fluorescence-based imaging techniques over the past 3 decades has improved the ability of researchers to scrutinize live cell biology at increased spatial and temporal resolution. In microbiology, these real-time vivisections structurally changed the view on the bacterial cell away from the "watery bag of enzymes" paradigm toward the perspective that these organisms are as complex as their eukaryotic counterparts. Capitalizing on the enormous potential of (time-lapse) fluorescence microscopy and the ever-extending pallet of corresponding probes, initial breakthroughs were made in unraveling the localization of proteins and monitoring real-time gene expression. However, later it became clear that the potential of this technique extends much further, paving the way for a focus-shift from observing single events within bacterial cells or populations to obtaining a more global picture at the intra- and intercellular level. In this review, we outline the current state of the art in fluorescence-based vivisection of bacteria and provide an overview of important case studies to exemplify how to use or combine different strategies to gain detailed information on the cell's physiology. The manuscript therefore consists of two separate (but interconnected) parts that can be read and consulted individually. The first part focuses on the fluorescent probe pallet and provides a perspective on modern methodologies for microscopy using these tools. The second section of the review takes the reader on a tour through the bacterial cell from cytoplasm to outer shell, describing strategies and methods to highlight architectural features and overall dynamics within cells.
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Affiliation(s)
- Alexander Cambré
- KU Leuven, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Leuven, Belgium
| | - Abram Aertsen
- KU Leuven, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Leuven, Belgium
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11
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Bachollet SPJT, Addi C, Pietrancosta N, Mallet JM, Dumat B. Fluorogenic Protein Probes with Red and Near-Infrared Emission for Genetically Targeted Imaging*. Chemistry 2020; 26:14467-14473. [PMID: 32691883 DOI: 10.1002/chem.202002911] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Indexed: 11/09/2022]
Abstract
Fluorogenic probes are important tools to image proteins with high contrast and no wash protocols. In this work, we rationally designed and synthesized a small set of four protein fluorogens with red or near-infrared emission. The fluorophores were characterized in the presence of albumin as a model protein environment and exhibited good fluorogenicity and brightness (fluorescence quantum yield up to 36 %). Once conjugated to a haloalkane ligand, the probes reacted with the protein self-labeling tag HaloTag with a high fluorescence enhancement (up to 156-fold). The spectroscopic properties of the fluorogens and their reaction with HaloTag were investigated experimentally in vitro and with the help of molecular dynamics. The two most promising probes, one in the red and one in the near-infrared range, were finally applied to image the nucleus or actin in live-cell and in wash-free conditions using fluorogenic and chemogenetic targeting of HaloTag fusion proteins.
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Affiliation(s)
- Sylvestre P J T Bachollet
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Cyril Addi
- Membrane Traffic and Cell Division Lab, Cell Biology and Infection Department, Institut Pasteur, CNRS UMR3691, Sorbonne Université, 75005, Paris, France
| | - Nicolas Pietrancosta
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France.,Neuroscience Paris Seine-Institut de Biologie Paris Seine (NPS-IBPS) INSERM, CNRS, Sorbonne Université, Paris, France
| | - Jean-Maurice Mallet
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Blaise Dumat
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
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12
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Li L, Xiong Z, Dang Y, Li Y, Zhang A, Ding C, Xu Z, Zhang W. A red-emissive D-A-D type fluorescent probe for lysosomal pH imaging. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:2978-2984. [PMID: 32930157 DOI: 10.1039/d0ay00418a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Visual detection of pH changes in lysosomes is critical because lysosomes not only play an important role in diverse cellular functions but also are closely related to various physiological and pathological processes. Herein, we disclose a donor-acceptor-donor (D-A-D) type fluorescent probe DBTD for detecting pH fluctuation in lysosomes. DBTD was rationally designed by using benzothiadiazole as the electron acceptor and N,N-diethylamino groups as the electron donor. Owing to its unique D-A-D structure, DBTD displayed a red-emission centered at 614 nm. It showed a sensitive and a linear response to pH from 4.5 to 5.2 with a pKa of 5.0, which is very suitable for lysosomal pH imaging. The response was based on the intramolecular charge transfer (ICT) effect owing to the protonation of the diethylamino group. Furthermore, DBTD could accurately monitor lysosomal pH variations in SGC-7901 cells. More importantly, it was able to image the pH change in lysosomes during the autophagy process successfully, suggesting the great potential of DBTD acting as a powerful tool for monitoring lysosomal pH-related biological processes.
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Affiliation(s)
- Lingling Li
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China.
| | - Zhi Xiong
- CAS Key Laboratory of Receptor Research, Synthetic Organic and Medicinal Chemistry Laboratory, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yijing Dang
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China.
| | - Yang Li
- CAS Key Laboratory of Receptor Research, Synthetic Organic and Medicinal Chemistry Laboratory, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ao Zhang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Chunyong Ding
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Zhiai Xu
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China.
| | - Wen Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China.
