1
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Chen S, Wang J, Guan D, Tan B, Zhai T, Yang L, Han Y, Liu Y, Liu Q, Zhang Y. Near-Infrared Spontaneously Blinking Fluorophores for Live Cell Super-Resolution Imaging with Minimized Phototoxicity. Anal Chem 2024; 96:10860-10869. [PMID: 38889184 DOI: 10.1021/acs.analchem.4c02445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Single-molecule localization microscopy (SMLM) requires high-intensity laser irradiation, typically exceeding kW/cm2, to yield a sufficient photon count. However, this intense visible light exposure incurs substantial cellular toxicity, hindering its use in living cells. Here, we developed a class of near-infrared (NIR) spontaneously blinking fluorophores for SMLM. These NIR fluorophores are a combination of rhodamine spirolactams and merocyanine derivatives, where the rhodamine spirolactam component converts between a bright and dark state based on pH-dependent spirocyclization and merocyanine derivatives shift the excitation wavelength into the infrared. Single-molecule characterizations demonstrated their potential for SMLM. At a moderate power density of 3.93 kW/cm2, these probes exhibit duty cycle as low as 0.18% and an emission rate as high as 26,700 photons/s. Phototoxicity assessment under single-molecule imaging conditions reveals that NIR illumination (721 nm) minimizes harm to living cells. Employing these NIR fluorophores, we successfully captured time-lapse super-resolution tracking of mitochondria at a Fourier ring correlation (FRC) resolution of 69.4 nm and reconstructed the ultrastructures of endoplasmic reticulum (ER) in living cells.
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Affiliation(s)
- Song Chen
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Jing Wang
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Daoming Guan
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Baojin Tan
- School of Engineering, China Pharmaceutical University, Nanjing 211198, China
| | - Tianli Zhai
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Lu Yang
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Yuheng Han
- School of Engineering, China Pharmaceutical University, Nanjing 211198, China
| | - Yi Liu
- School of Engineering, China Pharmaceutical University, Nanjing 211198, China
| | - Qian Liu
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Yunxiang Zhang
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
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2
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Ghasemi S, Shamsabadi M, Olesund A, Najera F, Erbs Hillers-Bendtsen A, Edhborg F, Aslam AS, Larsson W, Wang Z, Amombo Noa FM, Salthouse RJ, Öhrström L, Hölzel H, Perez-Inestrosa E, Mikkelsen KV, Hanrieder J, Albinsson B, Dreos A, Moth-Poulsen K. Pyrene Functionalized Norbornadiene-Quadricyclane Fluorescent Photoswitches: Characterization of their Spectral Properties and Application in Imaging of Amyloid Beta Plaques. Chemistry 2024; 30:e202400322. [PMID: 38629212 DOI: 10.1002/chem.202400322] [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: 01/26/2024] [Indexed: 05/23/2024]
Abstract
This study presents the synthesis and characterization of two fluorescent norbornadiene (NBD) photoswitches, each incorporating two conjugated pyrene units. Expanding on the limited repertoire of reported photoswitchable fluorescent NBDs, we explore their properties with a focus on applications in bioimaging of amyloid beta (Aβ) plaques. While the fluorescence emission of the NBD decreases upon photoisomerization, aligning with what has been previously reported, for the first time we observed luminescence after irradiation of the quadricyclane (QC) isomer. We deduce how the observed emission is induced by photoisomerization to the excited state of the parent isomer (NBD) which is then the emitting species. Thorough characterizations including NMR, UV-Vis, fluorescence, X-ray structural analysis and density functional theory (DFT) calculations provide a comprehensive understanding of these systems. Notably, one NBD-QC system exhibits exceptional durability. Additionally, these molecules serve as effective fluorescent stains targeting Aβ plaques in situ, with observed NBD/QC switching within the plaques. Molecular docking simulations explore NBD interactions with amyloid, unveiling novel binding modes. These insights mark a crucial advancement in the comprehension and design of future photochromic NBDs for bioimaging applications and beyond, emphasizing their potential in studying and addressing protein aggregates.
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Affiliation(s)
- Shima Ghasemi
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Monika Shamsabadi
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Axel Olesund
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Francisco Najera
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma Bionand, 29590, Malaga, Spain
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Málaga, 29071, Málaga, Spain
| | | | - Fredrik Edhborg
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Adil S Aslam
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Wera Larsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Zhihang Wang
- Department of Materials Science and Metallurgy, University of Cambridge, 27 Charles Babbage Rd, Cambridge, CB3 0FS, U.K
| | - Francoise M Amombo Noa
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Rebecca Jane Salthouse
- Department of Chemical Engineering, Universitat Politècnica de Catalunya, EEBE, Eduard Maristany 10-14, 08019, Barcelona, Spain
| | - Lars Öhrström
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Helen Hölzel
- Department of Chemical Engineering, Universitat Politècnica de Catalunya, EEBE, Eduard Maristany 10-14, 08019, Barcelona, Spain
| | - E Perez-Inestrosa
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma Bionand, 29590, Malaga, Spain
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Málaga, 29071, Málaga, Spain
| | - Kurt V Mikkelsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen Ø, Denmark
| | - Jörg Hanrieder
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy, University of Gothenburg, 43180, Mölndal, Sweden
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Bo Albinsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Ambra Dreos
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma Bionand, 29590, Malaga, Spain
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy, University of Gothenburg, 43180, Mölndal, Sweden
| | - Kasper Moth-Poulsen
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
- The Institute of Materials Science of Barcelona, ICMAB-CSIC, Bellaterra, 08193, Barcelona, Spain
- Catalan Institution for Research & Advanced Studies, ICREA, Pg. Llu'ıs Companys 23, 08010, Barcelona, Spain
- Department of Chemical Engineering, Universitat Politècnica de Catalunya, EEBE, Eduard Maristany 10-14, 08019, Barcelona, Spain
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3
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Jradi FM, English BP, Brown TA, Aaron J, Khuon S, Galbraith JA, Galbraith CG, Lavis LD. Coumarin as a general switching auxiliary to prepare photochromic and spontaneously blinking fluorophores. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.12.593749. [PMID: 38766036 PMCID: PMC11100827 DOI: 10.1101/2024.05.12.593749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Single-molecule localization microscopy (SMLM) uses activatable or switchable fluorophores to create non-diffraction limited maps of molecular location in biological samples. Despite the utility of this imaging technique, the portfolio of appropriate labels for SMLM remains limited. Here, we describe a general strategy for the construction of "glitter bomb" labels by simply combining rhodamine and coumarin dyes though an amide bond. Condensation of the ortho-carboxyl group on the pendant phenyl ring of rhodamine dyes with a 7-aminocoumarin yields photochromic or spontaneously blinking fluorophores depending on the parent rhodamine structure. We apply this strategy to prepare labels useful super-resolution experiments in fixed cells using different attachment techniques. This general glitter bomb strategy should lead to improved labels for SMLM, ultimately enabling the creation of detailed molecular maps in biological samples.
