51
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Diverse protocols for correlative super-resolution fluorescence imaging and electron microscopy of chemically fixed samples. Nat Protoc 2017; 12:916-946. [PMID: 28384138 DOI: 10.1038/nprot.2017.017] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Our groups have recently developed related approaches for sample preparation for super-resolution imaging within endogenous cellular environments using correlative light and electron microscopy (CLEM). Four distinct techniques for preparing and acquiring super-resolution CLEM data sets for aldehyde-fixed specimens are provided, including Tokuyasu cryosectioning, whole-cell mount, cell unroofing and platinum replication, and resin embedding and sectioning. The choice of the best protocol for a given application depends on a number of criteria that are discussed in detail. Tokuyasu cryosectioning is relatively rapid but is limited to small, delicate specimens. Whole-cell mount has the simplest sample preparation but is restricted to surface structures. Cell unroofing and platinum replication creates high-contrast, 3D images of the cytoplasmic surface of the plasma membrane but is more challenging than whole-cell mount. Resin embedding permits serial sectioning of large samples but is limited to osmium-resistant probes, and is technically difficult. Expected results from these protocols include super-resolution localization (∼10-50 nm) of fluorescent targets within the context of electron microscopy ultrastructure, which can help address cell biological questions. These protocols can be completed in 2-7 d, are compatible with a number of super-resolution imaging protocols, and are broadly applicable across biology.
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52
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Jazi AA, Ploetz E, Arizki M, Dhandayuthapani B, Waclawska I, Krämer R, Ziegler C, Cordes T. Caging and Photoactivation in Single-Molecule Förster Resonance Energy Transfer Experiments. Biochemistry 2017; 56:2031-2041. [PMID: 28362086 PMCID: PMC5390306 DOI: 10.1021/acs.biochem.6b00916] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Caged
organic fluorophores are established tools for localization-based
super-resolution imaging. Their use relies on reversible deactivation
of standard organic fluorophores by chemical reduction or commercially
available caged dyes with ON switching of the fluorescent signal by
ultraviolet (UV) light. Here, we establish caging of cyanine fluorophores
and caged rhodamine dyes, i.e., chemical deactivation of fluorescence,
for single-molecule Förster resonance energy transfer (smFRET)
experiments with freely diffusing molecules. They allow temporal separation
and sorting of multiple intramolecular donor–acceptor pairs
during solution-based smFRET. We use this “caged FRET”
methodology for the study of complex biochemical species such as multisubunit
proteins or nucleic acids containing more than two fluorescent labels.
Proof-of-principle experiments and a characterization of the uncaging
process in the confocal volume are presented. These reveal that chemical
caging and UV reactivation allow temporal uncoupling of convoluted
fluorescence signals from, e.g., multiple spectrally similar donor
or acceptor molecules on nucleic acids. We also use caging without
UV reactivation to remove unwanted overlabeled species in experiments
with the homotrimeric membrane transporter BetP. We finally outline
further possible applications of the caged FRET methodology, such
as the study of weak biochemical interactions, which are otherwise
impossible with diffusion-based smFRET techniques because of the required
low concentrations of fluorescently labeled biomolecules.
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Affiliation(s)
- Atieh Aminian Jazi
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands.,Institute of Biophysics and Biophysical Chemistry, Universität Regensburg , 95053 Regensburg, Germany
| | - Evelyn Ploetz
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Muhamad Arizki
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | | | - Izabela Waclawska
- Institute of Biophysics and Biophysical Chemistry, Universität Regensburg , 95053 Regensburg, Germany
| | - Reinhard Krämer
- Institute for Biochemistry, Universität Köln , 50674 Köln, Germany
| | - Christine Ziegler
- Institute of Biophysics and Biophysical Chemistry, Universität Regensburg , 95053 Regensburg, Germany
| | - Thorben Cordes
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
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53
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Abstract
Super-resolution fluorescence imaging by photoactivation or photoswitching of single fluorophores and position determination (single-molecule localization microscopy, SMLM) provides microscopic images with subdiffraction spatial resolution. This technology has enabled new insights into how proteins are organized in a cellular context, with a spatial resolution approaching virtually the molecular level. A unique strength of SMLM is that it delivers molecule-resolved information, along with super-resolved images of cellular structures. This allows quantitative access to cellular structures, for example, how proteins are distributed and organized and how they interact with other biomolecules. Ultimately, it is even possible to determine protein numbers in cells and the number of subunits in a protein complex. SMLM thus has the potential to pave the way toward a better understanding of how cells function at the molecular level. In this review, we describe how SMLM has contributed new knowledge in eukaryotic biology, and we specifically focus on quantitative biological data extracted from SMLM images.
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Affiliation(s)
- Markus Sauer
- Department of Biotechnology & Biophysics, Julius-Maximilian-University of Würzburg , 97074 Würzburg, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt , 60438 Frankfurt, Germany
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54
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Minoshima M, Kikuchi K. Photostable and photoswitching fluorescent dyes for super-resolution imaging. J Biol Inorg Chem 2017; 22:639-652. [PMID: 28083655 DOI: 10.1007/s00775-016-1435-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 12/28/2016] [Indexed: 12/18/2022]
Abstract
Super-resolution fluorescence microscopy is a recently developed imaging tool for biological researches. Several methods have been developed for detection of fluorescence signals from molecules in a subdiffraction-limited area, breaking the diffraction limit of the conventional optical microscopies and allowing visualization of detailed macromolecular structures in cells. As objectives are exposed to intense laser in the optical systems, fluorophores for super-resolution microscopy must be tolerated even under severe light irradiation conditions. The fluorophores must also be photoactivatable and photoswitchable for single-molecule localization-based super-resolution microscopy, because the number of active fluorophores must be controlled by light irradiation. This has led to growing interest in these properties in the development of fluorophores. In this mini-review, we focus on the development of photostable and photoswitching fluorescent dyes for super-resolution microscopy. We introduce recent efforts, including improvement of fluorophore photostability and control of photoswitching behaviors of fluorophores based on photochemical and photophysical processes. Understanding and manipulation of chemical reactions in excited fluorophores can develop highly photostable and efficiently photoswitchable fluorophores that are suitable for super-resolution imaging applications.
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Affiliation(s)
- Masafumi Minoshima
- Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan. .,Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, 565-0871, Japan.
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55
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Ni M, Zhuo S, So PTC, Yu H. Fluorescent probes for nanoscopy: four categories and multiple possibilities. JOURNAL OF BIOPHOTONICS 2017; 10:11-23. [PMID: 27221311 PMCID: PMC5775479 DOI: 10.1002/jbio.201600042] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 04/08/2016] [Accepted: 05/03/2016] [Indexed: 05/08/2023]
Abstract
Nanoscopy enables breaking down the light diffraction limit and reveals the nanostructures of objects being studied using light. In 2014, three scientists pioneered the development of nanoscopy and won the Nobel Prize in Chemistry. This recognized the achievement of the past twenty years in the field of nanoscopy. However, fluorescent probes used in the field of nanoscopy are still numbered. Here, we review the currently available four categories of probes and existing methods to improve the performance of probes.