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13
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Ma J, Yang M, Batchelor-McAuley C, Compton RG. Visualising electrochemical reaction layers: mediated vs. direct oxidation. Phys Chem Chem Phys 2020; 22:12422-12433. [PMID: 32459226 DOI: 10.1039/d0cp01904f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electrochemical treatments are widely used for 'clean up' in which toxic metals and organic compounds are removed using direct or mediated electrolysis. Herein we report novel studies offering proof of concept that spectrofluorometric electrochemistry can provide important mechanistic detail into these processes. A thin layer opto-electrochemical cell, with a carbon fibre (radius 3.5 μm) working electrode, is used to visualise the optical responses of the oxidative destruction of a fluorophore either directly, on an electrode, or via the indirect reaction of the analyte with an electrochemically formed species which 'mediates' the destruction. The optical responses of these two reaction mechanisms are first predicted by numerical simulation followed by experimental validation of each using two fluorescent probes, a redox inactive (in the electrochemical window) 1,3,6,8-pyrenetetrasulfonic acid and the redox-active derivative 8-hydroxypyrene-1,3,6-trisulfonic acid. In the vicinity of a carbon electrode held at different oxidative potentials, the contrast between indirect electro-destruction, chlorination, and direct oxidation is very obvious. Excellent agreement is seen between the numerically predicted fluorescence intensity profiles and experiment.
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Affiliation(s)
- Junling Ma
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK.
| | - Minjun Yang
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK.
| | - Christopher Batchelor-McAuley
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK.
| | - Richard G Compton
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK.
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14
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Dragwidge JM, VAN Damme D. Visualising endocytosis in plants: past, present, and future. J Microsc 2020; 280:104-110. [PMID: 32441767 DOI: 10.1111/jmi.12926] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/15/2020] [Accepted: 05/20/2020] [Indexed: 12/28/2022]
Abstract
Chris Hawes had a lively fascination for the immensely complex organisation of the endomembrane system, including the process of endocytosis. This is the method by which eukaryotic cells internalise membrane proteins, lipids, carbohydrates, and cell wall enzymes from the cell surface through membrane bound vesicles. Endocytosis occurs progressively, starting with early membrane deformation, scission, and finally the release of the vesicle into the cytoplasm. Next to secretion, endocytosis allows the cell to control the proteome composition of its inner and outer surface membrane and as such, its communication with the outside world. Whereas endocytosis was initially considered theoretically impossible in plants due to their high turgor pressure, it is now established as essential for plant life. Furthermore, endocytosis remains a highly active field of research, both in yeast, animal, and plant model systems. Over the past three decades, the tools and techniques used to visualise, quantify, and characterise endocytosis have resulted in an increasingly higher spatiotemporal understanding of this process. Here we provide a brief history of plant endocytosis research from the time when Chris Hawes was investigating the process, to the current state-of-the-art in the field. We will end this chapter with a discussion on some promising future developments for plant endocytosis research. LAY DESCRIPTION: Endocytosis is a key process whereby eukaryotic cells can selectively take up membrane proteins, extracellular material and lipids. As this process controls the abundance and protein composition of the plasma membrane, it also controls the communication of the cell with the outside world. Whereas endocytosis was initially considered theoretically impossible in plants due to their high turgor pressure, it is now established as essential for plant life. Today, endocytosis remains a highly active field of research, both in yeast, animal, and plant model systems. Endocytosis was one of the favourite research topics of Chris Hawes, which is why this mini-review is part of the Festschrift issue in his honour. We provide here a brief history of plant endocytosis research from the time when Chris Hawes was investigating the process, to the current state-of-the-art in the field. Over the past three decades, the tools and techniques that were developed to visualise, quantify, and characterise endocytosis have allowed to achieve an increasingly higher spatiotemporal understanding of this process. We end this chapter with a discussion on some promising future developments for plant endocytosis research.
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Affiliation(s)
- J M Dragwidge
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - D VAN Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
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15
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Perkins LA, Bruchez MP. Fluorogen activating protein toolset for protein trafficking measurements. Traffic 2020; 21:333-348. [PMID: 32080949 PMCID: PMC7462100 DOI: 10.1111/tra.12722] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 12/11/2022]
Abstract
Throughout the past decade the use of fluorogen activating proteins (FAPs) has expanded with several unique reporter dyes that support a variety of methods to specifically quantify protein trafficking events. The platform's capabilities have been demonstrated in several systems and shared for widespread use. This review will highlight the current FAP labeling techniques for protein traffic measurements and focus on the use of the different designed fluorogenic dyes for selective and specific labeling applications.