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Affiliation(s)
- Fadi M. Jradi
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| | - Brian P. English
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| | - Timothy A. Brown
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| | - Jesse Aaron
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| | - Satya Khuon
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| | - James A. Galbraith
- Department of Biomedical Engineering and Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Catherine G. Galbraith
- Department of Biomedical Engineering and Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Luke D. Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
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4
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Turnbull JL, Miller EW. An open and shut case? Chemistry to control xanthene dyes. TRENDS IN CHEMISTRY 2024; 6:164-172. [PMID: 39036609 PMCID: PMC11257214 DOI: 10.1016/j.trechm.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
Fluorescent dyes are an indispensable part of the scientific enterprise. Xanthene-based fluorophores, like fluorescein and rhodamine, have been in continual use across numerous fields since their invention in the late 19th century. Modern methods to synthesize and expand the scope of xanthene dye chemistry have enabled new colors, enhanced stability, and improved brightness. Modifications to the 3-position of xanthene dyes have been, until recently, less well-explored. Here, we discuss how small changes to the identity of the substituent at the 3-position of fluoresceins and rhodamines can profoundly alter the properties of xanthene dyes, with the potential to unlock new applications at the interface of chemistry and biology.
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Affiliation(s)
- Joshua L. Turnbull
- Department of Chemistry, University of California, Berkeley, CA 94720, United States of America
| | - Evan W. Miller
- Department of Chemistry, University of California, Berkeley, CA 94720, United States of America
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, United States of America
- Helen Wills Neuroscience Institute University of California, Berkeley, CA 94720, United States of America
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5
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Olesińska-Mönch M, Deo C. Small-molecule photoswitches for fluorescence bioimaging: engineering and applications. Chem Commun (Camb) 2023; 59:660-669. [PMID: 36622788 DOI: 10.1039/d2cc05870g] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Fluorescence microscopy has revolutionised our understanding of biological systems, enabling the visualisation of biomolecular structures and dynamics in complex systems. The possibility to reversibly control the optical or biochemical properties of fluorophores can unlock advanced applications ranging from super-resolution microscopy to the design of multi-stimuli responsive and functional biosensors. In this Highlight, we review recent progress in small-molecule photoswitches applied to biological imaging with an emphasis on molecular engineering strategies and promising applications, while underlining the main challenges in their design and implementation.
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Affiliation(s)
- Magdalena Olesińska-Mönch
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany.
| | - Claire Deo
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany.
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6
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Püntener S, Rivera-Fuentes P. Single-Molecule Peptide Identification Using Fluorescence Blinking Fingerprints. J Am Chem Soc 2023; 145:1441-1447. [PMID: 36603184 PMCID: PMC9853850 DOI: 10.1021/jacs.2c12561] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The ability to identify peptides with single-molecule sensitivity would lead to next-generation proteomics methods for basic research and clinical applications. Existing single-molecule peptide sequencing methods can read some amino acid sequences, but they are limited in their ability to distinguish between similar amino acids or post-translational modifications. Here, we demonstrate that the fluorescence intermittency of a peptide labeled with a spontaneously blinking fluorophore contains information about the structure of the peptide. Using a deep learning algorithm, this single-molecule blinking pattern can be used to identify the peptide. This method can distinguish between peptides with different sequences, peptides with the same sequence but different phosphorylation patterns, and even peptides that differ only by the presence of epimerized residues. This study builds the foundation for a targeted proteomics method with single-molecule sensitivity.
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Affiliation(s)
- Salome Püntener
- Institute
of Chemical Sciences and Engineering, Ecole
Polytechnique Fédéral de Lausanne, CH-1015 Lausanne, Switzerland,Department
of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Pablo Rivera-Fuentes
- Institute
of Chemical Sciences and Engineering, Ecole
Polytechnique Fédéral de Lausanne, CH-1015 Lausanne, Switzerland,Department
of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland,
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7
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Martin MI, Pati AK, Abeywickrama CS, Bar S, Kilic Z, Altman RB, Blanchard SC. Leveraging Baird aromaticity for advancement of bioimaging applications. J PHYS ORG CHEM 2023; 36:e4449. [PMID: 36590885 PMCID: PMC9799245 DOI: 10.1002/poc.4449] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 02/01/2023]
Abstract
In this perspective, we highlight the recent progress in utilizing Baird aromatic species to improve fluorophore performance in microscopy and imaging applications. We specifically focus on the origins of the use of Baird aromaticity in fluorescence applications, the development of “self‐healing” fluorophores leveraging cyclooctatetraene’ Baird aromaticity, and where developments need to occur to optimize this technology.
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Affiliation(s)
- Maxwell I. Martin
- Department of Structural BiologySt. Jude Children's Research HospitalMemphisTNUSA
- Department of Chemical Biology & TherapeuticsSt. Jude Children's Research HospitalMemphisTNUSA
| | - Avik K. Pati
- Department of Structural BiologySt. Jude Children's Research HospitalMemphisTNUSA
| | - Chathura S. Abeywickrama
- Department of Structural BiologySt. Jude Children's Research HospitalMemphisTNUSA
- Department of Chemical Biology & TherapeuticsSt. Jude Children's Research HospitalMemphisTNUSA
| | - Sukanta Bar
- Department of Structural BiologySt. Jude Children's Research HospitalMemphisTNUSA
- Department of Chemical Biology & TherapeuticsSt. Jude Children's Research HospitalMemphisTNUSA
| | - Zeliha Kilic
- Department of Structural BiologySt. Jude Children's Research HospitalMemphisTNUSA
| | - Roger B. Altman
- Department of Structural BiologySt. Jude Children's Research HospitalMemphisTNUSA
- Department of Chemical Biology & TherapeuticsSt. Jude Children's Research HospitalMemphisTNUSA
| | - Scott C. Blanchard
- Department of Structural BiologySt. Jude Children's Research HospitalMemphisTNUSA
- Department of Chemical Biology & TherapeuticsSt. Jude Children's Research HospitalMemphisTNUSA
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8
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Sanders EW, Carr AR, Bruggeman E, Körbel M, Benaissa SI, Donat RF, Santos AM, McColl J, O'Holleran K, Klenerman D, Davis SJ, Lee SF, Ponjavic A. resPAINT: Accelerating Volumetric Super-Resolution Localisation Microscopy by Active Control of Probe Emission. Angew Chem Int Ed Engl 2022; 61:e202206919. [PMID: 35876263 DOI: 10.1002/anie.202206919] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Indexed: 01/07/2023]
Abstract
Points for accumulation in nanoscale topography (PAINT) allows practically unlimited measurements in localisation microscopy but is limited by background fluorescence at high probe concentrations, especially in volumetric imaging. We present reservoir-PAINT (resPAINT), which combines PAINT and active control of probe photophysics. In resPAINT, an activatable probe "reservoir" accumulates on target, enabling a 50-fold increase in localisation rate versus conventional PAINT, without compromising contrast. By combining resPAINT with large depth-of-field microscopy, we demonstrate super-resolution imaging of entire cell surfaces. We generalise the approach by implementing various switching strategies and 3D imaging techniques. Finally, we use resPAINT with a Fab to image membrane proteins, extending the operating regime of PAINT to include a wider range of biological interactions.
