1
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Jantarug K, Tripathi V, Morin B, Iizuka A, Kuehl R, Morgenstern M, Clauss M, Khanna N, Bumann D, Rivera-Fuentes P. A Far-Red Fluorescent Probe to Visualize Gram-Positive Bacteria in Patient Samples. ACS Infect Dis 2024; 10:1545-1551. [PMID: 38632685 DOI: 10.1021/acsinfecdis.4c00060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Gram-positive bacteria, in particular Staphylococcus aureus (S. aureus), are the leading bacterial cause of death in high-income countries and can cause invasive infections at various body sites. These infections are associated with prolonged hospital stays, a large economic burden, considerable treatment failure, and high mortality rates. So far, there is only limited knowledge about the specific locations where S. aureus resides in the human body during various infections. Hence, the visualization of S. aureus holds significant importance in microbiological research. Herein, we report the development and validation of a far-red fluorescent probe to detect Gram-positive bacteria, with a focus on staphylococci, in human biopsies from deep-seated infections. This probe displays strong fluorescence and low background in human tissues, outperforming current tools for S. aureus detection. Several applications are demonstrated, including fixed- and live-cell imaging, flow cytometry, and super-resolution bacterial imaging.
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Affiliation(s)
| | | | - Benedict Morin
- Department of Biomedicine, University of Basel, Basel 4031, Switzerland
| | - Aya Iizuka
- Department of Biomedicine, University of Basel, Basel 4031, Switzerland
| | - Richard Kuehl
- Department of Biomedicine, University of Basel, Basel 4031, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel 4031, Switzerland
- Center for Musculoskeletal Infections (ZMSI), Department for Orthopaedics and Trauma Surgery, University Hospital Basel, Basel 4031, Switzerland
| | - Mario Morgenstern
- Center for Musculoskeletal Infections (ZMSI), Department for Orthopaedics and Trauma Surgery, University Hospital Basel, Basel 4031, Switzerland
| | - Martin Clauss
- Center for Musculoskeletal Infections (ZMSI), Department for Orthopaedics and Trauma Surgery, University Hospital Basel, Basel 4031, Switzerland
| | - Nina Khanna
- Department of Biomedicine, University of Basel, Basel 4031, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel 4031, Switzerland
- Department of Clinical Research, University Hospital of Basel, Basel 4031, Switzerland
| | - Dirk Bumann
- Biozentrum, University of Basel, Basel 4056, Switzerland
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2
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Martin A, Rivera-Fuentes P. Fluorogenic polymethine dyes by intramolecular cyclization. Curr Opin Chem Biol 2024; 80:102444. [PMID: 38520774 DOI: 10.1016/j.cbpa.2024.102444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/25/2024]
Abstract
Fluorescence imaging plays a pivotal role in the study of biological processes, and cell-permeable fluorogenic dyes are crucial to visualize intracellular structures with high specificity. Polymethine dyes are vitally important fluorophores in single-molecule localization microscopy and in vivo imaging, but their use in live cells has been limited by high background fluorescence and low membrane permeability. In this review, we summarize recent advances in the development of fluorogenic polymethine dyes via intramolecular cyclization. Finally, we offer an outlook on the prospects of fluorogenic polymethine dyes for bioimaging.
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Affiliation(s)
- Annabell Martin
- Department of Chemistry, University of Zurich, Zurich, Switzerland; École Polytechnique Fédérale de Lausanne, Institute of Chemical Sciences and Engineering, Lausanne, Switzerland
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3
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Martin A, Rivera-Fuentes P. A general strategy to develop fluorogenic polymethine dyes for bioimaging. Nat Chem 2024; 16:28-35. [PMID: 38012391 PMCID: PMC10774129 DOI: 10.1038/s41557-023-01367-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 10/12/2023] [Indexed: 11/29/2023]
Abstract
Fluorescence imaging is an invaluable tool to study biological processes and further progress depends on the development of advanced fluorogenic probes that reach intracellular targets and label them with high specificity. Excellent fluorogenic rhodamine dyes have been reported, but they often require long and low-yielding syntheses, and are spectrally limited to the visible range. Here we present a general strategy to transform polymethine compounds into fluorogenic dyes using an intramolecular ring-closure approach. We illustrate the generality of this method by creating both spontaneously blinking and no-wash, turn-on polymethine dyes with emissions across the visible and near-infrared spectrum. These probes are compatible with self-labelling proteins and small-molecule targeting ligands, and can be combined with rhodamine-based dyes for multicolour and fluorescence lifetime multiplexing imaging. This strategy provides access to bright, fluorogenic dyes that emit at wavelengths that are more red-shifted compared with those of existing rhodamine-based dyes.