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Affiliation(s)
- Lydia A. Perkins
- School of MedicineUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Marcel P. Bruchez
- The Department of Biological SciencesCarnegie MellonPittsburghPennsylvaniaUSA
- Department of ChemistryCarnegie MellonPittsburghPennsylvaniaUSA
- Molecular and Biosensor Imaging CenterCarnegie MellonPittsburghPennsylvaniaUSA
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16
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Zhang Y, Li S, Ma XT, He XW, Li WY, Zhang YK. Carbon dots-embedded epitope imprinted polymer for targeted fluorescence imaging of cervical cancer via recognition of epidermal growth factor receptor. Mikrochim Acta 2020; 187:228. [PMID: 32170469 DOI: 10.1007/s00604-020-4198-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 02/25/2020] [Indexed: 12/29/2022]
Abstract
A carbon dots-embedded epitope imprinted polymer (C-MIP) was fabricated for targeted fluorescence imaging of cervical cancer by specifically recognizing the epidermal growth factor receptor (EGFR). The core-shell C-MIP was prepared by a reverse microemulsion polymerization method. This method used silica nanoparticles embedded with carbon dots as carriers, acrylamide as the main functional monomer, and N-terminal nonapeptides of EGFR modified by palmitic acid as templates. A series of characterizations (transmission electron microscope, dynamic light scattering, X-ray photoelectron spectroscopy, Fourier transform infrared spectroscopy, zeta potential, and energy dispersive X-ray spectroscopy) prove the successful synthesis of C-MIP. The fluorescence of C-MIP is quenched by the epitopes of EGFR due to the specific recognition of epitopes of EGFR through their imprinted cavities (analytical excitation/emission wavelengths, 540 nm/610 nm). The linear range of fluorescence quenching is 2.0 to 15.0 μg mL-1 and the determination limit is 0.73 μg mL-1. The targeted imaging capabilities of C-MIP are demonstrated through in vitro and in vivo experiments. The laser confocal imaging results indicate that HeLa cells (over-expression EGFR) incubated with C-MIP show stronger fluorescence than that of MCF-7 cells (low-expression EGFR), revealing that C-MIP can target tumor cells overexpressing EGFR. The results of imaging experiments in tumor-bearing mice exhibit that C-MIP has a better imaging effect than C-NIP, which further proves the targeted imaging ability of C-MIP in vivo. Graphical abstract An oriented epitope imprinted polymer embedded with carbon dots was prepared for the determination of the epitopes of epidermal growth factor receptor and targeted fluorescence imaging of cervical cancer.
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Affiliation(s)
- Yue Zhang
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin, 300071, China
| | - Si Li
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin, 300071, China
| | - Xiao-Tong Ma
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin, 300071, China
| | - Xi-Wen He
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin, 300071, China
| | - Wen-You Li
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin, 300071, China.
| | - Yu-Kui Zhang
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin, 300071, China
- National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
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17
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Ozbakir HF, Anderson NT, Fan KC, Mukherjee A. Beyond the Green Fluorescent Protein: Biomolecular Reporters for Anaerobic and Deep-Tissue Imaging. Bioconjug Chem 2020; 31:293-302. [PMID: 31794658 PMCID: PMC7033020 DOI: 10.1021/acs.bioconjchem.9b00688] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fluorescence imaging represents cornerstone technology for studying biological function at the cellular and molecular levels. The technology's centerpiece is a prolific collection of genetic reporters based on the green fluorescent protein (GFP) and related analogs. More than two decades of protein engineering have endowed the GFP repertoire with an incredible assortment of fluorescent proteins, allowing scientists immense latitude in choosing reporters tailored to various cellular and environmental contexts. Nevertheless, GFP and derivative reporters have specific limitations that hinder their unrestricted use for molecular imaging. These challenges have inspired the development of new reporter proteins and imaging mechanisms. Here, we review how these developments are expanding the frontiers of reporter gene techniques to enable nondestructive studies of cell function in anaerobic environments and deep inside intact animals-two important biological contexts that are fundamentally incompatible with the use of GFP-based reporters.
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Affiliation(s)
- Harun F. Ozbakir
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Nolan T. Anderson
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Kang-Ching Fan
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Arnab Mukherjee
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Department of Chemistry, University of California, Santa Barbara, California 93106, United States
- Neuroscience Research Institute, University of California, Santa Barbara, California 93106, United States
- Center for Bioengineering, University of California, Santa Barbara, California 93106, United States
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18
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Chang Z, Liu F, Wang L, Deng M, Zhou C, Sun Q, Chu J. Near-infrared dyes, nanomaterials and proteins. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2019.08.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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19
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Povarova NV, Zaitseva SO, Baleeva NS, Smirnov AY, Myasnyanko IN, Zagudaylova MB, Bozhanova NG, Gorbachev DA, Malyshevskaya KK, Gavrikov AS, Mishin AS, Baranov MS. Red-Shifted Substrates for FAST Fluorogen-Activating Protein Based on the GFP-Like Chromophores. Chemistry 2019; 25:9592-9596. [PMID: 31111975 DOI: 10.1002/chem.201901151] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/14/2019] [Indexed: 11/10/2022]
Abstract
A genetically encoded fluorescent tag for live cell microscopy is presented. This tag is composed of previously published fluorogen-activating protein FAST and a novel fluorogenic derivative of green fluorescent protein (GFP)-like chromophore with red fluorescence. The reversible binding of the novel fluorogen and FAST is accompanied by three orders of magnitude increase in red fluorescence (580-650 nm). The proposed dye instantly stains target cellular proteins fused with FAST, washes out in a minute timescale, and exhibits higher photostability of the fluorescence signal in confocal and widefield microscopy, in contrast with previously published fluorogen:FAST complexes.