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Affiliation(s)
- Edward W Sanders
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Alexander R Carr
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Ezra Bruggeman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Markus Körbel
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Sarah I Benaissa
- Cambridge Advanced Imaging Centre, University of Cambridge, Cambridge, CB2 3DY, UK
| | - Robert F Donat
- Radcliffe Department of Medicine and United Kingdom Medical Research Council Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Ana M Santos
- Radcliffe Department of Medicine and United Kingdom Medical Research Council Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - James McColl
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Kevin O'Holleran
- Cambridge Advanced Imaging Centre, University of Cambridge, Cambridge, CB2 3DY, UK
| | - David Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Simon J Davis
- Radcliffe Department of Medicine and United Kingdom Medical Research Council Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Steven F Lee
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Aleks Ponjavic
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.,School of Physics and Astronomy, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.,School of Food Science and Nutrition, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
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9
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Sanders EW, Carr AR, Bruggeman E, Körbel M, Benaissa SI, Donat RF, Santos AM, McColl J, O'Holleran K, Klenerman D, Davis SJ, Lee SF, Ponjavic A. resPAINT: Accelerating Volumetric Super-Resolution Localisation Microscopy by Active Control of Probe Emission. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202206919. [PMID: 38505515 PMCID: PMC10946633 DOI: 10.1002/ange.202206919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Indexed: 03/21/2024]
Abstract
Points for accumulation in nanoscale topography (PAINT) allows practically unlimited measurements in localisation microscopy but is limited by background fluorescence at high probe concentrations, especially in volumetric imaging. We present reservoir-PAINT (resPAINT), which combines PAINT and active control of probe photophysics. In resPAINT, an activatable probe "reservoir" accumulates on target, enabling a 50-fold increase in localisation rate versus conventional PAINT, without compromising contrast. By combining resPAINT with large depth-of-field microscopy, we demonstrate super-resolution imaging of entire cell surfaces. We generalise the approach by implementing various switching strategies and 3D imaging techniques. Finally, we use resPAINT with a Fab to image membrane proteins, extending the operating regime of PAINT to include a wider range of biological interactions.
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Affiliation(s)
- Edward W. Sanders
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeCB2 1EWUK
| | - Alexander R. Carr
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeCB2 1EWUK
| | - Ezra Bruggeman
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeCB2 1EWUK
| | - Markus Körbel
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeCB2 1EWUK
| | - Sarah I. Benaissa
- Cambridge Advanced Imaging CentreUniversity of CambridgeCambridgeCB2 3DYUK
| | - Robert F. Donat
- Radcliffe Department of Medicine and United Kingdom Medical Research Council Human Immunology UnitJohn Radcliffe HospitalUniversity of OxfordOxfordOX3 9DSUK
| | - Ana M. Santos
- Radcliffe Department of Medicine and United Kingdom Medical Research Council Human Immunology UnitJohn Radcliffe HospitalUniversity of OxfordOxfordOX3 9DSUK
| | - James McColl
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeCB2 1EWUK
| | - Kevin O'Holleran
- Cambridge Advanced Imaging CentreUniversity of CambridgeCambridgeCB2 3DYUK
| | - David Klenerman
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeCB2 1EWUK
| | - Simon J. Davis
- Radcliffe Department of Medicine and United Kingdom Medical Research Council Human Immunology UnitJohn Radcliffe HospitalUniversity of OxfordOxfordOX3 9DSUK
| | - Steven F. Lee
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeCB2 1EWUK
| | - Aleks Ponjavic
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeCB2 1EWUK
- School of Physics and AstronomyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- School of Food Science and NutritionUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
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10
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Murali M, Murali VP, Joseph MM, Rajan S, Maiti KK. Elucidating cell surface glycan imbalance through SERS guided metabolic glycan labelling: An appraisal of metastatic potential in cancer cells. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 234:112506. [PMID: 35785648 DOI: 10.1016/j.jphotobiol.2022.112506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/14/2022] [Accepted: 06/25/2022] [Indexed: 06/15/2023]
Abstract
The intrinsic complexities of cell-surface glycans impede tracking the metabolic changes in cells. By coupling metabolic glycan labelling (MGL) and surface-enhanced Raman scattering (SERS), we employed the MGL-SERS strategy to elucidate the differential glycosylation pattern in cancer cell lines. Herein, for the first time, we are reporting an N-alkyl derivative of glucosamine (GlcNPhAlk) as a glycan labelling precursor. The extent of labelling was assessed by utilizing Raman imaging and verified by complementary fluorescence and Western blot analysis. MGL-SERS technique was implemented for a comparative evaluation of cell surface glycan imbalance in different cancer cells wherein a linear relationship between glycan expression and metastatic potential was established. Further, the effect of sialyltransferase inhibitor, P-3Fax-Neu5Ac, on metabolic labelling of GlcNPhAlk proved the incorporation of GlcNPhAlk to the terminal glycans through the sialic acid biosynthetic pathway. Hence, this methodology unveils the phenomenon of metastatic progression in cancer cells with inherent glycosylation-related dysplasia.
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Affiliation(s)
- Madhukrishnan Murali
- Chemical Sciences & Technology Division (CSTD), Organic Chemistry Section, CSIR- National Institute for Interdisciplinary Science & Technology (CSIR-NIIST), Industrial Estate, Pappanamcode, Thiruvananthapuram 695019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Vishnu Priya Murali
- Chemical Sciences & Technology Division (CSTD), Organic Chemistry Section, CSIR- National Institute for Interdisciplinary Science & Technology (CSIR-NIIST), Industrial Estate, Pappanamcode, Thiruvananthapuram 695019, Kerala, India
| | - Manu M Joseph
- Chemical Sciences & Technology Division (CSTD), Organic Chemistry Section, CSIR- National Institute for Interdisciplinary Science & Technology (CSIR-NIIST), Industrial Estate, Pappanamcode, Thiruvananthapuram 695019, Kerala, India
| | - Soumya Rajan
- Government College, Kasargod 671123, Kerala, India
| | - Kaustabh Kumar Maiti
- Chemical Sciences & Technology Division (CSTD), Organic Chemistry Section, CSIR- National Institute for Interdisciplinary Science & Technology (CSIR-NIIST), Industrial Estate, Pappanamcode, Thiruvananthapuram 695019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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11
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Stratton BFC, Pierre AJ, Riser EA, Grinalds NJ, Edwards CW, Wohlwend AM, Bauer JS, Spera RJ, Pferdmenges LS, Griffith KM, Hunter BW, Bobadova-Parvanova P, Day CS, Lundin PM, Fogarty KH. Synthesis and Optical Characterization of a Rhodamine B Spirolactam Dimer. J Phys Chem A 2022; 126:4211-4220. [PMID: 35749658 DOI: 10.1021/acs.jpca.2c02665] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amide derivatives of xanthene dyes such as rhodamine B are useful in a variety of sensing applications due to their colorimetric responses to stimuli such as acidity changes and UV light. The optical properties of these molecules can be influenced by intermolecular associations into dimeric structures, but the exact impact can be hard to predict. We have designed a covalently linked intramolecular dimer of the dye rhodamine B utilizing p-phenylenediamine to link the two dyes via amide bonds. The doubly closed spirolactam version of this dimer, RSL2, is isolated as a colorless solid. Under acidic conditions or UV exposure, RSL2 solutions develop a pink color that is expected for the ring-opened form of the molecule. However, nuclear magnetic resonance (NMR) and single-crystal diffraction data show that the equilibrium still prefers the closed dimer state. Interestingly, the emission profile of RSL2 shows solvatochromic blue fluorescence. Control studies of model compounds with similar structural motifs do not display similar blue fluorescence, indicating that this optical behavior is unique to the dimeric form. This behavior may lend itself to applications of such xanthene dimers to more sophisticated sensors beyond those with traditional binary on/off fluorescence profiles.