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Affiliation(s)
- Annabell Martin
- Department of Chemistry, University of Zurich, Zurich, Switzerland
- École Polytechnique Fédérale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering, Lausanne, Switzerland
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4
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Sollier J, Basler M, Broz P, Dittrich PS, Drescher K, Egli A, Harms A, Hierlemann A, Hiller S, King CG, McKinney JD, Moran-Gilad J, Neher RA, Page MGP, Panke S, Persat A, Picotti P, Rentsch KM, Rivera-Fuentes P, Sauer U, Stolz D, Tschudin-Sutter S, van Delden C, van Nimwegen E, Veening JW, Zampieri M, Zinkernagel AS, Khanna N, Bumann D, Jenal U, Dehio C. Revitalizing antibiotic discovery and development through in vitro modelling of in-patient conditions. Nat Microbiol 2024; 9:1-3. [PMID: 38177300 DOI: 10.1038/s41564-023-01566-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Affiliation(s)
| | - Marek Basler
- Biozentrum, University of Basel, Basel, Switzerland
| | - Petr Broz
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Petra S Dittrich
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Adrian Egli
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Alexander Harms
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Andreas Hierlemann
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Carolyn G King
- Department of Biomedicine, University Basel, Basel, Switzerland
| | - John D McKinney
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Jacob Moran-Gilad
- Department of Health Policy and Management, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | | | - Sven Panke
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Alexandre Persat
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Paola Picotti
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | | | | | - Uwe Sauer
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Daiana Stolz
- Clinic of Respiratory Medicine and Pulmonary Cell Research, University Hospital Basel, Basel, Switzerland
- Department of Pneumology, University Medical Center, Freiburg, Germany
| | - Sarah Tschudin-Sutter
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
- Department of Clinical Research, University Hospital Basel, Basel, Switzerland
| | | | | | - Jan-Willem Veening
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Mattia Zampieri
- Department of Biomedicine, University Basel, Basel, Switzerland
| | - Annelies S Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Nina Khanna
- Department of Biomedicine, University Basel, Basel, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
- Department of Clinical Research, University Hospital Basel, Basel, Switzerland
| | - Dirk Bumann
- Biozentrum, University of Basel, Basel, Switzerland
| | - Urs Jenal
- Biozentrum, University of Basel, Basel, Switzerland
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5
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Emmert S, Quargnali G, Thallmair S, Rivera-Fuentes P. A locally activatable sensor for robust quantification of organellar glutathione. Nat Chem 2023; 15:1415-1421. [PMID: 37322101 PMCID: PMC10533397 DOI: 10.1038/s41557-023-01249-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/22/2023] [Indexed: 06/17/2023]
Abstract
Glutathione (GSH) is the main determinant of intracellular redox potential and participates in multiple cellular signalling pathways. Achieving a detailed understanding of intracellular GSH homeostasis depends on the development of tools to map GSH compartmentalization and intra-organelle fluctuations. Here we present a GSH-sensing platform for live-cell imaging, termed targetable ratiometric quantitative GSH (TRaQ-G). This chemogenetic sensor possesses a unique reactivity turn-on mechanism, ensuring that the small molecule is only sensitive to GSH in a desired location. Furthermore, TRaQ-G can be fused to a fluorescent protein to give a ratiometric response. Using TRaQ-G fused to a redox-insensitive fluorescent protein, we demonstrate that the nuclear and cytosolic GSH pools are independently regulated during cell proliferation. This sensor was used in combination with a redox-sensitive fluorescent protein to quantify redox potential and GSH concentration simultaneously in the endoplasmic reticulum. Finally, by exchanging the fluorescent protein, we created a near-infrared, targetable and quantitative GSH sensor.
