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Ceballos-Ávila D, Vázquez-Sandoval I, Ferrusca-Martínez F, Jiménez-Sánchez A. Conceptually innovative fluorophores for functional bioimaging. Biosens Bioelectron 2024; 264:116638. [PMID: 39153261 DOI: 10.1016/j.bios.2024.116638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/30/2024] [Accepted: 08/06/2024] [Indexed: 08/19/2024]
Abstract
Fluorophore chemistry is at the forefront of bioimaging, revolutionizing the visualization of biological processes with unparalleled precision. From the serendipitous discovery of mauveine in 1856 to cutting-edge fluorophore engineering, this field has undergone transformative evolution. Today, the synergy of chemistry, biology, and imaging technologies has produced diverse, specialized fluorophores that enhance brightness, photostability, and targeting capabilities. This review delves into the history and innovation of fluorescent probes, showcasing their pivotal role in advancing our understanding of cellular dynamics and disease mechanisms. We highlight groundbreaking molecules and their applications, envisioning future breakthroughs that promise to redefine biomedical research and diagnostics.
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Affiliation(s)
- Daniela Ceballos-Ávila
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior s/n. Coyoacán, 04510, Ciudad de México, Mexico
| | - Ixsoyen Vázquez-Sandoval
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior s/n. Coyoacán, 04510, Ciudad de México, Mexico
| | - Fernanda Ferrusca-Martínez
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior s/n. Coyoacán, 04510, Ciudad de México, Mexico
| | - Arturo Jiménez-Sánchez
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior s/n. Coyoacán, 04510, Ciudad de México, Mexico.
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2
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Tang Z, Zhou P. Elaborating the Fluorescence Regulation and Quenching Mechanism of Sulfur-for-Oxygen Replacement for Fluorophores. Chemphyschem 2024:e202400503. [PMID: 39080510 DOI: 10.1002/cphc.202400503] [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: 05/01/2024] [Revised: 07/10/2024] [Indexed: 10/01/2024]
Abstract
Thio-caged fluorophores can be effectively desulfurized into their oxygenated derivatives through visible light, thereby restoring the strong emission of fluorophores, and are applied in the field of live cell super-resolution imaging. Herein, we theoretically investigated the reasons for the low fluorescence quantum yields of a series of thio-caged fluorophores and the underlying reasons for the differences in fluorescence quantum yields of their oxygenated derivatives. The calculation results show that the S atom on the thiocarbonyl group is more likely to excite n electrons to form the nπ* state, which reduces the energy of the nπ* state and leads to fluorescence quenching. In contrast, the O atom on the carbonyl group is more likely to excite π electrons to form ππ* state, which is the main reason for restoring the strong emission of fluorophore. Meanwhile, the calculation results show that the difference of fluorescence intensity caused by oxygenated derivatives is determined by the number of the carbonyl group, which affects the vibronic coupling between ππ* and nπ* states and thereby leads to fluorescence quenching. These results can effectively reveal the fluorescence quenching mechanism of thio-caged fluorophores and the luminescence mechanism of their oxygenated derivatives, and provide correct and guiding design strategies for the development of new thio-caged fluorophores.
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Affiliation(s)
- Zhe Tang
- Tianjin Key Laboratory of Life and Health Detection, Life and Health Intelligent Research Institute, Tianjin University of Technology, Tianjin, 300384, P. R. China
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Panwang Zhou
- State Key Laboratory of Catalysis, Dalian National Laboratory for Clean Energy, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Institute of Frontier Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Qingdao, 266237, China
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3
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Zheng Y, Ye Z, Zhang X, Xiao Y. Photo-uncaging Triggers on Self-Blinking to Control Single-Molecule Fluorescence Kinetics for Super-resolution Imaging. ACS NANO 2024; 18:18477-18484. [PMID: 38941491 DOI: 10.1021/acsnano.4c03809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Super-resolution imaging, especially a single-molecule localization approach, has raised a fluorophore engineering revolution chasing sparse single-molecule dark-bright blinking transforms. Yet, it is a challenge to structurally devise fluorophores manipulating the single-molecule blinking kinetics. In this pursuit, we have developed a triggering strategy by innovatively integrating the photoactivatable nitroso-caging strategy into self-blinking sulfonamide to form a nitroso-caged sulfonamide rhodamine (NOSR). Our fluorophore demonstrated controllable self-blinking events upon phototriggered caging unit release. This exceptional blink kinetics improved the super-resolution imaging integrity on microtubules compared to self-blinking analogues. With the aid of paramount single-molecule fluorescence kinetics, we successfully reconstructed the ring structure of nuclear pores and the axial morphology of mitochondrial outer membranes. We foresee that our synthetic approach of photoactivation and self-blinking would facilitate rhodamine devising for super-resolution imaging.
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Affiliation(s)
- Ying Zheng
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Linggong Road 2, Dalian 116024, China
- College of Medical Laboratory, Dalian Medical University, Dalian 116044, China
| | - Zhiwei Ye
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Linggong Road 2, Dalian 116024, China
| | - Xue Zhang
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Linggong Road 2, Dalian 116024, China
| | - Yi Xiao
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Linggong Road 2, Dalian 116024, China
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4
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Remmel M, Matthias J, Lincoln R, Keller-Findeisen J, Butkevich AN, Bossi ML, Hell SW. Photoactivatable Xanthone (PaX) Dyes Enable Quantitative, Dual Color, and Live-Cell MINFLUX Nanoscopy. SMALL METHODS 2024:e2301497. [PMID: 38497095 DOI: 10.1002/smtd.202301497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 02/06/2024] [Indexed: 03/19/2024]
Abstract
The single-molecule localization concept MINFLUX has triggered a reevaluation of the features of fluorophores for attaining nanometer-scale resolution. MINFLUX nanoscopy benefits from temporally controlled fluorescence ("on"/"off") photoswitching. Combined with an irreversible switching behavior, the localization process is expected to turn highly efficient and quantitative data analysis simple. The potential in the recently reported photoactivable xanthone (PaX) dyes is recognized to extend the list of molecular switches used for MINFLUX with 561 nm excitation beyond the fluorescent protein mMaple. The MINFLUX localization success rates of PaX560 , PaX+560, and mMaple are quantitatively compared by analyzing the effective labeling efficiency of endogenously tagged nuclear pore complexes. The PaX dyes prove to be superior to mMaple and on par with the best reversible molecular switches routinely used in single-molecule localization microscopy. Moreover, the rationally designed PaX595 is introduced for complementing PaX560 in dual color 561 nm MINFLUX imaging based on spectral classification and the deterministic, irreversible, and additive-independent nature of PaX photoactivation is showcased in fast live-cell MINFLUX imaging. The PaX dyes meet the demands of MINFLUX for a robust readout of each label position and fill the void of reliable fluorophores dedicated to 561 nm MINFLUX imaging.
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Affiliation(s)
- Michael Remmel
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, 69120, Heidelberg, Germany
| | - Jessica Matthias
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, 69120, Heidelberg, Germany
| | - Richard Lincoln
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, 69120, Heidelberg, Germany
| | - Jan Keller-Findeisen
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Alexey N Butkevich
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, 69120, Heidelberg, Germany
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Mariano L Bossi
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, 69120, Heidelberg, Germany
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Stefan W Hell
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, 69120, Heidelberg, Germany
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
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5
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Samanta S, Lai K, Wu F, Liu Y, Cai S, Yang X, Qu J, Yang Z. Xanthene, cyanine, oxazine and BODIPY: the four pillars of the fluorophore empire for super-resolution bioimaging. Chem Soc Rev 2023; 52:7197-7261. [PMID: 37743716 DOI: 10.1039/d2cs00905f] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
In the realm of biological research, the invention of super-resolution microscopy (SRM) has enabled the visualization of ultrafine sub-cellular structures and their functions in live cells at the nano-scale level, beyond the diffraction limit, which has opened up a new window for advanced biomedical studies to unravel the complex unknown details of physiological disorders at the sub-cellular level with unprecedented resolution and clarity. However, most of the SRM techniques are highly reliant on the personalized special photophysical features of the fluorophores. In recent times, there has been an unprecedented surge in the development of robust new fluorophore systems with personalized features for various super-resolution imaging techniques. To date, xanthene, cyanine, oxazine and BODIPY cores have been authoritatively utilized as the basic fluorophore units in most of the small-molecule-based organic fluorescent probe designing strategies for SRM owing to their excellent photophysical characteristics and easy synthetic acquiescence. Since the future of next-generation SRM studies will be decided by the availability of advanced fluorescent probes and these four fluorescent building blocks will play an important role in progressive new fluorophore design, there is an urgent need to review the recent advancements in designing fluorophores for different SRM methods based on these fluorescent dye cores. This review article not only includes a comprehensive discussion about the recent developments in designing fluorescent probes for various SRM techniques based on these four important fluorophore building blocks with special emphasis on their effective integration into live cell super-resolution bio-imaging applications but also critically evaluates the background of each of the fluorescent dye cores to highlight their merits and demerits towards developing newer fluorescent probes for SRM.