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Affiliation(s)
- Ming Ni
- Fujian Provincial Key Laboratory for Photonics Technology & Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Normal University, Fuzhou 350007, China
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore
- Corresponding authors: ; ;
| | - Shuangmu Zhuo
- Fujian Provincial Key Laboratory for Photonics Technology & Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Normal University, Fuzhou 350007, China
- Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, #10-01 CREATE Tower, Singapore 138602, Singapore
- Corresponding authors: ; ;
| | - Peter T. C. So
- Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, #10-01 CREATE Tower, Singapore 138602, Singapore
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Hanry Yu
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore
- Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, #10-01 CREATE Tower, Singapore 138602, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, MD9-04-11, 2 Medical Drive, Singapore 117597, Singapore
- Mechanobiology Institute, National University of Singapore, T-Lab, #05-01, 5A Engineering Drive 1, Singapore 117411, Singapore
- Corresponding authors: ; ;
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56
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Hauke S, von Appen A, Quidwai T, Ries J, Wombacher R. Specific protein labeling with caged fluorophores for dual-color imaging and super-resolution microscopy in living cells. Chem Sci 2017; 8:559-566. [PMID: 28451202 PMCID: PMC5351804 DOI: 10.1039/c6sc02088g] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 09/01/2016] [Indexed: 01/10/2023] Open
Abstract
We present new fluorophore-conjugates for dual-color photoactivation and super-resolution imaging inside live mammalian cells. These custom-designed, photo-caged Q-rhodamines and fluoresceins are cell-permeable, bright and localize specifically to intracellular targets. We utilized established orthogonal protein labeling strategies to precisely attach the photoactivatable fluorophores to proteins with subsequent activation of fluorescence by irradiation with UV light. That way, diffusive cytosolic proteins, histone proteins as well as filigree mitochondrial networks and focal adhesion proteins were visualized inside living cells. We applied the new photoactivatable probes in inverse fluorescence recovery after photo-bleaching (iFRAP) experiments, gaining real-time access to protein dynamics from live biological settings with resolution in space and time. Finally, we used the caged Q-rhodamine for photo-activated localization microscopy (PALM) on both fixed and live mammalian cells, where the superior molecular brightness and photo-stability directly resulted in improved localization precisions for different protein targets.
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Affiliation(s)
- Sebastian Hauke
- Institute of Pharmacy and Molecular Biotechnology , Ruprecht-Karls-University Heidelberg , Im Neuenheimer Feld 364 , 69120 Heidelberg , Germany . ; ; Tel: +49 6221 544879
| | - Alexander von Appen
- Institute of Pharmacy and Molecular Biotechnology , Ruprecht-Karls-University Heidelberg , Im Neuenheimer Feld 364 , 69120 Heidelberg , Germany . ; ; Tel: +49 6221 544879
| | - Tooba Quidwai
- European Molecular Biology Laboratory , Meyerhofstraße 1 , 69117 Heidelberg , Germany
| | - Jonas Ries
- European Molecular Biology Laboratory , Meyerhofstraße 1 , 69117 Heidelberg , Germany
| | - Richard Wombacher
- Institute of Pharmacy and Molecular Biotechnology , Ruprecht-Karls-University Heidelberg , Im Neuenheimer Feld 364 , 69120 Heidelberg , Germany . ; ; Tel: +49 6221 544879
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Abstract
![]()
Pd-catalyzed
cross-coupling reactions that form C–N bonds
have become useful methods to synthesize anilines and aniline derivatives,
an important class of compounds throughout chemical research. A key
factor in the widespread adoption of these methods has been the continued
development of reliable and versatile catalysts that function under
operationally simple, user-friendly conditions. This review provides
an overview of Pd-catalyzed N-arylation reactions found in both basic
and applied chemical research from 2008 to the present. Selected examples
of C–N cross-coupling reactions between nine classes of nitrogen-based
coupling partners and (pseudo)aryl halides are described for the synthesis
of heterocycles, medicinally relevant compounds, natural products,
organic materials, and catalysts.
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Affiliation(s)
- Paula Ruiz-Castillo
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Stephen L Buchwald
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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58
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Ong MJH, Srinivasan R, Romieu A, Richard JA. Divergent Synthesis of Dihydroxanthene-Hemicyanine Fused Near-Infrared Fluorophores through the Late-Stage Amination of a Bifunctional Precursor. Org Lett 2016; 18:5122-5125. [DOI: 10.1021/acs.orglett.6b02564] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Michelle Jui Hsien Ong
- Organic
Chemistry, Institute of Chemical and Engineering Sciences (ICES),
Agency for Science, Technology and Research (A*STAR), 8 Biomedical
Grove, Neuros, #07-01, Singapore, Singapore 138665
| | - Rajavel Srinivasan
- Organic
Chemistry, Institute of Chemical and Engineering Sciences (ICES),
Agency for Science, Technology and Research (A*STAR), 8 Biomedical
Grove, Neuros, #07-01, Singapore, Singapore 138665
| | - Anthony Romieu
- ICMUB, UMR 6302,
CNRS, Univ. Bourgogne Franche-Comté, 9, Avenue Alain Savary, 21078 Dijon cedex, France
- Institut Universitaire de France, 103 Boulevard Saint-Michel, 75005 Paris, France
| | - Jean-Alexandre Richard
- Organic
Chemistry, Institute of Chemical and Engineering Sciences (ICES),
Agency for Science, Technology and Research (A*STAR), 8 Biomedical
Grove, Neuros, #07-01, Singapore, Singapore 138665
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59
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From single molecules to life: microscopy at the nanoscale. Anal Bioanal Chem 2016; 408:6885-911. [PMID: 27613013 PMCID: PMC5566169 DOI: 10.1007/s00216-016-9781-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 06/30/2016] [Accepted: 07/07/2016] [Indexed: 01/08/2023]
Abstract
Super-resolution microscopy is the term commonly given to fluorescence microscopy techniques with resolutions that are not limited by the diffraction of light. Since their conception a little over a decade ago, these techniques have quickly become the method of choice for many biologists studying structures and processes of single cells at the nanoscale. In this review, we present the three main approaches used to tackle the diffraction barrier of ∼200 nm: stimulated-emission depletion (STED) microscopy, structured illumination microscopy (SIM), and single-molecule localization microscopy (SMLM). We first present a theoretical overview of the techniques and underlying physics, followed by a practical guide to all of the facets involved in designing a super-resolution experiment, including an approachable explanation of the photochemistry involved, labeling methods available, and sample preparation procedures. Finally, we highlight some of the most exciting recent applications of and developments in these techniques, and discuss the outlook for this field. Super-resolution microscopy techniques. Working principles of the common approaches stimulated-emission depletion (STED) microscopy, structured illumination microscopy (SIM), and single-molecule localization microscopy (SMLM). ![]()
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60
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Wu H, Alexander SC, Jin S, Devaraj NK. A Bioorthogonal Near-Infrared Fluorogenic Probe for mRNA Detection. J Am Chem Soc 2016; 138:11429-32. [PMID: 27510580 DOI: 10.1021/jacs.6b01625] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
There is significant interest in developing methods that visualize and detect RNA. Bioorthogonal template-driven tetrazine ligations could be a powerful route to visualizing nucleic acids in native cells, yet past work has been limited with respect to the diversity of fluorogens that can be activated via a tetrazine reaction. Herein we report a novel bioorthogonal tetrazine uncaging reaction that harnesses tetrazine reactivity to unmask vinyl ether caged fluorophores spanning the visible spectrum, including a near-infrared (NIR)-emitting cyanine dye. Vinyl ether caged fluorophores and tetrazine partners are conjugated to high-affinity antisense nucleic acid probes, which show highly selective fluorogenic reactivity when annealed to their respective target RNA sequences. A target sequence in the 3' untranslated region of an expressed mRNA was detected in live cells employing appropriate nucleic acid probes bearing a tetrazine-reactive NIR fluorogen. Given the expansion of tetrazine fluorogenic chemistry to NIR dyes, we believe highly selective proximity-induced fluorogenic tetrazine reactions could find broad uses in illuminating endogenous biomolecules in cells and tissues.