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Affiliation(s)
- Natalia V Povarova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Snizhana O Zaitseva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Alexander Yu Smirnov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Marina B Zagudaylova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Nina G Bozhanova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Dmitriy A Gorbachev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Blvd 30, Moscow, 121205, Russia
| | - Kseniya K Malyshevskaya
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Blvd 30, Moscow, 121205, Russia
| | - Alexey S Gavrikov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Alexander S Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia.,Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow, 117997, Russia
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20
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Santra K, Geraskin I, Nilsen-Hamilton M, Kraus GA, Petrich JW. Characterization of the Photophysical Behavior of DFHBI Derivatives: Fluorogenic Molecules that Illuminate the Spinach RNA Aptamer. J Phys Chem B 2019; 123:2536-2545. [PMID: 30807171 DOI: 10.1021/acs.jpcb.8b11166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
( Z)-5-(3,5-Difluoro-4-hydroxybenzylidene)-2,3-dimethyl-3,5-dihydro-4 H-imidazol-4-one (DFHBI) and its analogues are fluorogenic molecules that bind the Spinach aptamer (a small RNA molecule), which was selected for imaging RNA. They are extremely weakly fluorescent in liquid solvents. It had been hypothesized that photoisomerization is a very efficient nonradiative process of deactivation. We show, consistent with the results of other studies, that if the isomerization is impeded, the fluorescence signal is enhanced significantly. In addition, we provide a thorough characterization of the photophysical behavior of DFHBI and its derivatives, notably that of ( Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2-methyl-3-((perfluorophenyl)methyl)-3,5-dihydro-4 H-imidazol-4-one (PFP-DFHBI) in various solvent environments. Solvent-dependent studies were performed with various mixtures of solvents. The results suggest that hydrogen bonding or strong interactions of the solvents with the phenolic-OH group change the absorption band near 420-460 nm and the nature of emission near 430 and 500 nm through various degrees of stabilization and the transformation between the neutral and the anionic species at both ground and excited states. These observations are confirmed by using a methoxy-substituted molecule (( Z)-5-(4-methoxybenzylidene)-2,3-dimethyl-3,5-dihydro-4 H-imidazol-4-one), where the 420-460 nm band is absent in the presence of methanol and the spectra are similar to those of PFP-DFHBI in noninteracting solvents, such as acetonitrile and dichloromethane. Thus, in addition to the major role of photoisomerization as a nonradiative process of deactivation of the excited state, the fluorescence of DFHBI-type molecules is very sensitively dependent upon the pH of the medium as well as upon solvent-specific interactions, such as hydrogen-bonding ability and polarity.
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21
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Abstract
Fluorogenic probes efficiently reduce non-specific background signals, which often results in highly improved signal-to-noise ratios.
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Affiliation(s)
- Eszter Kozma
- Chemical Biology Research Group
- Institute of Organic Chemistry
- Research Centre for Natural Sciences
- Hungarian Academy of Sciences
- 1117 Budapest
| | - Péter Kele
- Chemical Biology Research Group
- Institute of Organic Chemistry
- Research Centre for Natural Sciences
- Hungarian Academy of Sciences
- 1117 Budapest
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22
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Tebo AG, Pimenta FM, Zoumpoulaki M, Kikuti C, Sirkia H, Plamont MA, Houdusse A, Gautier A. Circularly Permuted Fluorogenic Proteins for the Design of Modular Biosensors. ACS Chem Biol 2018; 13:2392-2397. [PMID: 30088915 DOI: 10.1021/acschembio.8b00417] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescent reporters are essential components for the design of optical biosensors that are able to image intracellular analytes in living cells. Herein, we describe the development of circularly permuted variants of Fluorescence-Activating and absorption-Shifting Tag (FAST) and demonstrate their potential as reporting module in biosensors. Circularly permutated FAST (cpFAST) variants allow one to condition the binding and activation of a fluorogenic ligand (and thus fluorescence) to analyte recognition by coupling them with analyte-binding domains. We demonstrated their use for biosensor design by generating multicolor plug-and-play fluorogenic biosensors for imaging the intracellular levels of Ca2+ in living mammalian cells in real time.