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Affiliation(s)
- Soham Samanta
- Center for Biomedical Optics and Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Kaitao Lai
- Center for Biomedical Optics and Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Feihu Wu
- Center for Biomedical Optics and Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Yingchao Liu
- Center for Biomedical Optics and Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Songtao Cai
- Center for Biomedical Optics and Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Xusan Yang
- Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Junle Qu
- Center for Biomedical Optics and Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Zhigang Yang
- Center for Biomedical Optics and Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
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6
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Aktalay A, Khan TA, Bossi ML, Belov VN, Hell SW. Photoactivatable Carbo- and Silicon-Rhodamines and Their Application in MINFLUX Nanoscopy. Angew Chem Int Ed Engl 2023; 62:e202302781. [PMID: 37555720 DOI: 10.1002/anie.202302781] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 08/05/2023] [Accepted: 08/08/2023] [Indexed: 08/10/2023]
Abstract
New photoactivatable fluorescent dyes (rhodamine, carbo- and silicon-rhodamines [SiR]) with emission ranging from green to far red have been prepared, and their photophysical properties studied. The photocleavable 2-nitrobenzyloxycarbonyl unit with an alpha-carboxyl group as a branching point and additional functionality was attached to a polycyclic and lipophilic fluorescent dye. The photoactivatable probes having the HaloTagTM amine (O2) ligand bound with a dye core were obtained and applied for live-cell staining in stable cell lines incorporating Vimentin (VIM) or Nuclear Pore Complex Protein NUP96 fused with the HaloTag. The probes were applied in 2D (VIM, NUP96) and 3D (VIM) MINFLUX nanoscopy, as well as in superresolution fluorescence microscopy with single fluorophore activation (VIM, live-cell labeling). Images of VIM and NUPs labeled with different dyes were acquired and their apparent dimensions and shapes assessed on a lower single-digit nanometer scale. Applicability and performance of the photoactivatable dye derivatives were evaluated in terms of photoactivation rate, labeling and detection efficiency, number of detected photons per molecule and other parameters related to MINFLUX nanoscopy.
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Affiliation(s)
- Ayse Aktalay
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research (MPI-MR), Jahnstraße 29, 69120, Heidelberg, Germany
| | - Taukeer A Khan
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences (MPI-NAT), Am Fassberg 11, 37077, Göttingen, Germany
| | - Mariano L Bossi
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research (MPI-MR), Jahnstraße 29, 69120, Heidelberg, Germany
| | - Vladimir N Belov
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences (MPI-NAT), Am Fassberg 11, 37077, Göttingen, Germany
| | - Stefan W Hell
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research (MPI-MR), Jahnstraße 29, 69120, Heidelberg, Germany
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences (MPI-NAT), Am Fassberg 11, 37077, Göttingen, Germany
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7
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Tsai CY, Chen PH, Chen AL, Wang TSA. Spatiotemporal Investigation of Intercellular Heterogeneity via Multiple Photocaged Probes. Chemistry 2023; 29:e202301067. [PMID: 37382047 DOI: 10.1002/chem.202301067] [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: 04/03/2023] [Revised: 06/14/2023] [Accepted: 06/28/2023] [Indexed: 06/30/2023]
Abstract
Intercellular heterogeneity occurs widely under both normal physiological environments and abnormal disease-causing conditions. Several attempts to couple spatiotemporal information to cell states in a microenvironment were performed to decipher the cause and effect of heterogeneity. Furthermore, spatiotemporal manipulation can be achieved with the use of photocaged/photoactivatable molecules. Here, we provide a platform to spatiotemporally analyze differential protein expression in neighboring cells by multiple photocaged probes coupled with homemade photomasks. We successfully established intercellular heterogeneity (photoactivable ROS trigger) and mapped the targets (directly ROS-affected cells) and bystanders (surrounding cells), which were further characterized by total proteomic and cysteinomic analysis. Different protein profiles were shown between bystanders and target cells in both total proteome and cysteinome. Our strategy should expand the toolkit of spatiotemporal mapping for elucidating intercellular heterogeneity.
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Affiliation(s)
- Chun-Yi Tsai
- Department of Chemistry, National Taiwan University and Center for, Emerging Material and Advanced Devices, National Taiwan University, Taipei, 10617, Taiwan (R.O.C
| | - Po-Hsun Chen
- Department of Chemistry, National Taiwan University and Center for, Emerging Material and Advanced Devices, National Taiwan University, Taipei, 10617, Taiwan (R.O.C
| | - Ai-Lin Chen
- Department of Chemistry, National Taiwan University and Center for, Emerging Material and Advanced Devices, National Taiwan University, Taipei, 10617, Taiwan (R.O.C
| | - Tsung-Shing Andrew Wang
- Department of Chemistry, National Taiwan University and Center for, Emerging Material and Advanced Devices, National Taiwan University, Taipei, 10617, Taiwan (R.O.C
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8
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Schnermann MJ, Lavis LD. Rejuvenating old fluorophores with new chemistry. Curr Opin Chem Biol 2023; 75:102335. [PMID: 37269674 PMCID: PMC10524207 DOI: 10.1016/j.cbpa.2023.102335] [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: 01/31/2023] [Revised: 04/26/2023] [Accepted: 05/02/2023] [Indexed: 06/05/2023]
Abstract
The field of organic chemistry began with 19th century scientists identifying and then expanding upon synthetic dye molecules for textiles. In the 20th century, dye chemistry continued with the aim of developing photographic sensitizers and laser dyes. Now, in the 21st century, the rapid evolution of biological imaging techniques provides a new driving force for dye chemistry. Of the extant collection of synthetic fluorescent dyes for biological imaging, two classes reign supreme: rhodamines and cyanines. Here, we provide an overview of recent examples where modern chemistry is used to build these old-but-venerable classes of optically responsive molecules. These new synthetic methods access new fluorophores, which then enable sophisticated imaging experiments leading to new biological insights.
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Affiliation(s)
- Martin J Schnermann
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Building 376, Frederick, MD 20850, USA.
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA, 20147, USA.
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9
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Rational Design of a Fluorescent Chromophore as a Calcium Receptor via DFT and Multivariate Approaches. Molecules 2022; 27:molecules27196248. [PMID: 36234784 PMCID: PMC9572636 DOI: 10.3390/molecules27196248] [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: 08/30/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/25/2022] Open
Abstract
Computational and experimental approaches were adopted to utilize a chromophore diglycolic functionalized fluorescein derivative as a Ca2+ receptor. Fluorescein diglycolic acid (Fl-DGA, 1) was synthesized and used in multivariate determination of Ca2+ and K+. Full-structure computation shows that the complexes of 1 and Ca2+ have comparable energies regardless of additional interaction with lactone moiety. The initial formation of diglycolic-Ca2+ complex followed by macrocyclization is thermodynamically disfavored. A U-shaped pre-organized 1 allows Ca2+ to interact simultaneously with diglycolic and lactone motifs. Both motifs actively participate in Ca2+ recognition and the eleven methylene units in the undecyl arm provides excellent flexibility for reorganization and optimum interaction. Principal component analysis (PCA) of computational molecular properties reveals a simple method in evaluating motifs for cation recognition. Fragment models support full-structure results that negative charge causes significant structural changes, but do not reproduce the full extent of C-O bond breaking observed in the latter. Experimental optical responses show that 1 is selective towards Ca2+ and discriminates against K+ and Mg2+. PCA of emission intensities affords distinct clusters of 0.01, 0.1 and 1 mM Ca2+ and K+, and suggests applicability of this technique for simultaneous determination of cationic plant macronutrients in precision agriculture and a wide variety of other applications.