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Affiliation(s)
- Haoxing Wu
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
| | - Seth C Alexander
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
| | - Shuaijiang Jin
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
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61
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Gu X, Zhao E, Zhao T, Kang M, Gui C, Lam JWY, Du S, Loy MMT, Tang BZ. A Mitochondrion-Specific Photoactivatable Fluorescence Turn-On AIE-Based Bioprobe for Localization Super-Resolution Microscope. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:5064-5071. [PMID: 27135807 DOI: 10.1002/adma.201505906] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 03/18/2016] [Indexed: 06/05/2023]
Abstract
A novel mitochondrion-specific photo-activatable fluorescence turn-on bioprobe, named as o-TPE-ON+, is designed and readily prepared, operating through a new photoactivatable mechanism of photocyclodehydrogenation. This bioprobe exhibits unique photoactivation behavior in cells, and is applied to super-resolution imaging of mitochondrion and its dynamic investigation in both fixed and live cells under physiological conditions without any external additives.
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Affiliation(s)
- Xinggui Gu
- HKUST-Shenzhen Research Institute, No. 9 Yuexing 1st RD, South Area, Hi-tech Park Nanshan, Shenzhen, 518057, China
- Departments of Chemistry and Physics, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Engui Zhao
- HKUST-Shenzhen Research Institute, No. 9 Yuexing 1st RD, South Area, Hi-tech Park Nanshan, Shenzhen, 518057, China
- Departments of Chemistry and Physics, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Teng Zhao
- Departments of Chemistry and Physics, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Miaomiao Kang
- Departments of Chemistry and Physics, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Department of Neurobiology and Anatomy, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Chen Gui
- HKUST-Shenzhen Research Institute, No. 9 Yuexing 1st RD, South Area, Hi-tech Park Nanshan, Shenzhen, 518057, China
- Departments of Chemistry and Physics, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Jacky W Y Lam
- HKUST-Shenzhen Research Institute, No. 9 Yuexing 1st RD, South Area, Hi-tech Park Nanshan, Shenzhen, 518057, China
- Departments of Chemistry and Physics, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Shengwang Du
- Departments of Chemistry and Physics, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Michael M T Loy
- Departments of Chemistry and Physics, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Ben Zhong Tang
- HKUST-Shenzhen Research Institute, No. 9 Yuexing 1st RD, South Area, Hi-tech Park Nanshan, Shenzhen, 518057, China
- Departments of Chemistry and Physics, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Guangdong Innovative Research Team, SCUT-HKUST Joint Research Laboratory, State Key Laboratory of Luminescent Materials and Device, South China University of Technology, Guangzhou, 51640, China
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62
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Grimm JB, Klein T, Kopek BG, Shtengel G, Hess HF, Sauer M, Lavis LD. Synthesis of a Far-Red Photoactivatable Silicon-Containing Rhodamine for Super-Resolution Microscopy. Angew Chem Int Ed Engl 2016; 55:1723-7. [PMID: 26661345 PMCID: PMC4736676 DOI: 10.1002/anie.201509649] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Indexed: 11/20/2022]
Abstract
The rhodamine system is a flexible framework for building small-molecule fluorescent probes. Changing N-substitution patterns and replacing the xanthene oxygen with a dimethylsilicon moiety can shift the absorption and fluorescence emission maxima of rhodamine dyes to longer wavelengths. Acylation of the rhodamine nitrogen atoms forces the molecule to adopt a nonfluorescent lactone form, providing a convenient method to make fluorogenic compounds. Herein, we take advantage of all of these structural manipulations and describe a novel photoactivatable fluorophore based on a Si-containing analogue of Q-rhodamine. This probe is the first example of a "caged" Si-rhodamine, exhibits higher photon counts compared to established localization microscopy dyes, and is sufficiently red-shifted to allow multicolor imaging. The dye is a useful label for super-resolution imaging and constitutes a new scaffold for far-red fluorogenic molecules.
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Affiliation(s)
- Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA, 20147, USA
| | - Teresa Klein
- Department of Biotechnology and Biophysics, Julius Maximilian University Wuerzburg, Am Hubland, 97074, Wuerzburg, Germany
| | - Benjamin G Kopek
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA, 20147, USA
- Hope College, Department of Biology, 35 E. 12th Street, Holland, MI, 49423, USA
| | - Gleb Shtengel
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA, 20147, USA
| | - Harald F Hess
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA, 20147, USA
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Julius Maximilian University Wuerzburg, Am Hubland, 97074, Wuerzburg, Germany
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA, 20147, USA.
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63
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Anzalone AV, Chen Z, Cornish VW. Synthesis of photoactivatable azido-acyl caged oxazine fluorophores for live-cell imaging. Chem Commun (Camb) 2016; 52:9442-5. [DOI: 10.1039/c6cc04882j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A new cell-permeable caged oxazine fluorophore was synthesized for protein specific labeling and photoactivation in living cells.
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Affiliation(s)
- Andrew V. Anzalone
- Department of Chemistry
- Columbia University
- New York
- USA
- Department of Systems Biology
| | - Zhixing Chen
- Department of Chemistry
- Columbia University
- New York
- USA
| | - Virginia W. Cornish
- Department of Chemistry
- Columbia University
- New York
- USA
- Department of Systems Biology
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64
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Gooch J, Abbate V, Daniel B, Frascione N. Solid-phase synthesis of Rhodamine-110 fluorogenic substrates and their application in forensic analysis. Analyst 2016; 141:2392-5. [DOI: 10.1039/c6an00686h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel synthesis demonstrates the rapid and efficient preparation of fluorogenic substrates containing Rhodamine-110 fluorophores for the detection of biological evidence.