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Affiliation(s)
- Brandy-Fey C Stratton
- Department of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Angelina J Pierre
- Department of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Elizabeth A Riser
- Department of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Nathan J Grinalds
- Department of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Charles W Edwards
- Department of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Anna M Wohlwend
- Department of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Jacob S Bauer
- Department of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Rachel J Spera
- Department of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Lauren S Pferdmenges
- Department of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Kaitlyn M Griffith
- Department of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Brandon W Hunter
- Department of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Petia Bobadova-Parvanova
- Department of Chemistry and Fermentation Sciences, Appalachian State University, Boone, North Carolina 28608, United States
| | - Cynthia S Day
- Department of Chemistry, Wake Forest University, Winston Salem, North Carolina 27109, United States
| | - Pamela M Lundin
- Department of Chemistry, High Point University, High Point, North Carolina 27268, United States
| | - Keir H Fogarty
- Department of Chemistry, High Point University, High Point, North Carolina 27268, United States
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12
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Ye Z, Zheng Y, Peng X, Xiao Y. Surpassing the Background Barrier for Multidimensional Single-Molecule Localization Super-Resolution Imaging: A Case of Lysosome-Exclusively Turn-on Probe. Anal Chem 2022; 94:7990-7995. [PMID: 35613079 DOI: 10.1021/acs.analchem.2c00987] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The background barrier restricts the dimensionality of live-cell single-molecule localization super-resolution imaging. Ideally, a probe exclusively turned on by its target, without any nonspecific fluorescence signals from off-target molecules, constitutes a practical solution to surpass this barrier. Yet, few such fluorophores have been developed. A lysosome with a unique acidic lumen was chosen as the target for demonstrating the concept advantage. A representative lyso-tracker Lyso-R (piperazine rhodamine) with high brightness has been spirocyclized with o-phenylenediamine to form Lyso-Ropa. This probe shifted its bright-dark spirocyclization balance to a strong acidity domain (pKa = -0.18). Consequently, under no-wash conditions, Lyso-Ropa showed almost undetectable background photons (only one-sixtieth of that of Lyso-R) in a neutral cellular environment, and it formed sparsely brightened molecules at a low ratio (∼1 × 10-3%) in lysosomes. This background-free probe enabled super-resolution imaging and modeling of live-cell lysosomes in four dimensions at 2 s resolution, with quantitative determination of lysosomal volume expansion and deformation at starvation. Our molecular approach sheds new light on surpassing the background barrier for multidimensional super-resolution imaging.
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Affiliation(s)
- Zhiwei Ye
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Ying Zheng
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Xiaojun Peng
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Yi Xiao
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
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13
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Mattedi F, Chennell G, Vagnoni A. Detailed Imaging of Mitochondrial Transport and Precise Manipulation of Mitochondrial Function with Genetically Encoded Photosensitizers in Adult Drosophila Neurons. Methods Mol Biol 2022; 2431:385-407. [PMID: 35412288 DOI: 10.1007/978-1-0716-1990-2_20] [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] [Indexed: 10/18/2022]
Abstract
Precise distribution of mitochondria is essential for maintaining neuronal homeostasis. Although detailed mechanisms governing the transport of mitochondria have emerged, it is still poorly understood how the regulation of transport is coordinated in space and time within the physiological context of an organism. How alteration in mitochondrial functionality may trigger changes in organellar dynamics also remains unclear in this context. Therefore, the use of genetically encoded tools to perturb mitochondrial functionality in real time would be desirable. Here we describe methods to interfere with mitochondrial function with high spatiotemporal precision with the use of photosensitizers in vivo in the intact wing nerve of adult Drosophila. We also provide details on how to visualize the transport of mitochondria and to improve the quality of the imaging to attain super-resolution in this tissue.
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Affiliation(s)
- Francesca Mattedi
- Department of Basic and Clinical Neurosciences, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - George Chennell
- Department of Basic and Clinical Neurosciences, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Wohl Cellular Imaging Centre, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Alessio Vagnoni
- Department of Basic and Clinical Neurosciences, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
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14
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Annuario E, Ng K, Vagnoni A. High-Resolution Imaging of Mitochondria and Mitochondrial Nucleoids in Differentiated SH-SY5Y Cells. Methods Mol Biol 2022; 2431:291-310. [PMID: 35412283 DOI: 10.1007/978-1-0716-1990-2_15] [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] [Indexed: 10/18/2022]
Abstract
Mitochondria are highly dynamic organelles which form intricate networks with complex dynamics. Mitochondrial transport and distribution are essential to ensure proper cell function, especially in cells with an extremely polarised morphology such as neurons. A layer of complexity is added when considering mitochondria have their own genome, packaged into nucleoids. Major mitochondrial morphological transitions, for example mitochondrial division, often occur in conjunction with mitochondrial DNA (mtDNA) replication and changes in the dynamic behaviour of the nucleoids. However, the relationship between mtDNA dynamics and mitochondrial motility in the processes of neurons has been largely overlooked. In this chapter, we describe a method for live imaging of mitochondria and nucleoids in differentiated SH-SY5Y cells by instant structured illumination microscopy (iSIM). We also include a detailed protocol for the differentiation of SH-SY5Y cells into cells with a pronounced neuronal-like morphology and show examples of coordinated mitochondrial and nucleoid motility in the long processes of these cells.