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10
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Lincoln R, Bossi ML, Remmel M, D'Este E, Butkevich AN, Hell SW. A general design of caging-group-free photoactivatable fluorophores for live-cell nanoscopy. Nat Chem 2022; 14:1013-1020. [PMID: 35864152 PMCID: PMC9417988 DOI: 10.1038/s41557-022-00995-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 06/09/2022] [Indexed: 11/17/2022]
Abstract
The controlled switching of fluorophores between non-fluorescent and fluorescent states is central to every super-resolution fluorescence microscopy (nanoscopy) technique, and the exploration of radically new switching mechanisms remains critical to boosting the performance of established, as well as emerging super-resolution methods. Photoactivatable dyes offer substantial improvements to many of these techniques, but often rely on photolabile protecting groups that limit their applications. Here we describe a general method to transform 3,6-diaminoxanthones into caging-group-free photoactivatable fluorophores. These photoactivatable xanthones (PaX) assemble rapidly and cleanly into highly fluorescent, photo- and chemically stable pyronine dyes upon irradiation with light. The strategy is extendable to carbon- and silicon-bridged xanthone analogues, yielding a family of photoactivatable labels spanning much of the visible spectrum. Our results demonstrate the versatility and utility of PaX dyes in fixed and live-cell labelling for conventional microscopy, as well as the coordinate-stochastic and deterministic nanoscopies STED, PALM and MINFLUX. ![]()
The design of photoactivatable fluorophores—which are required for some super-resolution fluorescence microscopy methods—usually relies on light-sensitive protecting groups imparting lipophilicity and generating reactive by-products. Now, it has been shown that by exploiting a unique intramolecular photocyclization, bright and highly photostable fluorophores can be rapidly generated in situ from appropriately substituted 1-alkenyl-3,6-diaminoxanthone precursors.
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Affiliation(s)
- Richard Lincoln
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Mariano L Bossi
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Michael Remmel
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Elisa D'Este
- Optical Microscopy Facility, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Alexey N Butkevich
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany.
| | - Stefan W Hell
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany. .,Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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11
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Jemas A, Xie Y, Pigga JE, Caplan JL, am Ende CW, Fox JM. Catalytic Activation of Bioorthogonal Chemistry with Light (CABL) Enables Rapid, Spatiotemporally Controlled Labeling and No-Wash, Subcellular 3D-Patterning in Live Cells Using Long Wavelength Light. J Am Chem Soc 2022; 144:1647-1662. [PMID: 35072462 PMCID: PMC9364228 DOI: 10.1021/jacs.1c10390] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Described is the spatiotemporally controlled labeling and patterning of biomolecules in live cells through the catalytic activation of bioorthogonal chemistry with light, referred to as "CABL". Here, an unreactive dihydrotetrazine (DHTz) is photocatalytically oxidized in the intracellular environment by ambient O2 to produce a tetrazine that immediately reacts with a trans-cyclooctene (TCO) dienophile. 6-(2-Pyridyl)dihydrotetrazine-3-carboxamides were developed as stable, cell permeable DHTz reagents that upon oxidation produce the most reactive tetrazines ever used in live cells with Diels-Alder kinetics exceeding k2 of 106 M-1 s-1. CABL photocatalysts are based on fluorescein or silarhodamine dyes with activation at 470 or 660 nm. Strategies for limiting extracellular production of singlet oxygen are described that increase the cytocompatibility of photocatalysis. The HaloTag self-labeling platform was used to introduce DHTz tags to proteins localized in the nucleus, mitochondria, actin, or cytoplasm, and high-yielding subcellular activation and labeling with a TCO-fluorophore were demonstrated. CABL is light-dose dependent, and two-photon excitation promotes CABL at the suborganelle level to selectively pattern live cells under no-wash conditions. CABL was also applied to spatially resolved live-cell labeling of an endogenous protein target by using TIRF microscopy to selectively activate intracellular monoacylglycerol lipase tagged with DHTz-labeled small molecule covalent inhibitor. Beyond spatiotemporally controlled labeling, CABL also improves the efficiency of "ordinary" tetrazine ligations by rescuing the reactivity of commonly used 3-aryl-6-methyltetrazine reporters that become partially reduced to DHTzs inside cells. The spatiotemporal control and fast rates of photoactivation and labeling of CABL should enable a range of biomolecular labeling applications in living systems.
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Affiliation(s)
- Andrew Jemas
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Yixin Xie
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Jessica E. Pigga
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Jeffrey L. Caplan
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19716, USA
| | - Christopher W. am Ende
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Joseph M. Fox
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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12
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Okada M, Nishimura Y. Electronic state of a fluoranthene–urea compound and the kinetics of its emissive tautomer state in the presence of acetate anions. NEW J CHEM 2022. [DOI: 10.1039/d1nj05270e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The fluorescence spectrum of 3FU–Ac around 600 nm agrees well with that of 3FU–DBU, indicating that the electronic state of tautomer has a proton-abstracted structure.
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Affiliation(s)
- Mahiro Okada
- Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8571, Japan
| | - Yoshinobu Nishimura
- Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8571, Japan
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13
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Heynck L, Matthias J, Bossi ML, Butkevich AN, Hell SW. N-Cyanorhodamines: cell-permeant, photostable and bathochromically shifted analogues of fluoresceins. Chem Sci 2022; 13:8297-8306. [PMID: 35919709 PMCID: PMC9297387 DOI: 10.1039/d2sc02448a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/24/2022] [Indexed: 11/23/2022] Open
Abstract
Fluorescein and its analogues have found only limited use in biological imaging because of the poor photostability and cell membrane impermeability of their O-unprotected forms. Herein, we report rationally designed N-cyanorhodamines as orange- to red-emitting, photostable and cell-permeant fluorescent labels negatively charged at physiological pH values and thus devoid of off-targeting artifacts often observed for cationic fluorophores. In combination with well-established fluorescent labels, self-labelling protein (HaloTag, SNAP-tag) ligands derived from N-cyanorhodamines permit up to four-colour confocal and super-resolution STED imaging in living cells. N-Cyanorhodamines – photostable, cell-permeant analogues of fluoresceins – provide fast labelling kinetics with the HaloTag protein and background-free images in multicolour super-resolution microscopy.![]()
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Affiliation(s)
- Lukas Heynck
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Jessica Matthias
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Mariano L. Bossi
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Alexey N. Butkevich
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Stefan W. Hell
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
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14
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Wang L, Wang S, Tang J, Espinoza VB, Loredo A, Tian Z, Weisman RB, Xiao H. Oxime as a general photocage for the design of visible light photo-activatable fluorophores. Chem Sci 2021; 12:15572-15580. [PMID: 35003586 PMCID: PMC8654061 DOI: 10.1039/d1sc05351e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/21/2021] [Indexed: 12/18/2022] Open
Abstract
Photoactivatable fluorophores have been widely used for tracking molecular and cellular dynamics with subdiffraction resolution. In this work, we have prepared a series of photoactivatable probes using the oxime moiety as a new class of photolabile caging group in which the photoactivation process is mediated by a highly efficient photodeoximation reaction. Incorporation of the oxime caging group into fluorophores results in loss of fluorescence. Upon light irradiation in the presence of air, the oxime-caged fluorophores are oxidized to their carbonyl derivatives, restoring strong fluorophore fluorescence. To demonstrate the utility of these oxime-caged fluorophores, we have created probes that target different organelles for live-cell confocal imaging. We also carried out photoactivated localization microscopy (PALM) imaging under physiological conditions using low-power light activation in the absence of cytotoxic additives. Our studies show that oximes represent a new class of visible-light photocages that can be widely used for cellular imaging, sensing, and photo-controlled molecular release.