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Affiliation(s)
- J. Gooch
- Analytical & Environmental Sciences Division
- King's College London
- Waterloo
- London
| | - V. Abbate
- Institute of Pharmaceutical Science
- King's College London
- Waterloo
- London
| | - B. Daniel
- Analytical & Environmental Sciences Division
- King's College London
- Waterloo
- London
| | - N. Frascione
- Analytical & Environmental Sciences Division
- King's College London
- Waterloo
- London
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65
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Grimm JB, Gruber TD, Ortiz G, Brown TA, Lavis LD. Virginia Orange: A Versatile, Red-Shifted Fluorescein Scaffold for Single- and Dual-Input Fluorogenic Probes. Bioconjug Chem 2015; 27:474-80. [DOI: 10.1021/acs.bioconjchem.5b00566] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Jonathan B. Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Todd D. Gruber
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Gloria Ortiz
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Timothy A. Brown
- 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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66
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Grimm JB, Klein T, Kopek BG, Shtengel G, Hess HF, Sauer M, Lavis LD. Synthesis of a Far-Red Photoactivatable Silicon-Containing Rhodamine for Super-Resolution Microscopy. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201509649] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jonathan B. Grimm
- Janelia Research Campus; Howard Hughes Medical Institute; 19700 Helix Drive Ashburn VA 20147 USA
| | - Teresa Klein
- Department of Biotechnology and Biophysics; Julius Maximilian University Wuerzburg; Am Hubland 97074 Wuerzburg Germany
| | - Benjamin G. Kopek
- Janelia Research Campus; Howard Hughes Medical Institute; 19700 Helix Drive Ashburn VA 20147 USA
- Hope College; Department of Biology; 35 E. 12th Street Holland MI 49423 USA
| | - Gleb Shtengel
- Janelia Research Campus; Howard Hughes Medical Institute; 19700 Helix Drive Ashburn VA 20147 USA
| | - Harald F. Hess
- Janelia Research Campus; Howard Hughes Medical Institute; 19700 Helix Drive Ashburn VA 20147 USA
| | - Markus Sauer
- Department of Biotechnology and Biophysics; Julius Maximilian University Wuerzburg; Am Hubland 97074 Wuerzburg Germany
| | - Luke D. Lavis
- Janelia Research Campus; Howard Hughes Medical Institute; 19700 Helix Drive Ashburn VA 20147 USA
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67
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Gu X, Zhao E, Lam JWY, Peng Q, Xie Y, Zhang Y, Wong KS, Sung HHY, Williams ID, Tang BZ. Mitochondrion-Specific Live-Cell Bioprobe Operated in a Fluorescence Turn-On Manner and a Well-Designed Photoactivatable Mechanism. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2015; 27:7093-7100. [PMID: 26445398 DOI: 10.1002/adma.201503751] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 09/04/2015] [Indexed: 06/05/2023]
Abstract
A novel mitochondrion-specific live-cell fluorescence turn-on photoactivatable bioprobe, named o-TPP3M, is designed and readily prepared, operating in a new photoactivatable mechanism based on a twisted intramolecular charge-transfer effect, the restriction of intramolecular rotations, and photocyclodehydrogenation. This bioprobe exhibits unique photoactivation behavior, a large signal-to-background ratio, and no cytotoxicity to living cells, providing a promising candidate for varied bioresearch.
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Affiliation(s)
- Xinggui Gu
- HKUST-Shenzhen Research Institute, No. 9 Yuexing 1st RD, South Area, Hi-Tech Park, Nanshan, Shenzhen, 518057, China
- Departments of Chemistry, Physics, and Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Engui Zhao
- HKUST-Shenzhen Research Institute, No. 9 Yuexing 1st RD, South Area, Hi-Tech Park, Nanshan, Shenzhen, 518057, China
- Departments of Chemistry, Physics, and Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Jacky W Y Lam
- HKUST-Shenzhen Research Institute, No. 9 Yuexing 1st RD, South Area, Hi-Tech Park, Nanshan, Shenzhen, 518057, China
- Departments of Chemistry, Physics, and Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Qian Peng
- Key Laboratory of Organic Solids, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yujun Xie
- Key Laboratory of Organic Solids, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yilin Zhang
- Departments of Chemistry, Physics, and Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Kam Sing Wong
- Departments of Chemistry, Physics, and Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Herman H Y Sung
- Departments of Chemistry, Physics, and Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Ian D Williams
- Departments of Chemistry, Physics, and Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Ben Zhong Tang
- HKUST-Shenzhen Research Institute, No. 9 Yuexing 1st RD, South Area, Hi-Tech Park, Nanshan, Shenzhen, 518057, China
- Departments of Chemistry, Physics, and Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Guangdong Innovative Research Team, SCUT-HKUST Joint Research Laboratory, State Key Laboratory of Luminescent Materials and Device, South China University of Technology, Guangzhou, 51640, China
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68
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Grenier V, Walker AS, Miller EW. A Small-Molecule Photoactivatable Optical Sensor of Transmembrane Potential. J Am Chem Soc 2015; 137:10894-7. [PMID: 26247778 DOI: 10.1021/jacs.5b05538] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper discloses the design, synthesis, and imaging applications of the first member of a new class of SPOTs, small-molecule photoactivatable optical sensors of transmembrane potential. SPOT2.1.Cl features an established voltage-sensitive dye, VoltageFluor2.1.Cl--or VF--capped with a dimethoxy-o-nitrobenzyl (DMNB) caging group to effectively diminish fluorescence of the VF dye prior to uncaging. SPOT2.1.Cl localizes to cell membranes and displays weak fluorescence until photoactivated. Illumination generates the parent VF dye which then optically reports on changes in the membrane voltage. After photoactivation with spatially restricted light, SPOT2.1.Cl-loaded cells display bright, voltage-sensitive fluorescence associated with the plasma membrane, while neighboring cells remain dark. Activated SPOT reports on action potentials in single trials. SPOT can be activated in neuron cell bodies or uncaged in dendrites to enable structural tracing via "backfilling" of the dye to the soma, followed by functional imaging in the labeled cell. The combination of cellular specificity achieved through spatially defined patterns of illumination, coupled with the fast, sensitive, and noncapacitive voltage sensing characteristics of VF dyes makes SPOT2.1.Cl a useful tool for interrogating both structure and function of neuronal systems.
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Affiliation(s)
- Vincent Grenier
- Departments of †Chemistry, ‡Molecular & Cell Biology, and §Helen Wills Neuroscience Institute, University of California , Berkeley, California 94720, United States
| | - Alison S Walker
- Departments of †Chemistry, ‡Molecular & Cell Biology, and §Helen Wills Neuroscience Institute, University of California , Berkeley, California 94720, United States
| | - Evan W Miller
- Departments of †Chemistry, ‡Molecular & Cell Biology, and §Helen Wills Neuroscience Institute, University of California , Berkeley, California 94720, United States
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69
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Budyka MF, Li VM, Gavrishova TN, Potashova NI. Spectral and luminescent properties and photoisomerization of substituted styrylbenzoquinolines. HIGH ENERGY CHEMISTRY 2015. [DOI: 10.1134/s0018143915030054] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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70
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Jacquemet A, Rihn S, Ulrich G, Renard PY, Romieu A, Ziessel R. Rational Design of Latent Fluorophores from Water-Soluble Hydroxyphenyltriazine Dyes Suitable for Lipase Sensing. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500047] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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71
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Abstract
Photo-activated or "Caged" rhodamine dyes are the most useful for microscopic investigation of biological tissue by various fluorescent techniques. Novel precursor of the fluorescent dye (PFD813) has been studied for photosensitive staining of numerous animal cells. The functional rhodamine dye (Rho813) with intensive fluorescence has been obtained after photoactivation of its precursor PFD813 inside cells. The dye Rho813 has been successfully used for the optical detection of particular features in biological objects (HaCaT cells, HBL-100, MDCK, lymphocytes). Moreover, the chitosan conjugate with PFD molecules ("Chitosan-PFD813″) has been obtained and studied for the first time. The developed procedures and obtained data are important for further applications of novel precursors of fluorescent dyes ("caged" dyes) for microscopic probing of biological objects. As example, the synthesized "Chitosan-PFD813″ has been successfully applied in this study for intracellular transport visualization by fluorescent microscopy.