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Affiliation(s)
- Emily Annuario
- Department of Basic and Clinical Neurosciences, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Kristal Ng
- Department of Basic and Clinical Neurosciences, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Alessio Vagnoni
- Department of Basic and Clinical Neurosciences, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
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15
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Unsupervised selection of optimal single-molecule time series idealization criterion. Biophys J 2021; 120:4472-4483. [PMID: 34487708 PMCID: PMC8553667 DOI: 10.1016/j.bpj.2021.08.045] [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: 03/31/2021] [Revised: 07/22/2021] [Accepted: 08/31/2021] [Indexed: 11/30/2022] Open
Abstract
Single-molecule (SM) approaches have provided valuable mechanistic information on many biophysical systems. As technological advances lead to ever-larger data sets, tools for rapid analysis and identification of molecules exhibiting the behavior of interest are increasingly important. In many cases the underlying mechanism is unknown, making unsupervised techniques desirable. The divisive segmentation and clustering (DISC) algorithm is one such unsupervised method that idealizes noisy SM time series much faster than computationally intensive approaches without sacrificing accuracy. However, DISC relies on a user-selected objective criterion (OC) to guide its estimation of the ideal time series. Here, we explore how different OCs affect DISC’s performance for data typical of SM fluorescence imaging experiments. We find that OCs differing in their penalty for model complexity each optimize DISC’s performance for time series with different properties such as signal/noise and number of sample points. Using a machine learning approach, we generate a decision boundary that allows unsupervised selection of OCs based on the input time series to maximize performance for different types of data. This is particularly relevant for SM fluorescence data sets, which often have signal/noise near the derived decision boundary and include time series of nonuniform length because of stochastic bleaching. Our approach, AutoDISC, allows unsupervised per-molecule optimization of DISC, which will substantially assist in the rapid analysis of high-throughput SM data sets with noisy samples and nonuniform time windows.
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16
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Lardon N, Wang L, Tschanz A, Hoess P, Tran M, D'Este E, Ries J, Johnsson K. Systematic Tuning of Rhodamine Spirocyclization for Super-resolution Microscopy. J Am Chem Soc 2021; 143:14592-14600. [PMID: 34460256 DOI: 10.1021/jacs.1c05004] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Rhodamines are the most important class of fluorophores for applications in live-cell fluorescence microscopy. This is mainly because rhodamines exist in a dynamic equilibrium between a fluorescent zwitterion and a nonfluorescent but cell-permeable spirocyclic form. Different imaging applications require different positions of this dynamic equilibrium, and an adjustment of the equilibrium poses a challenge for the design of suitable probes. We describe here how the conversion of the ortho-carboxy moiety of a given rhodamine into substituted acyl benzenesulfonamides and alkylamides permits the systematic tuning of the equilibrium of spirocyclization with unprecedented accuracy and over a large range. This allows one to transform the same rhodamine into either a highly fluorogenic and cell-permeable probe for live-cell-stimulated emission depletion (STED) microscopy or a spontaneously blinking dye for single-molecule localization microscopy (SMLM). We used this approach to generate differently colored probes optimized for different labeling systems and imaging applications.
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Affiliation(s)
- Nicolas Lardon
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.,Faculty of Chemistry and Earth Sciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Lu Wang
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.,Key Laboratory of Smart Drug Delivery, Ministry of Education, School of Pharmacy, Fudan University, Zhangheng Road 826, 201203 Shanghai, China
| | - Aline Tschanz
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.,Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, 69120 Heidelberg, Germany
| | - Philipp Hoess
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.,Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, 69120 Heidelberg, Germany
| | - Mai Tran
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Elisa D'Este
- Optical Microscopy Facility, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Jonas Ries
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.,Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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17
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Wang K, Shao X, Tian Z, Liu L, Zhang C, Tan C, Zhang J, Ling P, Liu F, Chen Q, Diao J, Mao Z. A Continuous Add-On Probe Reveals the Nonlinear Enlargement of Mitochondria in Light-Activated Oncosis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2004566. [PMID: 34197052 PMCID: PMC8425930 DOI: 10.1002/advs.202004566] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 05/03/2021] [Indexed: 05/25/2023]
Abstract
Oncosis, depending on DNA damage and mitochondrial swelling, is an important approach for treating cancer and other diseases. However, little is known about the behavior of mitochondria during oncosis, due to the lack of probes for in situ visual illumination of the mitochondrial membrane and mtDNA. Herein, a mitochondrial lipid and mtDNA dual-labeled probe, MitoMN, and a continuous add-on assay, are designed to image the dynamic process of mitochondria in conditions that are unobservable with current mitochondrial probes. Meanwhile, the MitoMN can induce oncosis in a light-activated manner, which results in the enlargement of mitochondria and the death of cancer cells. Using structured illumination microscopy (SIM), MitoMN-stained mitochondria with a dual-color response reveals, for the first time, how swelled mitochondria interacts and fuses with each other for a nonlinear enlargement to accelerate oncosis into an irreversible stage. With this sign of irreversible oncosis revealed by MitoMN, oncosis can be segregated into three stages, including before oncosis, initial oncosis, and accelerated oncosis.
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Affiliation(s)
- Kang‐Nan Wang
- MOE Key Laboratory of Bioinorganic and Synthetic ChemistrySchool of ChemistryState Key Laboratory of Oncology in South ChinaSun Yat‐Sen UniversityGuangzhou510275P. R. China
| | - Xintian Shao
- Institute of Materia MedicaShandong First Medical University & Shandong Academy of Medical SciencesJinan250000P. R. China
- Department of Cancer BiologyUniversity of Cincinnati College of MedicineCincinnati45267USA
- Shandong Academy of Pharmaceutical ScienceKey Laboratory of BiopharmaceuticalsEngineering Laboratory of Polysaccharide DrugsNational‐Local Joint Engineering Laboratory of Polysaccharide DrugsJinan250101P. R. China
| | - Zhiqi Tian
- Department of Molecular Genetics, Biochemistry, and MicrobiologyUniversity of Cincinnati College of MedicineCincinnati45267USA
| | - Liu‐Yi Liu
- MOE Key Laboratory of Bioinorganic and Synthetic ChemistrySchool of ChemistryState Key Laboratory of Oncology in South ChinaSun Yat‐Sen UniversityGuangzhou510275P. R. China
| | - Chengying Zhang
- Institute of Materia MedicaShandong First Medical University & Shandong Academy of Medical SciencesJinan250000P. R. China
- Shandong Academy of Pharmaceutical ScienceKey Laboratory of BiopharmaceuticalsEngineering Laboratory of Polysaccharide DrugsNational‐Local Joint Engineering Laboratory of Polysaccharide DrugsJinan250101P. R. China
- School of Pharmaceutical SciencesShandong UniversityJinan250101P. R. China
| | - Cai‐Ping Tan
- MOE Key Laboratory of Bioinorganic and Synthetic ChemistrySchool of ChemistryState Key Laboratory of Oncology in South ChinaSun Yat‐Sen UniversityGuangzhou510275P. R. China
| | - Jie Zhang
- Advanced Medical Research Institute/Translational Medicine Core Facility of Advanced Medical Research InstituteShandong UniversityJinan250101P. R. China
| | - Peixue Ling
- Shandong Academy of Pharmaceutical ScienceKey Laboratory of BiopharmaceuticalsEngineering Laboratory of Polysaccharide DrugsNational‐Local Joint Engineering Laboratory of Polysaccharide DrugsJinan250101P. R. China
- School of Pharmaceutical SciencesShandong UniversityJinan250101P. R. China
| | - Fei Liu
- Shandong Academy of Pharmaceutical ScienceKey Laboratory of BiopharmaceuticalsEngineering Laboratory of Polysaccharide DrugsNational‐Local Joint Engineering Laboratory of Polysaccharide DrugsJinan250101P. R. China
- School of Pharmaceutical SciencesShandong UniversityJinan250101P. R. China
| | - Qixin Chen
- Institute of Materia MedicaShandong First Medical University & Shandong Academy of Medical SciencesJinan250000P. R. China
- Department of Cancer BiologyUniversity of Cincinnati College of MedicineCincinnati45267USA
- Shandong Academy of Pharmaceutical ScienceKey Laboratory of BiopharmaceuticalsEngineering Laboratory of Polysaccharide DrugsNational‐Local Joint Engineering Laboratory of Polysaccharide DrugsJinan250101P. R. China
| | - Jiajie Diao
- Department of Cancer BiologyUniversity of Cincinnati College of MedicineCincinnati45267USA
| | - Zong‐Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic ChemistrySchool of ChemistryState Key Laboratory of Oncology in South ChinaSun Yat‐Sen UniversityGuangzhou510275P. R. China
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18
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Tyson J, Hu K, Zheng S, Kidd P, Dadina N, Chu L, Toomre D, Bewersdorf J, Schepartz A. Extremely Bright, Near-IR Emitting Spontaneously Blinking Fluorophores Enable Ratiometric Multicolor Nanoscopy in Live Cells. ACS CENTRAL SCIENCE 2021; 7:1419-1426. [PMID: 34471685 PMCID: PMC8393207 DOI: 10.1021/acscentsci.1c00670] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Indexed: 05/16/2023]
Abstract
New bright, photostable, emission-orthogonal fluorophores that blink without toxic additives are needed to enable multicolor, live-cell, single-molecule localization microscopy (SMLM). Here we report the design, synthesis, and biological evaluation of Yale676sb, a photostable, near-IR-emitting fluorophore that achieves these goals in the context of an exceptional quantum yield (0.59). When used alongside HMSiR, Yale676sb enables simultaneous, live-cell, two-color SMLM of two intracellular organelles (ER + mitochondria) with only a single laser and no chemical additives.