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Affiliation(s)
- Sarah Emmert
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédéral de Lausanne, Lausanne, Switzerland
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Gianluca Quargnali
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédéral de Lausanne, Lausanne, Switzerland
| | | | - Pablo Rivera-Fuentes
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédéral de Lausanne, Lausanne, Switzerland.
- Department of Chemistry, University of Zurich, Zurich, Switzerland.
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6
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Yang X, Chen D, Sun Q, Wang Y, Xia Y, Yang J, Lin C, Dang X, Cen Z, Liang D, Wei R, Xu Z, Xi G, Xue G, Ye C, Wang LP, Zou P, Wang SQ, Rivera-Fuentes P, Püntener S, Chen Z, Liu Y, Zhang J, Zhao Y. A live-cell image-based machine learning strategy for reducing variability in PSC differentiation systems. Cell Discov 2023; 9:53. [PMID: 37280224 DOI: 10.1038/s41421-023-00543-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 03/13/2023] [Indexed: 06/08/2023] Open
Abstract
The differentiation of pluripotent stem cells (PSCs) into diverse functional cell types provides a promising solution to support drug discovery, disease modeling, and regenerative medicine. However, functional cell differentiation is currently limited by the substantial line-to-line and batch-to-batch variabilities, which severely impede the progress of scientific research and the manufacturing of cell products. For instance, PSC-to-cardiomyocyte (CM) differentiation is vulnerable to inappropriate doses of CHIR99021 (CHIR) that are applied in the initial stage of mesoderm differentiation. Here, by harnessing live-cell bright-field imaging and machine learning (ML), we realize real-time cell recognition in the entire differentiation process, e.g., CMs, cardiac progenitor cells (CPCs), PSC clones, and even misdifferentiated cells. This enables non-invasive prediction of differentiation efficiency, purification of ML-recognized CMs and CPCs for reducing cell contamination, early assessment of the CHIR dose for correcting the misdifferentiation trajectory, and evaluation of initial PSC colonies for controlling the start point of differentiation, all of which provide a more invulnerable differentiation method with resistance to variability. Moreover, with the established ML models as a readout for the chemical screen, we identify a CDK8 inhibitor that can further improve the cell resistance to the overdose of CHIR. Together, this study indicates that artificial intelligence is able to guide and iteratively optimize PSC differentiation to achieve consistently high efficiency across cell lines and batches, providing a better understanding and rational modulation of the differentiation process for functional cell manufacturing in biomedical applications.
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Affiliation(s)
- Xiaochun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, MOE Key Laboratory of Cell Proliferation and Differentiation, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Daichao Chen
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Qiushi Sun
- Beijing Key Lab of Traffic Data Analysis and Mining, School of Computer and Information Technology, Beijing Jiaotong University, Beijing, China
| | - Yao Wang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yu Xia
- College of Engineering, Peking University, Beijing, China
| | - Jinyu Yang
- College of Engineering, Peking University, Beijing, China
| | - Chang Lin
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China
| | - Xin Dang
- State Key Laboratory of Natural and Biomimetic Drugs, MOE Key Laboratory of Cell Proliferation and Differentiation, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Zimu Cen
- State Key Laboratory of Natural and Biomimetic Drugs, MOE Key Laboratory of Cell Proliferation and Differentiation, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Dongdong Liang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Rong Wei
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Ze Xu
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, China
| | - Guangyin Xi
- State Key Laboratory of Natural and Biomimetic Drugs, MOE Key Laboratory of Cell Proliferation and Differentiation, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Gang Xue
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Can Ye
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Li-Peng Wang
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, China
| | - Peng Zou
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Shi-Qiang Wang
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, China
| | | | - Salome Püntener
- Department of Chemistry, University of Zurich, Zurich, Switzerland
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédéral de Lausanne, Lausanne, Switzerland
| | - Zhixing Chen
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Yi Liu
- Beijing Key Lab of Traffic Data Analysis and Mining, School of Computer and Information Technology, Beijing Jiaotong University, Beijing, China.
| | - Jue Zhang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
- College of Engineering, Peking University, Beijing, China.