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Affiliation(s)
- Lushun Wang
- Department of Chemistry, Rice University 6100 Main Street Houston Texas 77005 USA
| | - Shichao Wang
- Department of Chemistry, Rice University 6100 Main Street Houston Texas 77005 USA
| | - Juan Tang
- Department of Chemistry, Rice University 6100 Main Street Houston Texas 77005 USA
| | - Vanessa B Espinoza
- Department of Chemistry, Rice University 6100 Main Street Houston Texas 77005 USA
| | - Axel Loredo
- Department of Chemistry, Rice University 6100 Main Street Houston Texas 77005 USA
| | - Zeru Tian
- Department of Chemistry, Rice University 6100 Main Street Houston Texas 77005 USA
| | - R Bruce Weisman
- Department of Chemistry, Rice University 6100 Main Street Houston Texas 77005 USA
| | - Han Xiao
- Department of Chemistry, Rice University 6100 Main Street Houston Texas 77005 USA
- Department of Biosciences, Rice University 6100 Main Street Houston Texas 77005 USA
- Department of Bioengineering, Rice University 6100 Main Street Houston Texas 77005 USA
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15
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Darrah K, Wesalo J, Lukasak B, Tsang M, Chen JK, Deiters A. Small Molecule Control of Morpholino Antisense Oligonucleotide Function through Staudinger Reduction. J Am Chem Soc 2021; 143:18665-18671. [PMID: 34705461 DOI: 10.1021/jacs.1c08723] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Conditionally activated, caged morpholino antisense agents (cMOs) are tools that enable the temporal and spatial investigation of gene expression, regulation, and function during embryonic development. Cyclic MOs are conformationally gated oligonucleotide analogs that do not block gene expression until they are linearized through the application of an external trigger, such as light or enzyme activity. Here, we describe the first examples of small molecule-responsive cMOs, which undergo rapid and efficient decaging via a Staudinger reduction. This is enabled by a highly flexible linker design that offers opportunities for the installation of chemically activated, self-immolative motifs. We synthesized cyclic cMOs against two distinct, developmentally relevant genes and demonstrated phosphine-triggered knockdown of gene expression in zebrafish embryos. This represents the first report of a small molecule-triggered antisense agent for gene knockdown, adding another bioorthogonal entry to the growing arsenal of gene knockdown tools.
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Affiliation(s)
- Kristie Darrah
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Joshua Wesalo
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Bradley Lukasak
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Michael Tsang
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - James K Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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16
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17
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Zhang Y, Zheng Y, Meana Y, Raymo FM. BODIPYs with Photoactivatable Fluorescence. Chemistry 2021; 27:11257-11267. [PMID: 34062023 DOI: 10.1002/chem.202101628] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Indexed: 12/11/2022]
Abstract
The borondipyrromethene (BODIPY) chromophore is a versatile platform for the construction of photoresponsive dyes with unique properties. Specifically, its covalent connection to a photocleavable group can be exploited to engineer compounds with photoswitchable fluorescence. The resulting photoactivatable fluorophores can increase their emission intensity or shift their emission wavelengths in response to switching. Such changes permit the spatiotemporal control of fluorescence with optical stimulations and the implementation of imaging strategies that would be impossible to replicate with conventional fluorophores. Indeed, BODIPYs with photoactivatable fluorescence enable the selective highlighting of intracellular targets, the nanoscaled visualization of sub-cellular components, the real-time monitoring of dynamic events and the photochemical writing of optical barcodes.
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Affiliation(s)
- Yang Zhang
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Yeting Zheng
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, USA
| | - Yasniel Meana
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, USA
| | - Françisco M Raymo
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, USA
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18
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Zhu S, Li H, Fu R, Hao W, Wang S, Tu S, Jiang B. Regio‐ and Stereoselective Synthesis of Rotationally Hindered C
12
‐Naphthylated Tribenzo[
a,c,j
]xanthenes through Catalytic Tricyclization of Yne‐Allenones. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202100061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Shan‐Shan Zhu
- School of Chemistry and Material Science Jiangsu Key Laboratory of Green Synthetic Chemistry for Functional Materials Jiangsu Normal University Xuzhou 211116 People's Republic of China
| | - Heng Li
- School of Chemistry and Material Science Jiangsu Key Laboratory of Green Synthetic Chemistry for Functional Materials Jiangsu Normal University Xuzhou 211116 People's Republic of China
| | - Rong Fu
- School of Chemistry and Material Science Jiangsu Key Laboratory of Green Synthetic Chemistry for Functional Materials Jiangsu Normal University Xuzhou 211116 People's Republic of China
| | - Wen‐Juan Hao
- School of Chemistry and Material Science Jiangsu Key Laboratory of Green Synthetic Chemistry for Functional Materials Jiangsu Normal University Xuzhou 211116 People's Republic of China
| | - Shu‐Liang Wang
- School of Chemistry and Material Science Jiangsu Key Laboratory of Green Synthetic Chemistry for Functional Materials Jiangsu Normal University Xuzhou 211116 People's Republic of China
| | - Shu‐Jiang Tu
- School of Chemistry and Material Science Jiangsu Key Laboratory of Green Synthetic Chemistry for Functional Materials Jiangsu Normal University Xuzhou 211116 People's Republic of China
| | - Bo Jiang
- School of Chemistry and Material Science Jiangsu Key Laboratory of Green Synthetic Chemistry for Functional Materials Jiangsu Normal University Xuzhou 211116 People's Republic of China
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19
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Recent Applications of Heteropolyacids and Related Compounds in Heterocycle Synthesis. Contributions between 2010 and 2020. Catalysts 2021. [DOI: 10.3390/catal11020291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Over the past two decades, polyoxometalates (POM) have received considerable attention as solid catalysts, due to their unique physicochemical characteristics, since, first, they have very strong Bronsted acidity, approaching the region of a superacid, and second, they are efficient oxidizers that exhibit rapid redox transformations under fairly mild conditions. Their structural mobility is also highlighted, since they are complex molecules that can be modified by changing their structure or the elements that compose them to model their size, charge density, redox potentials, acidity, and solubility. Finally, they can be used in substoichiometric amounts and reused without an appreciable loss of catalytic activity, all of which postulate them as versatile, economic and ecological catalysts. Therefore, in 2009, we wrote a review article highlighting the great variety of organic reactions, mainly in the area of the synthesis of bioactive heterocycles in which they can be used, and this new review completes that article with the contributions made in the same area for the period 2010 to 2020. The synthesized heterocycles to be covered include pyrimidines, pyridines, pyrroles, indoles, chromenes, xanthenes, pyrans, azlactones, azoles, diazines, azepines, flavones, and formylchromones, among others.
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20
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Budyka MF, Gavrishova TN, Li VM, Dozmorov SA, Kozlovskii VI. Spectral, Luminescent, and Photochemical Properties of 3-Styrybenzo[f]quinolines Substituted in the Styryl Moiety. HIGH ENERGY CHEMISTRY 2021. [DOI: 10.1134/s0018143921010082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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21
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Budyka MF, Gavrishova TN, Li VM, Dozmorov SA. Photoisomerization and Energy Transfer in an Unsymmetrical Biphotochromic Dyad with a Longitudinal Shift of Photochromes—Derivatives of 3-Styrylbenzo[f]quinoline and Oxymethylene Bridging Group. HIGH ENERGY CHEMISTRY 2021. [DOI: 10.1134/s0018143921010094] [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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22
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Weber M, Khan TA, Patalag LJ, Bossi M, Leutenegger M, Belov VN, Hell SW. Photoactivatable Fluorophore for Stimulated Emission Depletion (STED) Microscopy and Bioconjugation Technique for Hydrophobic Labels. Chemistry 2021; 27:451-458. [PMID: 33095954 PMCID: PMC7839434 DOI: 10.1002/chem.202004645] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Indexed: 02/01/2023]
Abstract
The use of photoactivatable dyes in STED microscopy has so far been limited by two-photon activation through the STED beam and by the fact that photoactivatable dyes are poorly solvable in water. Herein, we report ONB-2SiR, a fluorophore that can be both photoactivated in the UV and specifically de-excited by STED at 775 nm. Likewise, we introduce a conjugation and purification protocol to effectively label primary and secondary antibodies with moderately water-soluble dyes. Greatly reducing dye aggregation, our technique provides a defined and tunable degree of labeling, and improves the imaging performance of dye conjugates in general.