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Affiliation(s)
- Jonathan Tyson
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Kevin Hu
- Department
of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, United States
- Department
of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, United States
| | - Shuai Zheng
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Phylicia Kidd
- Department
of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, United States
| | - Neville Dadina
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Ling Chu
- Department
of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, United States
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Derek Toomre
- Department
of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, United States
- Nanobiology
Institute, Yale University, West Haven, Connecticut 06516, United States
| | - Joerg Bewersdorf
- Department
of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, United States
- Department
of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, United States
- Kavli
Institute for Neuroscience, Yale School
of Medicine, New Haven, Connecticut 06510, United States
- Nanobiology
Institute, Yale University, West Haven, Connecticut 06516, United States
| | - Alanna Schepartz
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Molecular and Cellular Biology, University
of California, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Department
of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, United States
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19
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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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20
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Li W, Pan W, Huang M, Yang Z, He Y, Zhang W, Zhang J, Gu Z, Zhang D, Yan W, Qu J. Disulfide-Reduction-Triggered Spontaneous Photoblinking Cy5 Probe for Nanoscopic Imaging of Mitochondrial Dynamics in Live Cells. Anal Chem 2021; 93:2596-2602. [PMID: 33464055 DOI: 10.1021/acs.analchem.0c04658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mitochondria are highly dynamic organelles with interconnected tubule structures that are sensitive to environmental stress and light illumination. Super-resolution optical imaging of mitochondrial dynamics is of significance for understanding such biological events. Direct stochastic optical reconstruction microscopy has the advantages of a high spatial resolution, low phototoxicity in live-cell imaging, and the capacity to incorporate smart fluorescent probes. However, dSTORM imaging in live cells is challenging because of the requirement for an imaging buffer and a low temporal resolution. In this work, we achieved dSTORM imaging of mitochondrial dynamics in live cells with a disulfide-substituted Cy5 probe without using any toxic imaging buffer. Under the illumination of very low laser power, the probe exhibited spontaneous photoblinking triggered by disulfide-bond reduction in mitochondria of live cells. The obtained thiol attacked nearby carbon to form a six-membered ring and the reversible opening/closing of the ring produced spontaneous photoblinking behavior. With this new STORM strategy, we achieved observation of mitochondrial dynamics for more than 3 min, which provides a promising tool for further studies of mitochondria with an ultrafine structure.
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Affiliation(s)
- Wen Li
- Center for Biomedical 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
| | - Wenhui Pan
- Center for Biomedical 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
| | - Meina Huang
- Center for Biomedical 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 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
| | - Ying He
- Center for Biomedical 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
| | - Wei Zhang
- Center for Biomedical 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
| | - Jianguo Zhang
- Center for Biomedical 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
| | - Zhenyu Gu
- Center for Biomedical 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
| | - Dan Zhang
- Center for Biomedical 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
| | - Wei Yan
- Center for Biomedical 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
| | - Junle Qu
- Center for Biomedical 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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21
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Affiliation(s)
- Keke Hu
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Tho D. K. Nguyen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Stefania Rabasco
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Pieter E. Oomen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
- ParaMedir B.V., 1e Energieweg 13, 9301 LK Roden, The Netherlands
| | - Andrew G. Ewing
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
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22
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Carvalhais LG, Martinho VC, Ferreiro E, Pinheiro PS. Unraveling the Nanoscopic Organization and Function of Central Mammalian Presynapses With Super-Resolution Microscopy. Front Neurosci 2021; 14:578409. [PMID: 33584169 PMCID: PMC7874199 DOI: 10.3389/fnins.2020.578409] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/03/2020] [Indexed: 12/22/2022] Open
Abstract
The complex, nanoscopic scale of neuronal function, taking place at dendritic spines, axon terminals, and other minuscule structures, cannot be adequately resolved using standard, diffraction-limited imaging techniques. The last couple of decades saw a rapid evolution of imaging methods that overcome the diffraction limit imposed by Abbe's principle. These techniques, including structured illumination microscopy (SIM), stimulated emission depletion (STED), photo-activated localization microscopy (PALM), and stochastic optical reconstruction microscopy (STORM), among others, have revolutionized our understanding of synapse biology. By exploiting the stochastic nature of fluorophore light/dark states or non-linearities in the interaction of fluorophores with light, by using modified illumination strategies that limit the excitation area, these methods can achieve spatial resolutions down to just a few tens of nm or less. Here, we review how these advanced imaging techniques have contributed to unprecedented insight into the nanoscopic organization and function of mammalian neuronal presynapses, revealing new organizational principles or lending support to existing views, while raising many important new questions. We further discuss recent technical refinements and newly developed tools that will continue to expand our ability to delve deeper into how synaptic function is orchestrated at the nanoscopic level.
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Affiliation(s)
- Lia G Carvalhais
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Vera C Martinho
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Elisabete Ferreiro
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Paulo S Pinheiro
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
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23
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G. Keller S, Kamiya M, Urano Y. Recent Progress in Small Spirocyclic, Xanthene-Based Fluorescent Probes. Molecules 2020; 25:E5964. [PMID: 33339370 PMCID: PMC7766215 DOI: 10.3390/molecules25245964] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 12/13/2022] Open
Abstract
The use of fluorescent probes in a multitude of applications is still an expanding field. This review covers the recent progress made in small molecular, spirocyclic xanthene-based probes containing different heteroatoms (e.g., oxygen, silicon, carbon) in position 10'. After a short introduction, we will focus on applications like the interaction of probes with enzymes and targeted labeling of organelles and proteins, detection of small molecules, as well as their use in therapeutics or diagnostics and super-resolution microscopy. Furthermore, the last part will summarize recent advances in the synthesis and understanding of their structure-behavior relationship including novel computational approaches.