| | - Yang Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, MOE Key Laboratory of Cell Proliferation and Differentiation, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
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7
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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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8
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Eördögh Á, Martin A, Rivera-Fuentes P. Long‐Term, Single‐Molecule Imaging of Proteins in Live Cells with Photoregulated Fluxional Fluorophores. Chemistry 2022; 28:e202202832. [PMID: 36125781 PMCID: PMC10092635 DOI: 10.1002/chem.202202832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Indexed: 11/08/2022]
Abstract
Single-molecule localization microscopy (SMLM) can reveal nanometric details of biological samples, but its high phototoxicity hampers long-term imaging in live specimens. A significant part of this phototoxicity stems from repeated irradiations that are necessary for controlled switching of fluorophores to maintain the sparse labeling of the sample. Lower phototoxicity can be obtained using fluorophores that blink spontaneously, but controlling the density of single-molecule emitters is challenging. We recently developed photoregulated fluxional fluorophores (PFFs) that combine the benefits of spontaneously blinking dyes with photocontrol of emitter density. These dyes, however, were limited to imaging acidic organelles in live cells. Herein, we report a systematic study of PFFs that culminates in probes that are functional at physiological pH and operate at longer wavelengths than their predecessors. Moreover, these probes are compatible with HaloTag labeling, thus enabling timelapse, single-molecule imaging of specific protein targets for exceptionally long times.
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Affiliation(s)
- Ádám Eördögh
- University of Zurich Faculty of Science: Universitat Zurich Mathematisch-Naturwissenschaftliche Fakultat Chemistry SWITZERLAND
| | - Annabell Martin
- EPFL FSB: Ecole polytechnique federale de Lausanne Faculte des sciences de base Institute of Chemical Sciences and Engineering SWITZERLAND
| | - Pablo Rivera-Fuentes
- University of Zurich Faculty of Science: Universitat Zurich Mathematisch-Naturwissenschaftliche Fakultat Department of Chemistry Winterthurerstrasse 190 8057 Zurich SWITZERLAND
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9
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Rivera-Fuentes P, Deo C. Editorial Overview: Molecular Imaging. Curr Opin Chem Biol 2022; 69:102168. [PMID: 35696741 DOI: 10.1016/j.cbpa.2022.102168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
| | - Claire Deo
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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10
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Guidotti N, Eördögh Á, Mivelaz M, Rivera-Fuentes P, Fierz B. Multivalent Peptide Ligands To Probe the Chromocenter Microenvironment in Living Cells. ACS Chem Biol 2022; 18:1066-1075. [PMID: 35447032 DOI: 10.1021/acschembio.2c00203] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chromatin is spatially organized into functional states that are defined by both the presence of specific histone post-translational modifications (PTMs) and a defined set of chromatin-associated "reader" proteins. Different models for the underlying mechanism of such compartmentalization have been proposed, including liquid-liquid phase separation (LLPS) of chromatin-associated proteins to drive spatial organization. Heterochromatin, characterized by lysine 9 methylation on histone H3 (H3K9me3) and the presence of heterochromatin protein 1 (HP1) as a multivalent reader, represents a prime example of a spatially defined chromatin state. Heterochromatin foci exhibit features of protein condensates driven by LLPS; however, the exact nature of the physicochemical environment within heterochromatin in different cell types is not completely understood. Here we present tools to interrogate the environment of chromatin subcompartments in the form of modular, cell-permeable, multivalent, and fluorescent peptide probes. These probes can be tuned to target specific chromatin states by providing binding sites to reader proteins and can thereby integrate into the PTM-reader interaction network. Here we generate probes specific to HP1, directing them to heterochromatin at chromocenters in mouse fibroblasts. Moreover, we use a polarity-sensing photoactivatable probe that photoconverts to a fluorescent state in phase-separated protein droplets and thereby reports on the local microenvironment. Equipped with this dye, our probes indeed turn fluorescent in murine chromocenters. Image analysis and single-molecule tracking experiments reveal that the compartments are less dense and more dynamic than HP1 condensates obtained in vitro. Our results thus demonstrate that the local organization of heterochromatin in chromocenters is internally more complex than an HP1 condensate.