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Affiliation(s)
- Michael Weber
- Department of NanoBiophotonicsMax Planck Institute for Biophysical ChemistryAm Faßberg 1137077GöttingenGermany
| | - Taukeer A. Khan
- Department of NanoBiophotonicsMax Planck Institute for Biophysical ChemistryAm Faßberg 1137077GöttingenGermany
| | - Lukas J. Patalag
- Department of NanoBiophotonicsMax Planck Institute for Biophysical ChemistryAm Faßberg 1137077GöttingenGermany
- present address: Stratingh Institute for ChemistryZernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Mariano Bossi
- Department of Optical NanoscopyMax Planck Institute for Medical ResearchJahnstraße 2969120HeidelbergGermany
| | - Marcel Leutenegger
- Department of NanoBiophotonicsMax Planck Institute for Biophysical ChemistryAm Faßberg 1137077GöttingenGermany
| | - Vladimir N. Belov
- Department of NanoBiophotonicsMax Planck Institute for Biophysical ChemistryAm Faßberg 1137077GöttingenGermany
| | - Stefan W. Hell
- Department of NanoBiophotonicsMax Planck Institute for Biophysical ChemistryAm Faßberg 1137077GöttingenGermany
- Department of Optical NanoscopyMax Planck Institute for Medical ResearchJahnstraße 2969120HeidelbergGermany
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23
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24
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Tang W, Gao H, Li J, Wang X, Zhou Z, Gai L, Feng XJ, Tian J, Lu H, Guo Z. A General Strategy for the Construction of NIR-emitting Si-rhodamines and Their Application for Mitochondrial Temperature Visualization. Chem Asian J 2020; 15:2724-2730. [PMID: 32666700 DOI: 10.1002/asia.202000660] [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: 06/04/2020] [Revised: 07/07/2020] [Indexed: 11/07/2022]
Abstract
Si-rhodamine (SiR) is an ideal fluorophore because it possesses bright emission in the NIR region and can be implemented flexibly in living cells. Currently, several promising approaches for synthesizing SiR are being developed. However, challenges remain in the construction of SiR containing functional groups for bioimaging application. Herein, we introduce a general and simple approach by a condensation reaction of diarylsilylether and arylaldehyde in o-dichlorobenzene to synthesize a series of SiRs bearing various functional substituents. These SiRs have moderate to high quantum efficiency, tolerance to photobleaching, and high water solubility as well as NIR emitting, and their NIR fluorescence properties can be controlled through the photoinduced electron transfer (PET) mechanism. Fluorescence OFF-ON switching effect is observed for SiR 9 in the presence of acid, which is rationalized by DFT/TDDFT calculations. Moreover, reversible stimuli response toward temperature is achieved. Since positive charge enables mitochondrial targeting ability and chloromethyl unit can covalently immobilize the dyes onto the mitochondrial via click reaction between the benzyl choride and protein sulfhydryls, SiR 8 is identified as a valuable fluorescent marker to visualize the morphology and monitor the temperature change of mitochondria with high photostability.
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Affiliation(s)
- Weiguo Tang
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education and Key Laboratory of Organosilicon Material of Zhejiang Province, Hangzhou Normal University, No. 2318, Yuhangtang Road, Hangzhou, 311121, P. R. China
| | - Han Gao
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, China Pharmaceutical University, Nanjing, 211198, P. R. China
| | - Jiaxin Li
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education and Key Laboratory of Organosilicon Material of Zhejiang Province, Hangzhou Normal University, No. 2318, Yuhangtang Road, Hangzhou, 311121, P. R. China
| | - Xianhui Wang
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education and Key Laboratory of Organosilicon Material of Zhejiang Province, Hangzhou Normal University, No. 2318, Yuhangtang Road, Hangzhou, 311121, P. R. China
| | - Zhikuan Zhou
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education and Key Laboratory of Organosilicon Material of Zhejiang Province, Hangzhou Normal University, No. 2318, Yuhangtang Road, Hangzhou, 311121, P. R. China
| | - Lizhi Gai
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education and Key Laboratory of Organosilicon Material of Zhejiang Province, Hangzhou Normal University, No. 2318, Yuhangtang Road, Hangzhou, 311121, P. R. China
| | - Xin Jiang Feng
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education and Key Laboratory of Organosilicon Material of Zhejiang Province, Hangzhou Normal University, No. 2318, Yuhangtang Road, Hangzhou, 311121, P. R. China
| | - Jiangwei Tian
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, China Pharmaceutical University, Nanjing, 211198, P. R. China
| | - Hua Lu
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education and Key Laboratory of Organosilicon Material of Zhejiang Province, Hangzhou Normal University, No. 2318, Yuhangtang Road, Hangzhou, 311121, P. R. China
| | - Zijian Guo
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
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25
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A general method to optimize and functionalize red-shifted rhodamine dyes. Nat Methods 2020; 17:815-821. [PMID: 32719532 PMCID: PMC7396317 DOI: 10.1038/s41592-020-0909-6] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 06/22/2020] [Indexed: 12/29/2022]
Abstract
Expanding the palette of fluorescent dyes is vital to push the frontier of biological imaging. Although rhodamine dyes remain the premier type of small-molecule fluorophore due to their bioavailability and brightness, variants excited with far-red or near-infrared light suffer from poor performance due to their propensity to adopt a lipophilic, nonfluorescent form. We report a framework for rationalizing rhodamine behavior in biological environments and a general chemical modification for rhodamines that optimizes long-wavelength variants and enables facile functionalization with different chemical groups.
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26
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Liu Z, Liu J, Wang X, Mi F, Wang D, Wu C. Fluorescent Bioconjugates for Super-Resolution Optical Nanoscopy. Bioconjug Chem 2020; 31:1857-1872. [DOI: 10.1021/acs.bioconjchem.0c00320] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Zhihe Liu
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 510855, China
| | - Jie Liu
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 510855, China
- Department of Biology, Hong Kong Baptist University, Hong Kong 999077, China
| | - Xiaodong Wang
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 510855, China
| | - Feixue Mi
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 510855, China
| | - Dan Wang
- Key Laboratory of Functional Inorganic Material Chemistry, Ministry of Education, School of Chemistry and Materials Science, Heilongjiang University, Harbin 150080, China
| | - Changfeng Wu
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 510855, China
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27
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Zhang Y, Raymo FM. Live-Cell Imaging at the Nanoscale with Bioconjugatable and Photoactivatable Fluorophores. Bioconjug Chem 2020; 31:1052-1062. [PMID: 32150390 DOI: 10.1021/acs.bioconjchem.0c00073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Optical diffraction fundamentally limits the spatial resolution of conventional fluorescence images to length scales that are, at least, 2 orders of magnitude longer than the dimensions of individual molecules. As a result, the development of innovative probes and imaging schemes to overcome diffraction is very much needed to enable the investigation of the fundamental factors regulating cellular functions at the molecular level. In this context, the chemical synthesis of molecular constructs with photoactivatable fluorescence and the ability to label subcellular components of live cells can have transformative implications. Indeed, the fluorescence of the resulting assemblies can be activated with spatiotemporal control, even in the intracellular environment, to permit the sequential localization of individual emissive labels with precision at the nanometer level and the gradual reconstruction of images with subdiffraction resolution. The implementation of these operating principles for subdiffraction imaging, however, is only possible if demanding photochemical and photophysical requirements to enable photoactivation and localization as well as stringent structural requisites to allow the covalent labeling of intracellular targets in live cells are satisfied. Because of these complications, only a few synthetic photoactivatable fluorophores with appropriate performance for live-cell imaging at the nanoscale have been developed so far. Significant synthetic efforts in conjunction with spectroscopic analyses are still very much needed to advance this promising research area further and turn photoactivatable fluorophores into the imaging probes of choice for the investigation of live cells.
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Affiliation(s)
- Yang Zhang
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, Coral Gables, Florida 33146-0431, United States
| | - Françisco M Raymo
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, Coral Gables, Florida 33146-0431, United States
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28
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Frei MS, Hoess P, Lampe M, Nijmeijer B, Kueblbeck M, Ellenberg J, Wadepohl H, Ries J, Pitsch S, Reymond L, Johnsson K. Photoactivation of silicon rhodamines via a light-induced protonation. Nat Commun 2019; 10:4580. [PMID: 31594948 PMCID: PMC6783549 DOI: 10.1038/s41467-019-12480-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 09/13/2019] [Indexed: 12/17/2022] Open
Abstract
Photoactivatable fluorophores are important for single-particle tracking and super-resolution microscopy. Here we present a photoactivatable fluorophore that forms a bright silicon rhodamine derivative through a light-dependent protonation. In contrast to other photoactivatable fluorophores, no caging groups are required, nor are there any undesired side-products released. Using this photoactivatable fluorophore, we create probes for HaloTag and actin for live-cell single-molecule localization microscopy and single-particle tracking experiments. The unusual mechanism of photoactivation and the fluorophore's outstanding spectroscopic properties make it a powerful tool for live-cell super-resolution microscopy.