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Affiliation(s)
- Sascha G. Keller
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (S.G.K.); (M.K.)
| | - Mako Kamiya
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (S.G.K.); (M.K.)
| | - Yasuteru Urano
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (S.G.K.); (M.K.)
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
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24
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Li B, Haris U, Aljowni M, Nakatsuka A, Patel SK, Lippert AR. Tuning the Photophysical Properties of Spirolactam Rhodamine Photoswitches. Isr J Chem 2020. [DOI: 10.1002/ijch.202000083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Bo Li
- Department of Chemistry Southern Methodist University 3215 Daniel Avenue Dallas TX 75206 USA
| | - Uroob Haris
- Department of Chemistry Southern Methodist University 3215 Daniel Avenue Dallas TX 75206 USA
| | - Maha Aljowni
- Department of Chemistry Southern Methodist University 3215 Daniel Avenue Dallas TX 75206 USA
| | - Andrew Nakatsuka
- Department of Chemistry Southern Methodist University 3215 Daniel Avenue Dallas TX 75206 USA
| | - Shreya K. Patel
- Department of Chemistry Southern Methodist University 3215 Daniel Avenue Dallas TX 75206 USA
- Department of Chemistry and Biochemistry University of California, Los Angeles 607 Charles E. Young Drive East Los Angeles CA 90095-1569 USA
| | - Alexander R. Lippert
- Department of Chemistry Southern Methodist University 3215 Daniel Avenue Dallas TX 75206 USA
- Center for Drug Discovery Design and Delivery (CD4) Southern Methodist University Dallas TX 75206 USA
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25
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Chai X, Han HH, Sedgwick AC, Li N, Zang Y, James TD, Zhang J, Hu XL, Yu Y, Li Y, Wang Y, Li J, He XP, Tian H. Photochromic Fluorescent Probe Strategy for the Super-resolution Imaging of Biologically Important Biomarkers. J Am Chem Soc 2020; 142:18005-18013. [DOI: 10.1021/jacs.0c05379] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xianzhi Chai
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Hai-Hao Han
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
- National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 189 Guo Shoujing Road, Shanghai 201203, P. R. China
| | - Adam C. Sedgwick
- Department of Chemistry, The University of Texas at Austin, 105 East 24th Street A5300, Austin, Texas 78712-1224, United States
| | - Na Li
- National Center for Protein Science Shanghai, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, P. R. China
| | - Yi Zang
- National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 189 Guo Shoujing Road, Shanghai 201203, P. R. China
| | - Tony D. James
- Department of Chemistry, University of Bath, Bath BA2 7AY, U.K
| | - Junji Zhang
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Xi-Le Hu
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Yang Yu
- National Center for Protein Science Shanghai, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, P. R. China
| | - Yao Li
- National Center for Protein Science Shanghai, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, P. R. China
| | - Yan Wang
- National Center for Protein Science Shanghai, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, P. R. China
| | - Jia Li
- National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 189 Guo Shoujing Road, Shanghai 201203, P. R. China
| | - Xiao-Peng He
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - He Tian
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
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26
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Liu S, Huh H, Lee SH, Huang F. Three-Dimensional Single-Molecule Localization Microscopy in Whole-Cell and Tissue Specimens. Annu Rev Biomed Eng 2020; 22:155-184. [PMID: 32243765 PMCID: PMC7430714 DOI: 10.1146/annurev-bioeng-060418-052203] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Super-resolution microscopy techniques are versatile and powerful tools for visualizing organelle structures, interactions, and protein functions in biomedical research. However, whole-cell and tissue specimens challenge the achievable resolution and depth of nanoscopy methods. We focus on three-dimensional single-molecule localization microscopy and review some of the major roadblocks and developing solutions to resolving thick volumes of cells and tissues at the nanoscale in three dimensions. These challenges include background fluorescence, system- and sample-induced aberrations, and information carried by photons, as well as drift correction, volume reconstruction, and photobleaching mitigation. We also highlight examples of innovations that have demonstrated significant breakthroughs in addressing the abovementioned challenges together with their core concepts as well as their trade-offs.
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Affiliation(s)
- Sheng Liu
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, USA;
| | - Hyun Huh
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Sang-Hyuk Lee
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, USA
- Department of Physics and Astronomy, Rutgers University, Piscataway, New Jersey 08854, USA;
| | - Fang Huang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, USA;
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, Indiana 47907, USA
- Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, USA
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27
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Zhang Y, Raymo FM. Photoactivatable fluorophores for single-molecule localization microscopy of live cells. Methods Appl Fluoresc 2020; 8:032002. [PMID: 32325443 DOI: 10.1088/2050-6120/ab8c5c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Photochemical reactions can be designed to convert either irreversibly or reversibly a nonemissive reactant into an emissive product. The irreversible disconnection of a photocleavable group from an emissive chromophore or the reversible interconversion of a photochromic component is generally exploited to implement these operating principles for fluorescence switching. In both instances, the interplay of activating radiation, to convert the nonemissive state into the emissive species, and exciting radiation, to produce fluorescence from the latter, can be exploited to switch fluorescence on in a given area of interest at a precise interval of time. Such a level of spatiotemporal control provides the opportunity to reconstruct sub-diffraction images with resolution at the nanometer level. Indeed, closely-spaced emitters can be switched on under photochemical control at distinct intervals of time and localized independently at the single-molecule level. In combination with appropriate intracellular targeting strategies, some of these photoactivatable fluorophores can be switched and localized inside live cells to permit the visualization of sub-cellular structures with a spatial resolution that would be impossible to achieve with conventional fluorophores. As a result, photoactivatable fluorophores can become invaluable probes for the implementation of super-resolution imaging schemes aimed at the elucidation of the fundamental factors controlling cellular functions at the molecular level.
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Affiliation(s)
- Yang Zhang
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, Coral Gables, FL, United States of America
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28
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Thiel Z, Nguyen J, Rivera‐Fuentes P. Genetically Encoded Activators of Small Molecules for Imaging and Drug Delivery. Angew Chem Int Ed Engl 2020; 59:7669-7677. [PMID: 31898373 PMCID: PMC7318188 DOI: 10.1002/anie.201915521] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Indexed: 12/30/2022]
Abstract
Chemical biologists have developed many tools based on genetically encoded macromolecules and small, synthetic compounds. The two different approaches are extremely useful, but they have inherent limitations. In this Minireview, we highlight examples of strategies that combine both concepts to tackle challenging problems in chemical biology. We discuss applications in imaging, with a focus on super-resolved techniques, and in probe and drug delivery. We propose future directions in this field, hoping to inspire chemical biologists to develop new combinations of synthetic and genetically encoded probes.