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72
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Ballister ER, Aonbangkhen C, Mayo AM, Lampson MA, Chenoweth DM. Localized light-induced protein dimerization in living cells using a photocaged dimerizer. Nat Commun 2014; 5:5475. [PMID: 25400104 PMCID: PMC4308733 DOI: 10.1038/ncomms6475] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 10/06/2014] [Indexed: 12/17/2022] Open
Abstract
Regulated protein localization is critical for many cellular processes. Several techniques have been developed for experimental control over protein localization, including chemically induced and light-induced dimerization, which both provide temporal control. Light-induced dimerization offers the distinct advantage of spatial precision within subcellular length scales. A number of elegant systems have been reported that utilize natural light-sensitive proteins to induce dimerization via direct protein-protein binding interactions, but the application of these systems at cellular locations beyond the plasma membrane has been limited. Here we present a new technique to rapidly and reversibly control protein localization in living cells with subcellular spatial resolution using a cell-permeable, photoactivatable chemical inducer of dimerization. We demonstrate light-induced recruitment of a cytosolic protein to individual centromeres, kinetochores, mitochondria and centrosomes in human cells, indicating that our system is widely applicable to many cellular locations.
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Affiliation(s)
- Edward R Ballister
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Chanat Aonbangkhen
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Alyssa M Mayo
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Michael A Lampson
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - David M Chenoweth
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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73
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Conjugates of a photoactivated rhodamine with biopolymers for cell staining. ScientificWorldJournal 2014; 2014:285405. [PMID: 25383365 PMCID: PMC4214035 DOI: 10.1155/2014/285405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 09/02/2014] [Indexed: 12/01/2022] Open
Abstract
Conjugates of the photoactivated rhodamine dyes with biopolymers (proteins, polysaccharides, and nucleic acids) are important tools for microscopic investigation of biological tissue. In this study, a precursor of the photoactivated fluorescent dye (PFD) has been successfully used for staining of numerous mammalian cells lines and for conjugate formation with chitosan (“Chitosan-PFD”) and histone H1 (“Histone H1.3-PFD”). The intensive fluorescence has been observed after photoactivation of these conjugates inside cells (A431, HaCaT, HEK239, HBL-100, and MDCK). Developed procedures and obtained data are important for further application of novel precursors of fluorescent dyes (“caged” dyes) for microscopic probing of biological objects. Thus, the synthesized “Chitosan-PFD” and “Histone H1-PFD” have been successfully applied in this study for intracellular transport visualization by fluorescent microscopy.
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74
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Nobel Prizes 2014: E. Betzig, S. W. Hell, W. E. Moerner, J. M. O'Keefe, M.-B. Moser, E. I. Moser, I. Akasaki, H. Amano, and S. Nakamura. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/anie.201409871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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75
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Nobelpreise 2014: E. Betzig, S. W. Hell, W. E. Moerner, J. M. O'Keefe, M.-B. Moser, E. I. Moser, I. Akasaki, H. Amano und S. Nakamura. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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76
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Lin Q, Du Z, Yang Y, Fang Q, Bao C, Yang Y, Zhu L. Intracellular Thiols and Photo-Illumination Sequentially Activate Doubly Locked Molecular Probes for Long-Term Cell Highlighting and Tracking with Precise Spatial Accuracy. Chemistry 2014; 20:16314-9. [DOI: 10.1002/chem.201403905] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Indexed: 01/08/2023]
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77
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Belov VN, Mitronova GY, Bossi ML, Boyarskiy VP, Hebisch E, Geisler C, Kolmakov K, Wurm CA, Willig KI, Hell SW. Masked rhodamine dyes of five principal colors revealed by photolysis of a 2-diazo-1-indanone caging group: synthesis, photophysics, and light microscopy applications. Chemistry 2014; 20:13162-73. [PMID: 25196166 DOI: 10.1002/chem.201403316] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Indexed: 12/17/2022]
Abstract
Caged rhodamine dyes (Rhodamines NN) of five basic colors were synthesized and used as "hidden" markers in subdiffractional and conventional light microscopy. These masked fluorophores with a 2-diazo-1-indanone group can be irreversibly photoactivated, either by irradiation with UV- or violet light (one-photon process), or by exposure to intense red light (λ∼750 nm; two-photon mode). All dyes possess a very small 2-diazoketone caging group incorporated into the 2-diazo-1-indanone residue with a quaternary carbon atom (C-3) and a spiro-9H-xanthene fragment. Initially they are non-colored (pale yellow), non-fluorescent, and absorb at λ=330-350 nm (molar extinction coefficient (ε)≈10(4) M(-1) cm(-1)) with a band edge that extends to about λ=440 nm. The absorption and emission bands of the uncaged derivatives are tunable over a wide range (λ=511-633 and 525-653 nm, respectively). The unmasked dyes are highly colored and fluorescent (ε=3-8×10(4) M(-1) cm(-1) and fluorescence quantum yields (ϕ)=40-85% in the unbound state and in methanol). By stepwise and orthogonal protection of carboxylic and sulfonic acid groups a highly water-soluble caged red-emitting dye with two sulfonic acid residues was prepared. Rhodamines NN were decorated with amino-reactive N-hydroxysuccinimidyl ester groups, applied in aqueous buffers, easily conjugated with proteins, and readily photoactivated (uncaged) with λ=375-420 nm light or intense red light (λ=775 nm). Protein conjugates with optimal degrees of labeling (3-6) were prepared and uncaged with λ=405 nm light in aqueous buffer solutions (ϕ=20-38%). The photochemical cleavage of the masking group generates only molecular nitrogen. Some 10-40% of the non-fluorescent (dark) byproducts are also formed. However, they have low absorbance and do not quench the fluorescence of the uncaged dyes. Photoactivation of the individual molecules of Rhodamines NN (e.g., due to reversible or irreversible transition to a "dark" non-emitting state or photobleaching) provides multicolor images with subdiffractional optical resolution. The applicability of these novel caged fluorophores in super-resolution optical microscopy is exemplified.
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Affiliation(s)
- Vladimir N Belov
- NanoBiophotonics Department, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen (Germany), Fax: (+49) 551-201-2505.
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78
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Nekongo EE, Popik VV. Photoactivatable fluorescein derivatives caged with a (3-hydroxy-2-naphthalenyl)methyl group. J Org Chem 2014; 79:7665-71. [PMID: 25036698 DOI: 10.1021/jo501116g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The (3-hydroxy-2-naphthalenyl)methyl (NQMP) group represents an efficient photocage for fluorescein-based dyes. Thus, irradiation of the 6-NQMP ether of 2'-hydroxymethylfluorescein with low-intensity UVA light results in a 4-fold increase in emission intensity. Photoactivation of nonfluorescent NQMP-caged 3-allyloxyfluorescein produces a highly emissive fluorescein monoether. To facilitate conjugation of the caged dye to the substrate of interest via click chemistry, the allyloxy appendage was functionalized with an azide moiety.