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Affiliation(s)
- Alison G. Tebo
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Frederico M. Pimenta
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Martha Zoumpoulaki
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Carlos Kikuti
- Structural Motility, Institut Curie, PSL Research University, CNRS, UMR 144, F-75005 Paris, France
| | - Helena Sirkia
- Structural Motility, Institut Curie, PSL Research University, CNRS, UMR 144, F-75005 Paris, France
| | - Marie-Aude Plamont
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Anne Houdusse
- Structural Motility, Institut Curie, PSL Research University, CNRS, UMR 144, F-75005 Paris, France
| | - Arnaud Gautier
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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23
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Tebo AG, Pimenta FM, Zhang Y, Gautier A. Improved Chemical-Genetic Fluorescent Markers for Live Cell Microscopy. Biochemistry 2018; 57:5648-5653. [PMID: 30204425 DOI: 10.1021/acs.biochem.8b00649] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Inducible chemical-genetic fluorescent markers are promising tools for live cell imaging requiring high spatiotemporal resolution and low background fluorescence. The fluorescence-activating and absorption shifting tag (FAST) was recently developed to form fluorescent molecular complexes with a family of small, synthetic fluorogenic chromophores (so-called fluorogens). Here, we use rational design to modify the binding pocket of the protein and screen for improved fluorescence performances with four different fluorogens. The introduction of a single mutation results in improvements in both quantum yield and dissociation constant with nearly all fluorogens tested. Our improved FAST (iFAST) allowed the generation of a tandem iFAST (td-iFAST) that forms green and red fluorescent reporters 1.6-fold and 2-fold brighter than EGFP and mCherry, respectively, while having a comparable size.
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Affiliation(s)
- Alison G Tebo
- PASTEUR, Département de Chimie , École Normale Supérieure, PSL University, Sorbonne Université, CNRS , Paris 75005 , France
| | - Frederico M Pimenta
- PASTEUR, Département de Chimie , École Normale Supérieure, PSL University, Sorbonne Université, CNRS , Paris 75005 , France
| | - Yu Zhang
- PASTEUR, Département de Chimie , École Normale Supérieure, PSL University, Sorbonne Université, CNRS , Paris 75005 , France
| | - Arnaud Gautier
- PASTEUR, Département de Chimie , École Normale Supérieure, PSL University, Sorbonne Université, CNRS , Paris 75005 , France
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24
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Gautier A, Tebo AG. Fluorogenic Protein‐Based Strategies for Detection, Actuation, and Sensing. Bioessays 2018; 40:e1800118. [DOI: 10.1002/bies.201800118] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/01/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Arnaud Gautier
- PASTEUR, Département de Chimie, École Normale SupérieurePSL University, Sorbonne Université, CNRS75005 ParisFrance
| | - Alison G. Tebo
- PASTEUR, Département de Chimie, École Normale SupérieurePSL University, Sorbonne Université, CNRS75005 ParisFrance
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25
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Reiffers A, Torres Ziegenbein C, Engelhardt A, Kühnemuth R, Gilch P, Czekelius C. Impact of Mono-Fluorination on the Photophysics of the Flavin Chromophore. Photochem Photobiol 2018; 94:667-676. [DOI: 10.1111/php.12921] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 03/25/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Anna Reiffers
- Institut für Physikalische Chemie; Heinrich-Heine-Universität Düsseldorf; Düsseldorf Germany
| | | | - Alyn Engelhardt
- Institut für Physikalische Chemie; Heinrich-Heine-Universität Düsseldorf; Düsseldorf Germany
| | - Ralf Kühnemuth
- Institut für Physikalische Chemie; Heinrich-Heine-Universität Düsseldorf; Düsseldorf Germany
| | - Peter Gilch
- Institut für Physikalische Chemie; Heinrich-Heine-Universität Düsseldorf; Düsseldorf Germany
| | - Constantin Czekelius
- Institut für Organische Chemie und Makromolekulare Chemie; Heinrich-Heine-Universität Düsseldorf; Düsseldorf Germany
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26
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Xu S, Hu HY. Fluorogen-activating proteins: beyond classical fluorescent proteins. Acta Pharm Sin B 2018; 8:339-348. [PMID: 29881673 PMCID: PMC5989828 DOI: 10.1016/j.apsb.2018.02.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 02/11/2018] [Accepted: 02/18/2018] [Indexed: 01/09/2023] Open
Abstract
Fluorescence imaging is a powerful technique for the real-time noninvasive monitoring of protein dynamics. Recently, fluorogen activating proteins (FAPs)/fluorogen probes for protein imaging were developed. Unlike the traditional fluorescent proteins (FPs), FAPs do not fluoresce unless bound to their specific small-molecule fluorogens. When using FAPs/fluorogen probes, a washing step is not required for the removal of free probes from the cells, thus allowing rapid and specific detection of proteins in living cells with high signal-to-noise ratio. Furthermore, with different fluorogens, living cell multi-color proteins labeling system was developed. In this review, we describe about the discovery of FAPs, the design strategy of FAP fluorogens, the application of the FAP technology and the advances of FAP technology in protein labeling systems.