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Affiliation(s)
- Zacharias Thiel
- Institute of Chemical Sciences and EngineeringEPF LausanneCH C2 425, Station 61015LausanneSwitzerland
- Laboratory of Organic ChemistryETH ZurichVladimir-Prelog-Weg 38093ZurichSwitzerland
| | - Jade Nguyen
- Institute of Chemical Sciences and EngineeringEPF LausanneCH C2 425, Station 61015LausanneSwitzerland
- Laboratory of Organic ChemistryETH ZurichVladimir-Prelog-Weg 38093ZurichSwitzerland
| | - Pablo Rivera‐Fuentes
- Institute of Chemical Sciences and EngineeringEPF LausanneCH C2 425, Station 61015LausanneSwitzerland
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29
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Thiel Z, Nguyen J, Rivera‐Fuentes P. Genetically Encoded Activators of Small Molecules for Imaging and Drug Delivery. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Zacharias Thiel
- Institute of Chemical Sciences and Engineering EPF Lausanne CH C2 425, Station 6 1015 Lausanne Switzerland
- Laboratory of Organic Chemistry ETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Jade Nguyen
- Institute of Chemical Sciences and Engineering EPF Lausanne CH C2 425, Station 6 1015 Lausanne Switzerland
- Laboratory of Organic Chemistry ETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Pablo Rivera‐Fuentes
- Institute of Chemical Sciences and Engineering EPF Lausanne CH C2 425, Station 6 1015 Lausanne Switzerland
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30
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Tosheva KL, Yuan Y, Matos Pereira P, Culley S, Henriques R. Between life and death: strategies to reduce phototoxicity in super-resolution microscopy. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2020; 53:163001. [PMID: 33994582 PMCID: PMC8114953 DOI: 10.1088/1361-6463/ab6b95] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/01/2019] [Accepted: 01/14/2020] [Indexed: 05/23/2023]
Abstract
Super-resolution microscopy (SRM) enables non-invasive, molecule-specific imaging of the internal structure and dynamics of cells with sub-diffraction limit spatial resolution. One of its major limitations is the requirement for high-intensity illumination, generating considerable cellular phototoxicity. This factor considerably limits the capacity for live-cell observations, particularly for extended periods of time. Here, we give an overview of new developments in hardware, software and probe chemistry aiming to reduce phototoxicity. Additionally, we discuss how the choice of biological model and sample environment impacts the capacity for live-cell observations.
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Affiliation(s)
- Kalina L Tosheva
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Yue Yuan
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | | | - Siân Culley
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - Ricardo Henriques
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
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31
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Yin J, Jiao Y, Peng X, He H, Duan C. Ionic fluorescent sensor targeting receptor tyrosine kinases for biosystems imaging and application in flow cytometry. Biosens Bioelectron 2020; 153:112026. [PMID: 31989936 DOI: 10.1016/j.bios.2020.112026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 01/06/2020] [Accepted: 01/13/2020] [Indexed: 01/09/2023]
Abstract
Fluorescent imaging of receptor tyrosine kinases in living biosystems is an important means for the early diagnosis of cancer, herein an ionic fluorescent sensor (SNB) composed of targeting unit (sunitinib) and nile blue fluorophore linked via long flexible chain has been designed and evaluated. The SNB sensor exhibits distinct fluorescence responses to receptor tyrosine kinases derived from unfolding strategy and targeting ability, which were evaluated through 2D NMR analyses, optical studies, kinase activity assays. The SNB sensor has excellent membrane fluorescent imaging by electrostatic adsorption and can selectively insert into receptor tyrosine kinases domain pocket on the membrane of cancer cell lines. The SNB sensor has been successfully applied in flow cytometry for cell sorting and fluorescence imaging with tumor mouse model in vivo. The SNB senor may help transition the technology into a widely suitable tool for flow cytometry, imaging with confocal microscopes, whole animal imaging and possibly facilitating early diagnoses and treatment of cancer.
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Affiliation(s)
- Jiqiu Yin
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, 116024, China; College of Medical Laboratory, Dalian Medical University, Dalian, 116044, China
| | - Yang Jiao
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, 116024, China.
| | - Xiaojun Peng
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, 116024, China
| | - Haiyang He
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, 116024, China
| | - Chunying Duan
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, 116024, China.
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32
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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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33
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Qi Q, Chi W, Li Y, Qiao Q, Chen J, Miao L, Zhang Y, Li J, Ji W, Xu T, Liu X, Yoon J, Xu Z. A H-bond strategy to develop acid-resistant photoswitchable rhodamine spirolactams for super-resolution single-molecule localization microscopy. Chem Sci 2019; 10:4914-4922. [PMID: 31160962 PMCID: PMC6510312 DOI: 10.1039/c9sc01284b] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 04/04/2019] [Indexed: 01/04/2023] Open
Abstract
Rhodamine spirolactam based photoswitches have been extensively applied in super-resolution single-molecule localization microscopy (SMLM). However, the ring-opening reactions of spirolactams are cross-sensitive to acid, limiting their photoswitch use to neutral pH conditions. In addition, the ring-closing reactions of spirolactams are environment-sensitive and slow (up to hours), virtually making rhodamine spirolactams caged fluorescent dyes instead of reversible photoswitches in SMLM. Herein, by introducing hydrogen bonds to stabilize spirolactams, we report a series of acid-resistant rhodamine spirolactams with accelerated ring-closing reactions from fluorescent xanthyliums to non-fluorescent spirolactams, endowing them with good photoswitchable properties even in acidic environments. By further substitution of 6-phenylethynyl naphthalimide on the spirolactam, we shifted the photoactivation wavelength into the visible region (>400 nm). Subsequently, we have successfully applied these dyes in labeling and imaging the cell surface of Bacillus subtilis at pH 4.5 using SMLM.
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Affiliation(s)
- Qingkai Qi
- CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China .
| | - Weijie Chi
- Singapore University of Technology and Design , 8 Somapah Road , Singapore 487372 , Singapore .
| | - Yuanyuan Li
- National Laboratory of Biomacromolecules , Institute of Biophysics , Chinese Academy of Sciences , Beijing 100101 , China .
| | - Qinglong Qiao
- CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China .
| | - Jie Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China .
| | - Lu Miao
- CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China .
| | - Yi Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China .
| | - Jin Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China .
| | - Wei Ji
- National Laboratory of Biomacromolecules , Institute of Biophysics , Chinese Academy of Sciences , Beijing 100101 , China .
| | - Tao Xu
- National Laboratory of Biomacromolecules , Institute of Biophysics , Chinese Academy of Sciences , Beijing 100101 , China .
| | - Xiaogang Liu
- Singapore University of Technology and Design , 8 Somapah Road , Singapore 487372 , Singapore .
| | - Juyoung Yoon
- Department of Chemistry and Nano Science , Ewha Womans University , Seoul 120-750 , Korea .
| | - Zhaochao Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China .
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34
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Bypassing bleaching with fluxional fluorophores. Nat Methods 2019; 16:357. [PMID: 31040423 DOI: 10.1038/s41592-019-0402-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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