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Affiliation(s)
- Nora Guidotti
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Station 6, CH-1015 Lausanne, Switzerland
| | - Ádám Eördögh
- EPFL, SB ISIC LOCBP, Station 6, CH-1015 Lausanne, Switzerland
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Maxime Mivelaz
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Station 6, CH-1015 Lausanne, Switzerland
| | | | - Beat Fierz
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Station 6, CH-1015 Lausanne, Switzerland
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11
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Nguyen J, Tirla A, Rivera-Fuentes P. Disruption of mitochondrial redox homeostasis by enzymatic activation of a trialkylphosphine probe. Org Biomol Chem 2021; 19:2681-2687. [PMID: 33634293 DOI: 10.1039/d0ob02259d] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Redox homeostasis is essential for cell function and its disruption is associated with multiple pathologies. Redox balance is largely regulated by the relative concentrations of reduced and oxidized glutathione. In eukaryotic cells, this ratio is different in each cell compartment, and disruption of the mitochondrial redox balance has been specifically linked to metabolic diseases. Here, we report a probe that is selectively activated by endogenous nitroreductases, and releases tributylphosphine to trigger redox stress in mitochondria. Mechanistic studies revealed that, counterintuitively, release of a reducing agent in mitochondria rapidly induced oxidative stress through accumulation of superoxide. This response is mediated by glutathione, suggesting a link between reductive and oxidative stress. Furthermore, mitochondrial redox stress activates a cellular response orchestrated by transcription factor ATF4, which upregulates genes involved in glutathione catabolism.
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Affiliation(s)
- Jade Nguyen
- Laboratory of Organic Chemistry, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland.
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12
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Eördögh Á, Paganini C, Pinotsi D, Arosio P, Rivera-Fuentes P. A Molecular Logic Gate Enables Single-Molecule Imaging and Tracking of Lipids in Intracellular Domains. ACS Chem Biol 2020; 15:2597-2604. [PMID: 32803945 DOI: 10.1021/acschembio.0c00639] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Photoactivatable dyes enable single-molecule imaging and tracking in biology. Despite progress in the development of new fluorophores and labeling strategies, many intracellular compartments remain difficult to image beyond the limit of diffraction in living cells. For example, lipid domains, e.g., membranes and droplets, remain difficult to image with nanometric resolution. To visualize these challenging subcellular targets, it is necessary to develop new fluorescent molecular devices beyond simple on/off switches. Here, we report a fluorogenic molecular logic gate that can be used to image single molecules associated with lipid domains, most notably droplets, with excellent specificity. This probe requires the subsequent action of light, a lipophilic environment, and a competent nucleophile to produce a fluorescent product. The combination of these inputs results in a probe that can be used to image the boundary of lipid droplets in three dimensions with resolution beyond the limit of diffraction. Moreover, this probe enables single-molecule tracking of lipid trafficking between droplets and the endoplasmic reticulum.
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Affiliation(s)
- Ádám Eördögh
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
- Institute of Chemical Sciences and Engineering, EPF Lausanne, 1015 Lausanne, Switzerland
| | - Carolina Paganini
- Institute for Chemical and Bioengineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Dorothea Pinotsi
- Scientific Center for Optical and Electron Microscopy, ETH Zurich, 8093 Zurich, Switzerland
| | - Paolo Arosio
- Institute for Chemical and Bioengineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Pablo Rivera-Fuentes
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
- Institute of Chemical Sciences and Engineering, EPF Lausanne, 1015 Lausanne, Switzerland
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13
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Halabi EA, Arasa J, Püntener S, Collado-Diaz V, Halin C, Rivera-Fuentes P. Dual-Activatable Cell Tracker for Controlled and Prolonged Single-Cell Labeling. ACS Chem Biol 2020; 15:1613-1620. [PMID: 32298071 PMCID: PMC7309267 DOI: 10.1021/acschembio.0c00208] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Cell
trackers are fluorescent chemical tools that facilitate imaging
and tracking cells within live organisms. Despite their versatility,
these dyes lack specificity, tend to leak outside of the cell, and
stain neighboring cells. Here, we report a dual-activatable cell tracker
for increased spatial and temporal staining control, especially for
single-cell tracking. This probe overcomes the typical problems of
current cell trackers: off-target staining, high background signal,
and leakage from the intracellular medium. Staining with this dye
is not cytotoxic, and it can be used in sensitive primary cells. Moreover,
this dye is resistant to harsh fixation and permeabilization conditions
and allows for multiwavelength studies with confocal microscopy and
fluorescence-activated cell sorting. Using this cell tracker, we performed in vivo homing experiments in mice with primary splenocytes
and tracked a single cell in a heterogeneous, multicellular culture
environment for over 20 h. These experiments, in addition to comparative
proliferation studies with other cell trackers, demonstrated that
the signal from this dye is retained in cells for over 72 h after
photoactivation. We envision that this type of probes will facilitate
the analysis of single-cell behavior and migration in cell culture
and in vivo experiments.