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Affiliation(s)
- Shengnan Xu
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Hai-Yu Hu
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
- Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
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27
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Li C, Plamont MA, Aujard I, Le Saux T, Jullien L, Gautier A. Design and characterization of red fluorogenic push-pull chromophores holding great potential for bioimaging and biosensing. Org Biomol Chem 2018; 14:9253-9261. [PMID: 27714200 DOI: 10.1039/c6ob01612j] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluorogenic chromophores have been used recently for fluorescence reporting and biosensing. Their ability to turn on upon specific interaction with a given target has been exploited in particular for the design of fluorogen-based reporters enabling biomolecule labeling and imaging. In this paper, we report the development and exhaustive characterization of a new family of red fluorogenic push-pull chromophores, holding great potential for the development of fluorogen-based reporters or intracellular fluorogenic markers. The proposed methodology is generic and should find general applicability in the discovery of new fluorogenic dyes suitable for the design of fluorogen-based reporters and biosensors.
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Affiliation(s)
- Chenge Li
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France. and Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Marie-Aude Plamont
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France. and Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Isabelle Aujard
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France. and Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Thomas Le Saux
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France. and Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Ludovic Jullien
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France. and Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Arnaud Gautier
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France. and Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
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28
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Zhang R, Chouket R, Plamont MA, Kelemen Z, Espagne A, Tebo AG, Gautier A, Gissot L, Faure JD, Jullien L, Croquette V, Le Saux T. Macroscale fluorescence imaging against autofluorescence under ambient light. LIGHT, SCIENCE & APPLICATIONS 2018; 7:97. [PMID: 30510693 PMCID: PMC6261969 DOI: 10.1038/s41377-018-0098-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 10/27/2018] [Accepted: 10/27/2018] [Indexed: 05/07/2023]
Abstract
Macroscale fluorescence imaging is increasingly used to observe biological samples. However, it may suffer from spectral interferences that originate from ambient light or autofluorescence of the sample or its support. In this manuscript, we built a simple and inexpensive fluorescence macroscope, which has been used to evaluate the performance of Speed OPIOM (Out of Phase Imaging after Optical Modulation), which is a reference-free dynamic contrast protocol, to selectively image reversibly photoswitchable fluorophores as labels against detrimental autofluorescence and ambient light. By tuning the intensity and radial frequency of the modulated illumination to the Speed OPIOM resonance and adopting a phase-sensitive detection scheme that ensures noise rejection, we enhanced the sensitivity and the signal-to-noise ratio for fluorescence detection in blot assays by factors of 50 and 10, respectively, over direct fluorescence observation under constant illumination. Then, we overcame the strong autofluorescence of growth media that are currently used in microbiology and realized multiplexed fluorescence observation of colonies of spectrally similar fluorescent bacteria with a unique configuration of excitation and emission wavelengths. Finally, we easily discriminated fluorescent labels from the autofluorescent and reflective background in labeled leaves, even under the interference of incident light at intensities that are comparable to sunlight. The proposed approach is expected to find multiple applications, from biological assays to outdoor observations, in fluorescence macroimaging.
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Affiliation(s)
- Ruikang Zhang
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Raja Chouket
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Marie-Aude Plamont
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Zsolt Kelemen
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Saclay Plant Science (SPS), Université Paris-Saclay, Versailles, France
| | - Agathe Espagne
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Alison G. Tebo
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Arnaud Gautier
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Lionel Gissot
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Saclay Plant Science (SPS), Université Paris-Saclay, Versailles, France
| | - Jean-Denis Faure
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Saclay Plant Science (SPS), Université Paris-Saclay, Versailles, France
| | - Ludovic Jullien
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Vincent Croquette
- Laboratoire de Physique Statistique, École Normale Supérieure, PSL Research University, Université Paris Diderot Sorbonne Paris-Cité, Sorbonne Université, CNRS, 75005 Paris, France
- Institut de biologie de l’École normale supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - Thomas Le Saux
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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29
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Jullien L, Gautier A. [Hybrid fluorescent probes for imaging cellular proteins on demand]. Med Sci (Paris) 2017; 33:576-578. [PMID: 28990551 DOI: 10.1051/medsci/20173306006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ludovic Jullien
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24, rue Lhomond, 75005 Paris, France - Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Arnaud Gautier
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24, rue Lhomond, 75005 Paris, France - Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
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Pimenta FM, Chiappetta G, Le Saux T, Vinh J, Jullien L, Gautier A. Chromophore Renewal and Fluorogen-Binding Tags: A Match Made to Last. Sci Rep 2017; 7:12316. [PMID: 28951577 PMCID: PMC5615068 DOI: 10.1038/s41598-017-12400-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 09/08/2017] [Indexed: 01/20/2023] Open
Abstract
Fluorogen-binding tags, which activate the fluorescence of a specific chromophore (so-called fluorogen) upon reversible binding, have recently been proposed as a way of reducing photobleaching via fluorogen renewal. However, no generic methodology has been proposed to systematically analyze the photodamage of the fluorogen and the protein tag. Using Y-FAST (Yellow Fluorescence-activating and Absorption-Shifting Tag) as a case study we propose here a generic experimental and theoretical approach to assess how fluorogen renewal reduces the apparent photobleaching rate of a fluorogen-binding tag. Y-FAST has its apparent photobleaching rate greatly reduced by fluorogen renewal and its photostability is mainly limited by oxidation of specific residues in the protein scaffold by reactive oxygen species generated by the bound fluorogen. This study sets the groundwork for the optimization of fluorogenic systems, helping guide rational improvements to their photostability.