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Affiliation(s)
- Michelle S Frei
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany
- Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Philipp Hoess
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Marko Lampe
- Advanced Light Microscopy Facility (ALMF), European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Bianca Nijmeijer
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Moritz Kueblbeck
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Hubert Wadepohl
- Anorganisch-Chemisches Institut, University of Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Jonas Ries
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Stefan Pitsch
- Spirochrome AG, Chalberweidstrasse 4, CH-8260, Stein am Rhein, Switzerland
| | - Luc Reymond
- Biomolecular Screening Facility, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
- National Centre of Competence in Research (NCCR) in Chemical Biology, 1015, Lausanne, Switzerland.
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany.
- Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
- National Centre of Competence in Research (NCCR) in Chemical Biology, 1015, Lausanne, Switzerland.
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29
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Kamino S. [Development of External Stimuli-responsive Organic π Molecules and the Creation of Novel Photo-functions]. YAKUGAKU ZASSHI 2019; 139:975-986. [PMID: 31257255 DOI: 10.1248/yakushi.19-00005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have found that the spiro form of aminobenzopyranoxanthene (ABPX) exhibits dual solvatochromic and nanoaggregate fluorescence in organic solvents by spectrophotometric and theoretical analyses. The dual fluorescence properties of ABPX were adjustable in response to water content, and served as a new detection principal for naked-eye visualization (above 0.5 wt%) and quantification (0.010-0.125 wt%) of water in tetrahydrofuran. In investigating the optical properties of a dicationic form of ABPX, ABPX containing linear n-alkyl chains at amino groups were then synthesized. These ABPX exhibited fluorescence emission in the far-red and NIR wavelength regions, and we noted an increased fluorescence quantum efficiency with increasing n-alkyl chain length. To further improve the fluorescence quantum yields, we have designed and synthesized ABPX with different nitrogen-containing fused rings. It was kinetically demonstrated that the structurally rigid conjugation of the xanthene moiety is an effective molecular design for the drastic enhancement of fluorescence emission efficiency.
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Affiliation(s)
- Shinichiro Kamino
- Fine Organic Synthesis Laboratory, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University.,Next-Generation Imaging Team, RIKEN Center for Biosystems Dynamics Research
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30
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Jradi FM, Lavis LD. Chemistry of Photosensitive Fluorophores for Single-Molecule Localization Microscopy. ACS Chem Biol 2019; 14:1077-1090. [PMID: 30997987 DOI: 10.1021/acschembio.9b00197] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Development of single-molecule localization microscopy (SMLM) has sparked a revolution in biological imaging, allowing "super-resolution" fluorescence microscopy below the diffraction limit of light. The past decade has seen an explosion in not only optical hardware for SMLM but also the development or repurposing of fluorescent proteins and small-molecule fluorescent probes for this technique. In this review, written by chemists for chemists, we detail the history of single-molecule localization microscopy and collate the collection of probes with demonstrated utility in SMLM. We hope it will serve as a primer for probe choice in localization microscopy as well as an inspiration for the development of new fluorophores that enable imaging of biological samples with exquisite detail.
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Affiliation(s)
- Fadi M. Jradi
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Luke D. Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
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31
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Wang L, Du W, Hu Z, Uvdal K, Li L, Huang W. Hybrid Rhodamine Fluorophores in the Visible/NIR Region for Biological Imaging. Angew Chem Int Ed Engl 2019; 58:14026-14043. [DOI: 10.1002/anie.201901061] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Liulin Wang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM) Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM) Nanjing Tech University Nanjing 211816 P. R. China
| | - Wei Du
- Shaanxi Institute of Flexible Electronics (SIFE) Northwestern Polytechnical University Xi'an 710072 P. R. China
| | - Zhangjun Hu
- Department of Physics, Chemistry and Biology Linköping University Linköping 58183 Sweden
| | - Kajsa Uvdal
- Department of Physics, Chemistry and Biology Linköping University Linköping 58183 Sweden
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM) Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM) Nanjing Tech University Nanjing 211816 P. R. China
| | - Wei Huang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM) Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM) Nanjing Tech University Nanjing 211816 P. R. China
- Shaanxi Institute of Flexible Electronics (SIFE) Northwestern Polytechnical University Xi'an 710072 P. R. China
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32
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Wang L, Du W, Hu Z, Uvdal K, Li L, Huang W. Hybrid Rhodamine Fluorophores in the Visible/NIR Region for Biological Imaging. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901061] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Liulin Wang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM) Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM) Nanjing Tech University Nanjing 211816 P. R. China
| | - Wei Du
- Shaanxi Institute of Flexible Electronics (SIFE) Northwestern Polytechnical University Xi'an 710072 P. R. China
| | - Zhangjun Hu
- Department of Physics, Chemistry and Biology Linköping University Linköping 58183 Sweden
| | - Kajsa Uvdal
- Department of Physics, Chemistry and Biology Linköping University Linköping 58183 Sweden
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM) Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM) Nanjing Tech University Nanjing 211816 P. R. China
| | - Wei Huang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM) Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM) Nanjing Tech University Nanjing 211816 P. R. China
- Shaanxi Institute of Flexible Electronics (SIFE) Northwestern Polytechnical University Xi'an 710072 P. R. China
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33
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Yang Y, Jiang N, Lai YT, Chang YY, Yang X, Sun H, Li H. Green Fluorescent Probe for Imaging His 6-Tagged Proteins Inside Living Cells. ACS Sens 2019; 4:1190-1196. [PMID: 31012309 DOI: 10.1021/acssensors.8b01128] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Small molecule-based fluorescent probes offer great opportunities for specifically tracking proteins in living systems with minimal perturbation on the protein function and localization. Herein, we report a small green fluorescent probe (Ni2+- NTA-AF) consisting of a Ni2+-NTA moiety, a fluorescein, and an arylazide group, that binds specifically to His6-tagged proteins with fluorescence enhancement in vitro upon photoactivation of the arylazide group. Importantly, the probe can cross the cell membranes and stoichiometrically label His6-tagged proteins rapidly (∼15 min) in living prokaryotic and eukaryotic cells exemplified by a DNA repair protein Xeroderma pigmentosum group A (XPA). Using the probe, we successfully visualized Sirtuin 5, which is localized to the mitochondria. This probe exhibits high quantum yields and improved solubility, offering a new opportunity for imaging intracellular His6-tagged proteins inside living cells with better contrast.
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Affiliation(s)
- Ya Yang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Nan Jiang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yau-Tsz Lai
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yuen-Yan Chang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xinming Yang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Hongzhe Sun
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Hongyan Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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34
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Samanta S, Gong W, Li W, Sharma A, Shim I, Zhang W, Das P, Pan W, Liu L, Yang Z, Qu J, Kim JS. Organic fluorescent probes for stochastic optical reconstruction microscopy (STORM): Recent highlights and future possibilities. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2018.08.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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35
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Paredes J, Miguel D, Resa S, Gonzalez-Garcia M, Diaz-Torres Y, Cuerva J, Crovetto L. Design, synthesis and photophysical studies of improved xanthene dye to detect acetate. J Photochem Photobiol A Chem 2019. [DOI: 10.1016/j.jphotochem.2018.11.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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36
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Wang L, Frei MS, Salim A, Johnsson K. Small-Molecule Fluorescent Probes for Live-Cell Super-Resolution Microscopy. J Am Chem Soc 2019; 141:2770-2781. [PMID: 30550714 DOI: 10.1021/jacs.8b11134] [Citation(s) in RCA: 295] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Super-resolution fluorescence microscopy is a powerful tool to visualize biomolecules and cellular structures at the nanometer scale. Employing these techniques in living cells has opened up the possibility to study dynamic processes with unprecedented spatial and temporal resolution. Different physical approaches to super-resolution microscopy have been introduced over the last years. A bottleneck to apply these approaches for live-cell imaging has become the availability of appropriate fluorescent probes that can be specifically attached to biomolecules. In this Perspective, we discuss the role of small-molecule fluorescent probes for live-cell super-resolution microscopy and the challenges that need to be overcome for their generation. Recent trends in the development of labeling strategies are reviewed together with the required chemical and spectroscopic properties of the probes. Finally, selected examples of the use of small-molecule fluorescent probes in live-cell super-resolution microscopy are given.