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Affiliation(s)
- Elias A. Halabi
- Laboratory of Organic Chemistry, ETH Zürich, 8093, Zürich, Switzerland
| | - Jorge Arasa
- Institute of Pharmaceutical Sciences, ETH Zürich, 8093, Zürich, Switzerland
| | - Salome Püntener
- Laboratory of Organic Chemistry, ETH Zürich, 8093, Zürich, Switzerland
- Institute of Chemical Sciences and Engineering, EPF Lausanne, 1015, Lausanne, Switzerland
| | | | - Cornelia Halin
- Institute of Pharmaceutical Sciences, ETH Zürich, 8093, Zürich, Switzerland
| | - Pablo Rivera-Fuentes
- Laboratory of Organic Chemistry, ETH Zürich, 8093, Zürich, Switzerland
- Institute of Chemical Sciences and Engineering, EPF Lausanne, 1015, Lausanne, Switzerland
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14
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Affiliation(s)
- Rebecca J. B. Schäfer
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, Zurich 8093, Switzerland
| | - Mattia R. Monaco
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, Zurich 8093, Switzerland
| | - Mao Li
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, Zurich 8093, Switzerland
| | - Alina Tirla
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, Zurich 8093, Switzerland
| | - Pablo Rivera-Fuentes
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, Zurich 8093, Switzerland
| | - Helma Wennemers
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, Zurich 8093, Switzerland
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15
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Šolomek T, Rivera-Fuentes P, Merzc L. 12 th Young Faculty Meeting, 28 th May 2019. Chimia (Aarau) 2019; 73:772-775. [PMID: 31514784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023] Open
Affiliation(s)
- Tomáš Šolomek
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056 Basel;,
| | | | - Leo Merzc
- Swiss Academy of Sciences (SCNAT), Platform Chemistry, Laupenstrasse 7, Postfach, CH-3001 Bern;,
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16
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Halabi EA, Pinotsi D, Rivera-Fuentes P. Photoregulated fluxional fluorophores for live-cell super-resolution microscopy with no apparent photobleaching. Nat Commun 2019; 10:1232. [PMID: 30874551 PMCID: PMC6420572 DOI: 10.1038/s41467-019-09217-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 02/25/2019] [Indexed: 01/13/2023] Open
Abstract
Photoswitchable molecules have multiple applications in the physical and life sciences because their properties can be modulated with light. Fluxional molecules, which undergo rapid degenerate rearrangements in the electronic ground state, also exhibit switching behavior. The stochastic nature of fluxional switching, however, has hampered its application in the development of functional molecules and materials. Here we combine photoswitching and fluxionality to develop a fluorophore that enables very long (>30 min) time-lapse single-molecule localization microscopy in living cells with minimal phototoxicity and no apparent photobleaching. These long time-lapse experiments allow us to track intracellular organelles with unprecedented spatiotemporal resolution, revealing new information of the three-dimensional compartmentalization of synaptic vesicle trafficking in live human neurons. Super-resolution microscopy with spontaneously blinking dyes is dependent on pH and polarity of the medium. Here the authors introduce a photoactivatable fluxional fluorophore for live cell imaging that allows control over the fraction of spontaneously blinking molecules independently of medium properties.