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Affiliation(s)
- Frederico M Pimenta
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005, Paris, France
| | - Giovanni Chiappetta
- ESPCI Biological Mass Spectrometry and Proteomics USR 3149 CNRS/ESPCI-PSL, Paris, France
| | - Thomas Le Saux
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005, Paris, France
| | - Joëlle Vinh
- ESPCI Biological Mass Spectrometry and Proteomics USR 3149 CNRS/ESPCI-PSL, Paris, France
| | - Ludovic Jullien
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005, Paris, France. .,Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005, Paris, France.
| | - Arnaud Gautier
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005, Paris, France. .,Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005, Paris, France.
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31
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Li C, Tebo AG, Gautier A. Fluorogenic Labeling Strategies for Biological Imaging. Int J Mol Sci 2017; 18:ijms18071473. [PMID: 28698494 PMCID: PMC5535964 DOI: 10.3390/ijms18071473] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 07/03/2017] [Accepted: 07/06/2017] [Indexed: 12/27/2022] Open
Abstract
The spatiotemporal fluorescence imaging of biological processes requires effective tools to label intracellular biomolecules in living systems. This review presents a brief overview of recent labeling strategies that permits one to make protein and RNA strongly fluorescent using synthetic fluorogenic probes. Genetically encoded tags selectively binding the exogenously applied molecules ensure high labeling selectivity, while high imaging contrast is achieved using fluorogenic chromophores that are fluorescent only when bound to their cognate tag, and are otherwise dark. Beyond avoiding the need for removal of unbound synthetic dyes, these approaches allow the development of sophisticated imaging assays, and open exciting prospects for advanced imaging, particularly for multiplexed imaging and super-resolution microscopy.
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Affiliation(s)
- Chenge Li
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France.
- Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France.
| | - Alison G Tebo
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France.
- Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France.
| | - Arnaud Gautier
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France.
- Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France.
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32
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Li C, Plamont MA, Sladitschek HL, Rodrigues V, Aujard I, Neveu P, Le Saux T, Jullien L, Gautier A. Dynamic multicolor protein labeling in living cells. Chem Sci 2017; 8:5598-5605. [PMID: 28970939 PMCID: PMC5618792 DOI: 10.1039/c7sc01364g] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/20/2017] [Indexed: 12/13/2022] Open
Abstract
Yellow Fluorescence-Activating and absorption-Shifting Tag (Y-FAST, hereafter called FAST) is a 14 kDa protein tag giving a bright green-yellow fluorescent complex upon interaction with the fluorogenic dye 4-hydroxy-3-methylbenzylidene rhodanine (HMBR). Here, we report a collection of fluorogens enabling tuning of the fluorescence color of FAST from green-yellow to orange and red. Beyond allowing the multicolor imaging of FAST-tagged proteins in live cells, these fluorogens enable dynamic color switching because of FAST's reversible labeling. This unprecedented behavior allows for selective detection of FAST-tagged proteins in cells expressing both green and red fluorescent species through two-color cross-correlation, opening up exciting prospects to overcome spectral crowding and push the frontiers of multiplexed imaging.