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Affiliation(s)
- Emmanuel E Nekongo
- Department of Chemistry, University of Georgia , Athens, Georgia 30602, United States
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79
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Raulf A, Spahn CK, Zessin PJM, Finan K, Bernhardt S, Heckel A, Heilemann M. Click chemistry facilitates direct labelling and super-resolution imaging of nucleic acids and proteins†Electronic supplementary information (ESI) available. See DOI: 10.1039/c4ra01027bClick here for additional data file. RSC Adv 2014; 4:30462-30466. [PMID: 25580242 PMCID: PMC4285124 DOI: 10.1039/c4ra01027b] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 06/27/2014] [Indexed: 12/21/2022] Open
Abstract
We demonstrate high-density labelling of cellular DNA and RNA using click chemistry and perform confocal and super-resolution microscopy. We visualize the crescent and ring-like structure of densely packed RNA in nucleoli. We further demonstrate click chemistry with unnatural amino acids for super-resolution imaging of outer-membrane proteins of E. coli.
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Affiliation(s)
- Anika Raulf
- Institute of Physical & Theoretical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Str. 7 , 60438 Frankfurt/Main , Germany .
| | - Christoph K Spahn
- Institute of Physical & Theoretical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Str. 7 , 60438 Frankfurt/Main , Germany .
| | - Patrick J M Zessin
- Institute of Physical & Theoretical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Str. 7 , 60438 Frankfurt/Main , Germany .
| | | | - Stefan Bernhardt
- Institute for Organic Chemistry and Chemical Biology , Goethe-University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/Main , Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology , Goethe-University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/Main , Germany
| | - Mike Heilemann
- Institute of Physical & Theoretical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Str. 7 , 60438 Frankfurt/Main , Germany .
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80
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Chozinski TJ, Gagnon LA, Vaughan JC. Twinkle, twinkle little star: photoswitchable fluorophores for super-resolution imaging. FEBS Lett 2014; 588:3603-12. [PMID: 25010263 DOI: 10.1016/j.febslet.2014.06.043] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/14/2014] [Accepted: 06/16/2014] [Indexed: 01/01/2023]
Abstract
Photoswitchable fluorescent probes are key elements of newly developed super-resolution fluorescence microscopy techniques that enable far-field interrogation of biological systems with a resolution of 50 nm or better. In contrast to most conventional fluorescence imaging techniques, the performance achievable by most super-resolution techniques is critically impacted by the photoswitching properties of the fluorophores. Here we review photoswitchable fluorophores for super-resolution imaging with discussion of the fundamental principles involved, a focus on practical implementation with available tools, and an outlook on future directions.
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Affiliation(s)
| | - Lauren A Gagnon
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Joshua C Vaughan
- Department of Chemistry, University of Washington, Seattle, WA, USA; Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA.
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81
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Lavis LD, Raines RT. Bright building blocks for chemical biology. ACS Chem Biol 2014; 9:855-66. [PMID: 24579725 PMCID: PMC4006396 DOI: 10.1021/cb500078u] [Citation(s) in RCA: 360] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 02/28/2014] [Indexed: 02/08/2023]
Abstract
Small-molecule fluorophores manifest the ability of chemistry to solve problems in biology. As we noted in a previous review (Lavis, L. D.; Raines, R. T. ACS Chem. Biol. 2008, 3, 142-155), the extant collection of fluorescent probes is built on a modest set of "core" scaffolds that evolved during a century of academic and industrial research. Here, we survey traditional and modern synthetic routes to small-molecule fluorophores and highlight recent biological insights attained with customized fluorescent probes. Our intent is to inspire the design and creation of new high-precision tools that empower chemical biologists.
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Affiliation(s)
- Luke D. Lavis
- Janelia Farm Research
Campus, Howard Hughes Medical
Institute, Ashburn, Virginia 20147, United
States
| | - Ronald T. Raines
- Departments
of Biochemistry and Chemistry, University
of Wisconsin−Madison, Madison, Wisconsin 53706, United States
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82
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Ragab SS, Swaminathan S, Baker JD, Raymo FM. Activation of BODIPY fluorescence by the photoinduced dealkylation of a pyridinium quencher. Phys Chem Chem Phys 2014; 15:14851-5. [PMID: 23694991 DOI: 10.1039/c3cp51580j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The photoinduced cleavage of a 2-nitrobenzyl group from a pyridinium quencher covalently attached to the meso position of a BODIPY fluorophore activates the emission of the latter. This photochemical transformation prevents the transfer of one electron from the BODIPY platform to its heterocyclic appendage upon excitation and, as a result, permits the radiative deactivation of the excited fluorophore. This versatile mechanism for fluorescence switching can translate into the realization of an entire family of photoactivatable fluorophores based on the outstanding photophysical properties of BODIPY chromophores.
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Affiliation(s)
- Sherif Shaban Ragab
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, Coral Gables, Florida 33146-0431, USA
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83
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Hamers D, van Voorst Vader L, Borst JW, Goedhart J. Development of FRET biosensors for mammalian and plant systems. PROTOPLASMA 2014; 251:333-347. [PMID: 24337770 DOI: 10.1007/s00709-013-0590-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 11/19/2013] [Indexed: 06/03/2023]
Abstract
Genetically encoded biosensors are increasingly used in visualising signalling processes in different organisms. Sensors based on green fluorescent protein technology are providing a great opportunity for using Förster resonance energy transfer (FRET) as a tool that allows for monitoring dynamic processes in living cells. The development of these FRET biosensors requires careful selection of fluorophores, substrates and recognition domains. In this review, we will discuss recent developments, strategies to create and optimise FRET biosensors and applications of FRET-based biosensors for use in the two major eukaryotic kingdoms and elaborate on different methods for FRET detection.
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Affiliation(s)
- Danny Hamers
- Laboratory of Biochemistry and Microspectroscopy Centre, Wageningen University, Wageningen, The Netherlands
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84
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Carlini L, Benke A, Reymond L, Lukinavičius G, Manley S. Reduced dyes enhance single-molecule localization density for live superresolution imaging. Chemphyschem 2014; 15:750-5. [PMID: 24554553 DOI: 10.1002/cphc.201301004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 12/17/2013] [Indexed: 11/09/2022]
Abstract
Cell-permeable rhodamine dyes are reductively quenched by NaBH4 into a non-fluorescent leuco-rhodamine form. Quenching is reversible, and their fluorescence is recovered when the dyes are oxidized. In living cells, oxidation occurs spontaneously, and can result in up to ten-fold higher densities of single molecule localizations, and more photons per localization as compared with unmodified dyes. These two parameters directly impact the achievable resolution, and we see a significant improvement in the quality of live-cell point-localization super-resolution images taken with reduced dyes. These improvements carry over to increase the density of trajectories for single-molecule tracking experiments.