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Affiliation(s)
- Lu Wang
- Department of Chemical Biology , Max Planck Institute for Medical Research , Jahnstrasse 29 , 69120 Heidelberg , Germany
| | - Michelle S Frei
- Department of Chemical Biology , Max Planck Institute for Medical Research , Jahnstrasse 29 , 69120 Heidelberg , Germany.,Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Aleksandar Salim
- Department of Chemical Biology , Max Planck Institute for Medical Research , Jahnstrasse 29 , 69120 Heidelberg , Germany.,Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Kai Johnsson
- Department of Chemical Biology , Max Planck Institute for Medical Research , Jahnstrasse 29 , 69120 Heidelberg , Germany.,Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
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37
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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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38
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Gruber TD, Krishnamurthy C, Grimm JB, Tadross MR, Wysocki LM, Gartner ZJ, Lavis LD. Cell-Specific Chemical Delivery Using a Selective Nitroreductase-Nitroaryl Pair. ACS Chem Biol 2018; 13:2888-2896. [PMID: 30111097 DOI: 10.1021/acschembio.8b00524] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The utility of small molecules to probe or perturb biological systems is limited by the lack of cell-specificity. "Masking" the activity of small molecules using a general chemical modification and "unmasking" it only within target cells overcomes this limitation. To this end, we have developed a selective enzyme-substrate pair consisting of engineered variants of E. coli nitroreductase (NTR) and a 2-nitro- N-methylimidazolyl (NM) masking group. To discover and optimize this NTR-NM system, we synthesized a series of fluorogenic substrates containing different nitroaromatic masking groups, confirmed their stability in cells, and identified the best substrate for NTR. We then engineered the enzyme for improved activity in mammalian cells, ultimately yielding an enzyme variant (enhanced NTR, or eNTR) that possesses up to 100-fold increased activity over wild-type NTR. These improved NTR enzymes combined with the optimal NM masking group enable rapid, selective unmasking of dyes, indicators, and drugs to genetically defined populations of cells.
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Affiliation(s)
- Todd D Gruber
- Janelia Research Campus , Howard Hughes Medical Institute , Ashburn , Virginia 20147 , United States
| | - Chithra Krishnamurthy
- Janelia Research Campus , Howard Hughes Medical Institute , Ashburn , Virginia 20147 , United States
- Department of Pharmaceutical Chemistry , University of California , San Francisco , California 94158 , United States
| | - Jonathan B Grimm
- Janelia Research Campus , Howard Hughes Medical Institute , Ashburn , Virginia 20147 , United States
| | - Michael R Tadross
- Janelia Research Campus , Howard Hughes Medical Institute , Ashburn , Virginia 20147 , United States
| | - Laura M Wysocki
- Janelia Research Campus , Howard Hughes Medical Institute , Ashburn , Virginia 20147 , United States
| | - Zev J Gartner
- Department of Pharmaceutical Chemistry , University of California , San Francisco , California 94158 , United States
| | - Luke D Lavis
- Janelia Research Campus , Howard Hughes Medical Institute , Ashburn , Virginia 20147 , United States
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39
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Abstract
The past decade has witnessed an explosion in the use of super-resolution fluorescence microscopy methods in biology and other fields. Single-molecule localization microscopy (SMLM) is one of the most widespread of these methods and owes its success in large part to the ability to control the on-off state of fluorophores through various chemical, photochemical, or binding-unbinding mechanisms. We provide here a comprehensive overview of switchable fluorophores in SMLM including a detailed review of all major classes of SMLM fluorophores, and we also address strategies for labeling specimens, considerations for multichannel and live-cell imaging, potential pitfalls, and areas for future development.
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Affiliation(s)
- Honglin Li
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, USA, 98195
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40
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Wang L, Gao X, Wei Y, Liu K, Huang J, Wang J, Yan Y. Coordinating Self-Assembly of Copper Perylenetetracarboxylate Nanorods: Selectively Lighting up Normal Cells around Cancerous Ones for Better Cancer Diagnosis. ACS APPLIED MATERIALS & INTERFACES 2018; 10:17630-17638. [PMID: 29733187 DOI: 10.1021/acsami.8b03211] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Specific imaging of cancer cells has been well-accepted in cancer diagnosis although it cannot precisely mark the boundary between the normal and cancerous cells and report their mutual influence. We report a nanorod fluorescent probe of copper perylenetetracarbonate (PTC-Cu) that can specifically light up normal cells. In combination with cancer cell imaging, the cocultured normal and cancer cells can be lit up with different colors, offering a clear contrast between the normal and cancer cells when they coexist. Because cancerous cells are only 20-30% in cancer area, this provides a possibility to visibly detect the mutual influence between the cancer and normal cells during therapy. We expect this method is beneficial to better cancer diagnosis and therapy.
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Affiliation(s)
- Lizhi Wang
- Key Laboratory of Oil and Gas Fine Chemicals, Ministry of Education and Xinjiang Uygur Autonomous Region, College of Chemistry and Chemical Engineering , Xinjiang University , Urumqi 830046 , People's Republic of China
| | - Xuedong Gao
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , People's Republic of China
| | - Ying Wei
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , People's Republic of China
| | - Kaerdun Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , People's Republic of China
| | - Jianbin Huang
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , People's Republic of China
| | - Jide Wang
- Key Laboratory of Oil and Gas Fine Chemicals, Ministry of Education and Xinjiang Uygur Autonomous Region, College of Chemistry and Chemical Engineering , Xinjiang University , Urumqi 830046 , People's Republic of China
| | - Yun Yan
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , People's Republic of China
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41
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Rosenberg M, Rostgaard KR, Liao Z, Madsen AØ, Martinez KL, Vosch T, Laursen BW. Design, synthesis, and time-gated cell imaging of carbon-bridged triangulenium dyes with long fluorescence lifetime and red emission. Chem Sci 2018; 9:3122-3130. [PMID: 29780456 PMCID: PMC5932597 DOI: 10.1039/c8sc00089a] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 02/15/2018] [Indexed: 01/05/2023] Open
Abstract
Time-resolved fluorescence offers many advantages over normal steady-state detection and becomes increasingly important in bioimaging. However, only very few fluorophores with emission in the visible range and fluorescence lifetimes above 5 ns are available. In this work, we prepare a series of new aza/oxa-triangulenium dyes where one of the usual oxa or aza bridges is replaced by an isopropyl bridge. This leads to a significant redshift of fluorescence with only moderate reductions of quantum yields and a unique long fluorescence lifetime. The fluorescence of the isopropyl bridged diazatriangulenium derivative CDATA+ is red-shifted by 50 nm (1400 cm-1) as compared to the oxygen-bridged DAOTA+ chromophore and has intense emission in the red region (600-700 nm) with a quantum yield of 61%, and a fluorescence lifetime of 15.8 ns in apolar solution. When the CDATA+ dye is used as cell stain, high photostability and efficient time-gated cell imaging is demonstrated.
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Affiliation(s)
- M Rosenberg
- Nano-Science Center & Department of Chemistry , University of Copenhagen , Universitetsparken 5, DK-2100 , Copenhagen Ø , Denmark . ;
| | - K R Rostgaard
- Nano-Science Center & Department of Chemistry , University of Copenhagen , Universitetsparken 5, DK-2100 , Copenhagen Ø , Denmark . ;
| | - Z Liao
- Nano-Science Center & Department of Chemistry , University of Copenhagen , Universitetsparken 5, DK-2100 , Copenhagen Ø , Denmark . ;
| | - A Ø Madsen
- Department of Pharmacy , University of Copenhagen , Universitetsparken 2, DK-2100 , Copenhagen Ø , Denmark
| | - K L Martinez
- Nano-Science Center & Department of Chemistry , University of Copenhagen , Universitetsparken 5, DK-2100 , Copenhagen Ø , Denmark . ;
| | - T Vosch
- Nano-Science Center & Department of Chemistry , University of Copenhagen , Universitetsparken 5, DK-2100 , Copenhagen Ø , Denmark . ;
| | - B W Laursen
- Nano-Science Center & Department of Chemistry , University of Copenhagen , Universitetsparken 5, DK-2100 , Copenhagen Ø , Denmark . ;
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42
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Goldberg JM, Wang F, Sessler CD, Vogler NW, Zhang DY, Loucks WH, Tzounopoulos T, Lippard SJ. Photoactivatable Sensors for Detecting Mobile Zinc. J Am Chem Soc 2018; 140:2020-2023. [PMID: 29384658 PMCID: PMC5935517 DOI: 10.1021/jacs.7b12766] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Fluorescent sensors for mobile zinc are valuable for studying complex biological systems. Because these sensors typically bind zinc rapidly and tightly, there has been little temporal control over the activity of the probe after its application to a sample. The ability to control the activity of a zinc sensor in vivo during imaging experiments would greatly improve the time resolution of the measurement. Here, we describe photoactivatable zinc sensors that can be triggered with short pulses of UV light. These probes are prepared by functionalizing a zinc sensor with protecting groups that render the probe insensitive to metal ions. Photoinduced removal of the protecting groups restores the binding site, allowing for zinc-responsive changes in fluorescence that can be observed in live cells and tissues.