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Affiliation(s)
- Chenge Li
- École Normale Supérieure , PSL Research University , UPMC Univ Paris 06 , CNRS , Département de Chimie , PASTEUR , 24 rue Lhomond , 75005 Paris , France.,Sorbonne Universités , UPMC Univ Paris 06 , ENS , CNRS , PASTEUR , 75005 Paris , France . ;
| | - Marie-Aude Plamont
- École Normale Supérieure , PSL Research University , UPMC Univ Paris 06 , CNRS , Département de Chimie , PASTEUR , 24 rue Lhomond , 75005 Paris , France.,Sorbonne Universités , UPMC Univ Paris 06 , ENS , CNRS , PASTEUR , 75005 Paris , France . ;
| | - Hanna L Sladitschek
- Cell Biology and Biophysics Unit , European Molecular Biology Laboratory , Meyerhofstr. 1 , D-69117 Heidelberg , Germany
| | - Vanessa Rodrigues
- École Normale Supérieure , PSL Research University , UPMC Univ Paris 06 , CNRS , Département de Chimie , PASTEUR , 24 rue Lhomond , 75005 Paris , France.,Sorbonne Universités , UPMC Univ Paris 06 , ENS , CNRS , PASTEUR , 75005 Paris , France . ;
| | - Isabelle Aujard
- École Normale Supérieure , PSL Research University , UPMC Univ Paris 06 , CNRS , Département de Chimie , PASTEUR , 24 rue Lhomond , 75005 Paris , France.,Sorbonne Universités , UPMC Univ Paris 06 , ENS , CNRS , PASTEUR , 75005 Paris , France . ;
| | - Pierre Neveu
- Cell Biology and Biophysics Unit , European Molecular Biology Laboratory , Meyerhofstr. 1 , D-69117 Heidelberg , Germany
| | - Thomas Le Saux
- École Normale Supérieure , PSL Research University , UPMC Univ Paris 06 , CNRS , Département de Chimie , PASTEUR , 24 rue Lhomond , 75005 Paris , France.,Sorbonne Universités , UPMC Univ Paris 06 , ENS , CNRS , PASTEUR , 75005 Paris , France . ;
| | - Ludovic Jullien
- École Normale Supérieure , PSL Research University , UPMC Univ Paris 06 , CNRS , Département de Chimie , PASTEUR , 24 rue Lhomond , 75005 Paris , France.,Sorbonne Universités , UPMC Univ Paris 06 , ENS , CNRS , PASTEUR , 75005 Paris , France . ;
| | - Arnaud Gautier
- École Normale Supérieure , PSL Research University , UPMC Univ Paris 06 , CNRS , Département de Chimie , PASTEUR , 24 rue Lhomond , 75005 Paris , France.,Sorbonne Universités , UPMC Univ Paris 06 , ENS , CNRS , PASTEUR , 75005 Paris , France . ;
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Chung PH, Tregidgo C, Suhling K. Determining a fluorophore’s transition dipole moment from fluorescence lifetime measurements in solvents of varying refractive index. Methods Appl Fluoresc 2016; 4:045001. [DOI: 10.1088/2050-6120/4/4/045001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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34
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Sakin V, Paci G, Lemke EA, Müller B. Labeling of virus components for advanced, quantitative imaging analyses. FEBS Lett 2016; 590:1896-914. [PMID: 26987299 DOI: 10.1002/1873-3468.12131] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/08/2016] [Accepted: 03/09/2016] [Indexed: 12/31/2022]
Abstract
In recent years, investigation of virus-cell interactions has moved from ensemble measurements to imaging analyses at the single-particle level. Advanced fluorescence microscopy techniques provide single-molecule sensitivity and subdiffraction spatial resolution, allowing observation of subviral details and individual replication events to obtain detailed quantitative information. To exploit the full potential of these techniques, virologists need to employ novel labeling strategies, taking into account specific constraints imposed by viruses, as well as unique requirements of microscopic methods. Here, we compare strengths and limitations of various labeling methods, exemplify virological questions that were successfully addressed, and discuss challenges and future potential of novel approaches in virus imaging.
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Affiliation(s)
- Volkan Sakin
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Germany
| | - Giulia Paci
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Edward A Lemke
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Barbara Müller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Germany
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35
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Small fluorescence-activating and absorption-shifting tag for tunable protein imaging in vivo. Proc Natl Acad Sci U S A 2015; 113:497-502. [PMID: 26711992 DOI: 10.1073/pnas.1513094113] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
This paper presents Yellow Fluorescence-Activating and absorption-Shifting Tag (Y-FAST), a small monomeric protein tag, half as large as the green fluorescent protein, enabling fluorescent labeling of proteins in a reversible and specific manner through the reversible binding and activation of a cell-permeant and nontoxic fluorogenic ligand (a so-called fluorogen). A unique fluorogen activation mechanism based on two spectroscopic changes, increase of fluorescence quantum yield and absorption red shift, provides high labeling selectivity. Y-FAST was engineered from the 14-kDa photoactive yellow protein by directed evolution using yeast display and fluorescence-activated cell sorting. Y-FAST is as bright as common fluorescent proteins, exhibits good photostability, and allows the efficient labeling of proteins in various organelles and hosts. Upon fluorogen binding, fluorescence appears instantaneously, allowing monitoring of rapid processes in near real time. Y-FAST distinguishes itself from other tagging systems because the fluorogen binding is highly dynamic and fully reversible, which enables rapid labeling and unlabeling of proteins by addition and withdrawal of the fluorogen, opening new exciting prospects for the development of multiplexing imaging protocols based on sequential labeling.
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36
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Kele P. Focus on advanced molecular (bio)probes—probes that aregood, better, smarter. Methods Appl Fluoresc 2015. [DOI: 10.1088/2050-6120/4/1/010401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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