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Affiliation(s)
- Lina Carlini
- Laboratory of Experimental Biophysics, Institute of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne (EPFL), National Centre of Competence in Research (NCCR) in Chemical Biology, Lausanne (Switzerland)
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85
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Kamino S, Murakami M, Tanioka M, Shirasaki Y, Watanabe K, Horigome J, Ooyama Y, Enomoto S. Design and Syntheses of Highly Emissive Aminobenzopyrano-xanthene Dyes in the Visible and Far-Red Regions. Org Lett 2013; 16:258-61. [DOI: 10.1021/ol403262x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Shinichiro Kamino
- Next-generation
Imaging Team, RIKEN-CLST, Kobe-shi, Hyogo 650-0047, Japan
- Graduate
School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama-shi, Okayama 700-8530, Japan
| | - Miho Murakami
- Graduate
School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama-shi, Okayama 700-8530, Japan
| | - Masaru Tanioka
- Graduate
School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama-shi, Okayama 700-8530, Japan
| | - Yoshinao Shirasaki
- Graduate
School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama-shi, Okayama 700-8530, Japan
| | - Keiko Watanabe
- Next-generation
Imaging Team, RIKEN-CLST, Kobe-shi, Hyogo 650-0047, Japan
- Graduate
School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama-shi, Okayama 700-8530, Japan
| | - Jun Horigome
- Hitachi High-Tech
Science Co., Ltd., Hitachinaka-shi, Ibaraki 312-8504, Japan
| | - Yousuke Ooyama
- Department
of Applied Chemistry, Graduate School of Engineering, Hiroshima University, Higashi-Hiroshima 739-8527, Japan
| | - Shuichi Enomoto
- Next-generation
Imaging Team, RIKEN-CLST, Kobe-shi, Hyogo 650-0047, Japan
- Graduate
School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama-shi, Okayama 700-8530, Japan
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86
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Zhao D, Li G, Wu D, Qin X, Neuhaus P, Cheng Y, Yang S, Lu Z, Pu X, Long C, You J. Regiospecific N-Heteroarylation of Amidines for Full-Color-Tunable Boron Difluoride Dyes with Mechanochromic Luminescence. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201304824] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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87
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Zhao D, Li G, Wu D, Qin X, Neuhaus P, Cheng Y, Yang S, Lu Z, Pu X, Long C, You J. Regiospecific N-Heteroarylation of Amidines for Full-Color-Tunable Boron Difluoride Dyes with Mechanochromic Luminescence. Angew Chem Int Ed Engl 2013; 52:13676-80. [DOI: 10.1002/anie.201304824] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 07/28/2013] [Indexed: 01/28/2023]
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88
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Kopek BG, Shtengel G, Grimm JB, Clayton DA, Hess HF. Correlative photoactivated localization and scanning electron microscopy. PLoS One 2013; 8:e77209. [PMID: 24204771 PMCID: PMC3808397 DOI: 10.1371/journal.pone.0077209] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 09/03/2013] [Indexed: 11/26/2022] Open
Abstract
The ability to localize proteins precisely within subcellular space is crucial to understanding the functioning of biological systems. Recently, we described a protocol that correlates a precise map of fluorescent fusion proteins localized using three-dimensional super-resolution optical microscopy with the fine ultrastructural context of three-dimensional electron micrographs. While it achieved the difficult simultaneous objectives of high photoactivated fluorophore preservation and ultrastructure preservation, it required a super-resolution optical and specialized electron microscope that is not available to many researchers. We present here a faster and more practical protocol with the advantage of a simpler two-dimensional optical (Photoactivated Localization Microscopy (PALM)) and scanning electron microscope (SEM) system that retains the often mutually exclusive attributes of fluorophore preservation and ultrastructure preservation. As before, cryosections were prepared using the Tokuyasu protocol, but the staining protocol was modified to be amenable for use in a standard SEM without the need for focused ion beam ablation. We show the versatility of this technique by labeling different cellular compartments and structures including mitochondrial nucleoids, peroxisomes, and the nuclear lamina. We also demonstrate simultaneous two-color PALM imaging with correlated electron micrographs. Lastly, this technique can be used with small-molecule dyes as demonstrated with actin labeling using phalloidin conjugated to a caged dye. By retaining the dense protein labeling expected for super-resolution microscopy combined with ultrastructural preservation, simplifying the tools required for correlative microscopy, and expanding the number of useful labels we expect this method to be accessible and valuable to a wide variety of researchers.
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Affiliation(s)
- Benjamin G. Kopek
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
- * E-mail:
| | - Gleb Shtengel
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Jonathan B. Grimm
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - David A. Clayton
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Harald F. Hess
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
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89
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Shaban Ragab S, Swaminathan S, Deniz E, Captain B, Raymo FM. Fluorescence photoactivation by ligand exchange around the boron center of a BODIPY chromophore. Org Lett 2013; 15:3154-7. [PMID: 23738708 DOI: 10.1021/ol401380n] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Chelation of the boron center of the borondipyrromethene (BODIPY) platform by a catecholate ligand results in effective fluorescence suppression. Electron transfer from the chelating unit to the adjacent chromophore upon excitation is responsible for fluorescence quenching. Under the influence of a photoacid generator, the catecholate chelator can be exchanged with a pair of methoxide ligands. This photoinduced transformation prevents electron transfer and efficiently activates the fluorescence of the BODIPY chromophore.
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Affiliation(s)
- Sherif Shaban Ragab
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami , 1301 Memorial Drive, Coral Gables, Florida 33146-0431, United States
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90
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Grimm JB, Sung AJ, Legant WR, Hulamm P, Matlosz SM, Betzig E, Lavis LD. Carbofluoresceins and carborhodamines as scaffolds for high-contrast fluorogenic probes. ACS Chem Biol 2013; 8:1303-10. [PMID: 23557713 PMCID: PMC3691720 DOI: 10.1021/cb4000822] [Citation(s) in RCA: 155] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Fluorogenic molecules are important
tools for advanced biochemical
and biological experiments. The extant collection of fluorogenic probes
is incomplete, however, leaving regions of the electromagnetic spectrum
unutilized. Here, we synthesize green-excited fluorescent and fluorogenic
analogues of the classic fluorescein and rhodamine 110 fluorophores
by replacement of the xanthene oxygen with a quaternary carbon. These
anthracenyl “carbofluorescein” and “carborhodamine
110” fluorophores exhibit excellent fluorescent properties
and can be masked with enzyme- and photolabile groups to prepare high-contrast
fluorogenic molecules useful for live cell imaging experiments and
super-resolution microscopy. Our divergent approach to these red-shifted
dye scaffolds will enable the preparation of numerous novel fluorogenic
probes with high biological utility.