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Affiliation(s)
- Jacob M. Goldberg
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Fang Wang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Chanan D. Sessler
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Nathan W. Vogler
- Pittsburgh Hearing Research Center, Department of Otolaryngology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
| | - Daniel Y. Zhang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - William H. Loucks
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Thanos Tzounopoulos
- Pittsburgh Hearing Research Center, Department of Otolaryngology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
| | - Stephen J. Lippard
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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43
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Fischer C, Sparr C. Direct Transformation of Esters into Heterocyclic Fluorophores. Angew Chem Int Ed Engl 2018; 57:2436-2440. [DOI: 10.1002/anie.201711296] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Christian Fischer
- Department of Chemistry; University of Basel; St. Johanns-Ring 19 4056 Basel Switzerland
| | - Christof Sparr
- Department of Chemistry; University of Basel; St. Johanns-Ring 19 4056 Basel Switzerland
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44
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Fischer C, Sparr C. Direkte Umwandlung von Estern in heterocyclische Fluorophore. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201711296] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Christian Fischer
- Departement Chemie; Universität Basel; St. Johanns-Ring 19 4056 Basel Schweiz
| | - Christof Sparr
- Departement Chemie; Universität Basel; St. Johanns-Ring 19 4056 Basel Schweiz
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45
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A Red-Emitting, Multidimensional Sensor for the Simultaneous Cellular Imaging of Biothiols and Phosphate Ions. SENSORS 2018; 18:s18010161. [PMID: 29315248 PMCID: PMC5795539 DOI: 10.3390/s18010161] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 12/21/2017] [Accepted: 01/02/2018] [Indexed: 01/12/2023]
Abstract
The development of new fluorescent probes for cellular imaging is currently a very active field because of the large potential in understanding cell physiology, especially targeting anomalous behaviours due to disease. In particular, red-emitting dyes are keenly sought, as the light in this spectral region presents lower interferences and a deeper depth of penetration in tissues. In this work, we have synthesized a red-emitting, dual probe for the multiplexed intracellular detection of biothiols and phosphate ions. We have prepared a fluorogenic construct involving a silicon-substituted fluorescein for red emission. The fluorogenic reaction is selectively started by the presence of biothiols. In addition, the released fluorescent moiety undergoes an excited-state proton transfer reaction promoted by the presence of phosphate ions, which modulates its fluorescence lifetime, τ, with the total phosphate concentration. Therefore, in a multidimensional approach, the intracellular levels of biothiols and phosphate can be detected simultaneously using a single fluorophore and with spectral clearing of cell autofluorescence interferences. We have applied this concept to different cell lines, including photoreceptor cells, whose levels of biothiols are importantly altered by light irradiation and other oxidants.
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46
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Ziarani GM, Moradi R, Lashgari N, Kruger HG. Rhodamine Dyes. METAL-FREE SYNTHETIC ORGANIC DYES 2018:185-191. [DOI: 10.1016/b978-0-12-815647-6.00014-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
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47
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Grimm J, Brown TA, Tkachuk AN, Lavis LD. General Synthetic Method for Si-Fluoresceins and Si-Rhodamines. ACS CENTRAL SCIENCE 2017; 3:975-985. [PMID: 28979939 PMCID: PMC5620978 DOI: 10.1021/acscentsci.7b00247] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Indexed: 05/24/2023]
Abstract
The century-old fluoresceins and rhodamines persist as flexible scaffolds for fluorescent and fluorogenic compounds. Extensive exploration of these xanthene dyes has yielded general structure-activity relationships where the development of new probes is limited only by imagination and organic chemistry. In particular, replacement of the xanthene oxygen with silicon has resulted in new red-shifted Si-fluoresceins and Si-rhodamines, whose high brightness and photostability enable advanced imaging experiments. Nevertheless, efforts to tune the chemical and spectral properties of these dyes have been hindered by difficult synthetic routes. Here, we report a general strategy for the efficient preparation of Si-fluoresceins and Si-rhodamines from readily synthesized bis(2-bromophenyl)silane intermediates. These dibromides undergo metal/bromide exchange to give bis-aryllithium or bis(aryl Grignard) intermediates, which can then add to anhydride or ester electrophiles to afford a variety of Si-xanthenes. This strategy enabled efficient (3-5 step) syntheses of known and novel Si-fluoresceins, Si-rhodamines, and related dye structures. In particular, we discovered that previously inaccessible tetrafluorination of the bottom aryl ring of the Si-rhodamines resulted in dyes with improved visible absorbance in solution, and a convenient derivatization through fluoride-thiol substitution. This modular, divergent synthetic method will expand the palette of accessible xanthenoid dyes across the visible spectrum, thereby pushing further the frontiers of biological imaging.
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48
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A general method to fine-tune fluorophores for live-cell and in vivo imaging. Nat Methods 2017; 14:987-994. [PMID: 28869757 PMCID: PMC5621985 DOI: 10.1038/nmeth.4403] [Citation(s) in RCA: 399] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 07/25/2017] [Indexed: 12/18/2022]
Abstract
Pushing the frontier of fluorescence microscopy requires the design of enhanced fluorophores with finely tuned properties. We recently discovered that incorporation of four-membered azetidine rings into classic fluorophore structures elicits substantial increases in brightness and photostability, resulting in the ‘Janelia Fluor’ (JF) series of dyes. Here, we refine and extend this strategy, showing that incorporation of 3-substituted azetidine groups allows rational tuning of the spectral and chemical properties with unprecedented precision. This strategy yields a palette of new fluorescent and fluorogenic labels with excitation ranging from blue to the far-red with utility in cells, tissue, and animals.
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49
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Lavis LD. Teaching Old Dyes New Tricks: Biological Probes Built from Fluoresceins and Rhodamines. Annu Rev Biochem 2017; 86:825-843. [DOI: 10.1146/annurev-biochem-061516-044839] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Luke D. Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
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50
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Schuster BS, Allan DB, Kays JC, Hanes J, Leheny RL. Photoactivatable fluorescent probes reveal heterogeneous nanoparticle permeation through biological gels at multiple scales. J Control Release 2017; 260:124-133. [PMID: 28578189 DOI: 10.1016/j.jconrel.2017.05.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 05/19/2017] [Accepted: 05/30/2017] [Indexed: 11/24/2022]
Abstract
Diffusion through biological gels is crucial for effective drug delivery using nanoparticles. Here, we demonstrate a new method to measure diffusivity over a large range of length scales - from tens of nanometers to tens of micrometers - using photoactivatable fluorescent nanoparticle probes. We have applied this method to investigate the length-scale dependent mobility of nanoparticles in fibrin gels and in sputum from patients with cystic fibrosis (CF). Nanoparticles composed of poly(lactic-co-glycolic acid), with polyethylene glycol coatings to resist bioadhesion, were internally labeled with caged rhodamine to make the particles photoactivatable. We activated particles within a region of sample using brief, targeted exposure to UV light, uncaging the rhodamine and causing the particles in that region to become fluorescent. We imaged the subsequent spatiotemporal evolution in fluorescence intensity and observed the collective particle diffusion over tens of minutes and tens of micrometers. We also performed complementary multiple particle tracking experiments on the same particles, extending significantly the range over which particle motion and its heterogeneity can be observed. In fibrin gels, both methods showed an immobile fraction of particles and a mobile fraction that diffused over all measured length scales. In the CF sputum, particle diffusion was spatially heterogeneous and locally anisotropic but nevertheless typically led to unbounded transport extending tens of micrometers within tens of minutes. These findings provide insight into the mesoscale architecture of these gels and its role in setting their permeability on physiologically relevant length scales, pointing toward strategies for improving nanoparticle drug delivery.
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Affiliation(s)
- Benjamin S Schuster
- Center for Nanomedicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daniel B Allan
- Department of Physics & Astronomy, Johns Hopkins University, Baltimore, MD 21218, USA; NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Joshua C Kays
- Center for Nanomedicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Justin Hanes
- Center for Nanomedicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA.
| | - Robert L Leheny
- Department of Physics & Astronomy, Johns Hopkins University, Baltimore, MD 21218, USA.
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