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Affiliation(s)
- Jonathan B. Grimm
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, 20147, United
States
| | - Andrew J. Sung
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, 20147, United
States
| | - Wesley R. Legant
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, 20147, United
States
| | - Phuson Hulamm
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, 20147, United
States
| | - Sylwia M. Matlosz
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, 20147, United
States
| | - Eric Betzig
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, 20147, United
States
| | - Luke D. Lavis
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, 20147, United
States
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91
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Klán P, Šolomek T, Bochet CG, Blanc A, Givens R, Rubina M, Popik V, Kostikov A, Wirz J. Photoremovable protecting groups in chemistry and biology: reaction mechanisms and efficacy. Chem Rev 2013; 113:119-91. [PMID: 23256727 PMCID: PMC3557858 DOI: 10.1021/cr300177k] [Citation(s) in RCA: 1248] [Impact Index Per Article: 113.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Indexed: 02/06/2023]
Affiliation(s)
- Petr Klán
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
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92
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Socher E, Grossmann TN. Chemical biology 2012: from drug targets to biological systems and back. Chembiochem 2013. [PMID: 23184865 DOI: 10.1002/cbic.201200697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Multiple sites sharing a common target: This year's EMBO conference on chemical biology encouraged over 340 researchers to come to Heidelberg, Germany, and discuss the use of diverse chemical strategies and tools to investigate biological questions and better understand cellular processes.
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Affiliation(s)
- Elke Socher
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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93
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The chemistry of small-molecule fluorogenic probes. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 113:1-34. [PMID: 23244787 DOI: 10.1016/b978-0-12-386932-6.00001-6] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Chemical fluorophores find wide use in biology to detect and visualize different phenomena. A key advantage of small-molecule dyes is the ability to construct compounds where fluorescence is activated by chemical or biochemical processes. Fluorogenic molecules, in which fluorescence is activated by enzymatic activity, light, or environmental changes, enable advanced bioassays and sophisticated imaging experiments. Here, we detail the collection of fluorophores and highlight both general strategies and unique approaches that are employed to control fluorescence using chemistry.
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94
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95
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Abstract
Photoactivatable fluorophores switch from a nonemissive to an emissive state upon illumination at an activating wavelength and then emit after irradiation at an exciting wavelength. The interplay of such activation and excitation events can be exploited to switch fluorescence on in a defined region of space at a given interval of time. In turn, the spatiotemporal control of fluorescence translates into the opportunity to implement imaging and spectroscopic schemes that are not possible with conventional fluorophores. Specifically, photoactivatable fluorophores permit the monitoring of dynamic processes in real time as well as the reconstruction of images with subdiffraction resolution. These promising applications can have a significant impact on the characterization of the structures and functions of biomolecular systems. As a result, strategies to implement mechanisms for fluorescence photoactivation with synthetic fluorophores are particularly valuable. In fact, a number of versatile operating principles have already been identified to activate the fluorescence of numerous members of the main families of synthetic dyes. These methods are based on either the irreversible cleavage of covalent bonds or the reversible opening and closing of rings. This paper overviews the fundamental mechanisms that govern the behavior of these photoresponsive systems, illustrates structural designs for fluorescence photoactivation, and provides representative examples of photoactivatable fluorophores in actions.
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Affiliation(s)
- Françisco M. Raymo
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146-0431, USA
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96
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Raymo FM. Photoactivatable Synthetic Dyes for Fluorescence Imaging at the Nanoscale. J Phys Chem Lett 2012; 3:2379-2385. [PMID: 26292118 DOI: 10.1021/jz301021e] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The transition from conventional to photoactivatable fluorophores can bring the resolution of fluorescence images from the micrometer to the nanometer level. Indeed, fluorescence photoactivation can overcome the limitations that diffraction imposes on the resolution of optical microscopes. Specifically, distinct fluorophores positioned within the same subdiffraction volume can be resolved only if their emissions are activated independently at different intervals of time. Under these conditions, the sequential localization of multiple probes permits the reconstruction of images with a spatial resolution that is otherwise impossible to achieve with conventional fluorophores. The irreversible photolysis of protecting groups or the reversible transformations of photochromic compounds can be employed to control the emission of appropriate fluorescent chromophores and allow the implementation of these ingenious operating principles for superresolution imaging. Such molecular constructs enable the spatiotemporal control that is required to avoid diffraction and can become invaluable analytical tools for the optical visualization of biological specimens and nanostructured materials with unprecedented resolution.
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Affiliation(s)
- Françisco M Raymo
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146-0431, United States
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97
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Correlative 3D superresolution fluorescence and electron microscopy reveal the relationship of mitochondrial nucleoids to membranes. Proc Natl Acad Sci U S A 2012; 109:6136-41. [PMID: 22474357 DOI: 10.1073/pnas.1121558109] [Citation(s) in RCA: 174] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Microscopic images of specific proteins in their cellular context yield important insights into biological processes and cellular architecture. The advent of superresolution optical microscopy techniques provides the possibility to augment EM with nanometer-resolution fluorescence microscopy to access the precise location of proteins in the context of cellular ultrastructure. Unfortunately, efforts to combine superresolution fluorescence and EM have been stymied by the divergent and incompatible sample preparation protocols of the two methods. Here, we describe a protocol that preserves both the delicate photoactivatable fluorescent protein labels essential for superresolution microscopy and the fine ultrastructural context of EM. This preparation enables direct 3D imaging in 500- to 750-nm sections with interferometric photoactivatable localization microscopy followed by scanning EM images generated by focused ion beam ablation. We use this process to "colorize" detailed EM images of the mitochondrion with the position of labeled proteins. The approach presented here has provided a new level of definition of the in vivo nature of organization of mitochondrial nucleoids, and we expect this straightforward method to be applicable to many other biological questions that can be answered by direct imaging.
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98
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Banala S, Maurel D, Manley S, Johnsson K. A caged, localizable rhodamine derivative for superresolution microscopy. ACS Chem Biol 2012; 7:289-93. [PMID: 22026407 DOI: 10.1021/cb2002889] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A caged rhodamine 110 derivative for the specific labeling of SNAP-tag fusion proteins is introduced. The caged rhodamine 110 derivative permits the labeling of cell surface proteins in living cells and of intracellular proteins in fixed cells. The probe requires only a single caging group to maintain the fluorophore in a non-fluorescent state and becomes highly fluorescent after uncaging. The high contrast ratio is confirmed both in bulk and at the single molecule level. This property, together with its high photon yield makes it an excellent dye for photoactivated localization microscopy (PALM), as we demonstrate here.
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Affiliation(s)
- Sambashiva Banala
- Institute
of Chemical Sciences and Engineering and ‡Laboratory of Experimental Biophysics, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Damien Maurel
- Institute
of Chemical Sciences and Engineering and ‡Laboratory of Experimental Biophysics, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Suliana Manley
- Institute
of Chemical Sciences and Engineering and ‡Laboratory of Experimental Biophysics, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Kai Johnsson
- Institute
of Chemical Sciences and Engineering and ‡Laboratory of Experimental Biophysics, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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99
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Grimm JB, Lavis LD. Synthesis of rhodamines from fluoresceins using Pd-catalyzed C-N cross-coupling. Org Lett 2011; 13:6354-7. [PMID: 22091952 PMCID: PMC3235915 DOI: 10.1021/ol202618t] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A unified, convenient, and efficient strategy for the preparation of rhodamines and N,N'-diacylated rhodamines has been developed. Fluorescein ditriflates were found to undergo palladium-catalyzed C-N cross-coupling with amines, amides, carbamates, and other nitrogen nucleophiles to provide direct access to known and novel rhodamine derivatives, including fluorescent dyes, quenchers, and latent fluorophores.
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Affiliation(s)
- Jonathan B Grimm
- Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, USA
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