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Affiliation(s)
- Elias A Halabi
- Laboratory of Organic Chemistry, ETH Zurich, Zurich, 8093, Switzerland
| | - Dorothea Pinotsi
- Scientific Center for Optical and Electron Microscopy, ETH Zurich, Zurich, 8093, Switzerland
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17
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Abstract
The development of super-resolved optical microscopies has revolutionized the way we visualize cell biology. These techniques strongly rely on the use of photochemically active fluorophores that display changes in their photophysical properties upon irradiation with light. Many reversible and irreversible photochemical transformations have been explored for this purpose, and different imaging techniques require specific mechanisms of photoconversion. In this review, we provide an overview of the most common strategies used for the development of fluorophores for super-resolution microscopy and give specific examples of state-of-the-art fluorogenic probes. Furthermore, we discuss their main field of application and possible directions for future developments.
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Affiliation(s)
- Zacharias Thiel
- Laboratorium für Organische Chemie ETH Zurich Vladimir-Prelog-Weg 3, CH-8093 Zurich
| | - Pablo Rivera-Fuentes
- Laboratorium für Organische Chemie ETH Zurich Vladimir-Prelog-Weg 3, CH-8093 Zurich;,
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18
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Affiliation(s)
- Alina Tirla
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Pablo Rivera-Fuentes
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
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19
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Affiliation(s)
- Elias A. Halabi
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences; ETH Zürich; Vladimir-Prelog-Weg 1-5/10 CH-8093 Zürich Switzerland
| | - Salome Püntener
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences; ETH Zürich; Vladimir-Prelog-Weg 1-5/10 CH-8093 Zürich Switzerland
| | - Pablo Rivera-Fuentes
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences; ETH Zürich; Vladimir-Prelog-Weg 1-5/10 CH-8093 Zürich Switzerland
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20
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Abstract
Reductive stress is a condition present in cells that have an increased concentration of reducing species, and it has been associated with a number of pathologies, such as neurodegenerative diseases and cancer. The tools available to study reductive stress lack both in selectivity and specific targeting and some of these shortcomings can be addressed by using photoactivatable compounds. We developed a photoactivatable phosphonium probe, which upon irradiation releases a fluorescent molecule and a trialkyphosphine. The probes can permeate through the plasma membrane and the photoreleased phosphine can induce intracellular reductive stress as proven by the detection of protein aggregates.
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Affiliation(s)
- Alina Tirla
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland.
| | - Pablo Rivera-Fuentes
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland. rivera-fuentes.chem.ethz.ch
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21
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Rivera-Fuentes P, Bassolino G, Halabi E. Practical and Scalable Synthesis of 7-Azetidin-1-yl-4-(hydroxymethyl)coumarin: An Improved Photoremovable Group. SYNTHESIS-STUTTGART 2017. [DOI: 10.1055/s-0036-1591742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
7-Substituted 4-methylcoumarin derivatives are widely employed as photoprotecting groups in chemistry and biology. We have recently shown that the 7-azetidinylated version of this photocage releases carboxylic acids in aqueous solution more efficiently than the traditionally used 7-diethylamino variant. Here we present a robust and scalable route to prepare the 7-azetidinylated alcohol, a useful precursor for the photoprotection of a variety of leaving groups, and its use in the preparation of model phosphate, sulfonate, and carbamate derivatives.
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22
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Rivera-Fuentes P, Tirla A, Hansen M. Synthesis of Asparagusic Acid Modified Lysine and its Application in Solid-Phase Synthesis of Peptides with Enhanced Cellular Uptake. Synlett 2017. [DOI: 10.1055/s-0036-1591847] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Cyclic disulfides, such as asparagusic acid, enhance the uptake of a variety of cargoes into live cells. Here, we report a robust and scalable synthesis of an asparagusic acid modified lysine. This amino acid can be used in solid-phase peptide synthesis. We confirmed that incorporation of this building block into the sequence of a peptide increases its cellular uptake substantially.
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23
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Bassolino G, Nançoz C, Thiel Z, Bois E, Vauthey E, Rivera-Fuentes P. Photolabile coumarins with improved efficiency through azetidinyl substitution. Chem Sci 2017; 9:387-391. [PMID: 29629108 PMCID: PMC5868312 DOI: 10.1039/c7sc03627b] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/31/2017] [Indexed: 11/21/2022] Open
Abstract
The efficiency of photoactivatable coumarins in water has been enhanced by substitution with azetidine.
Azetidinyl substituents have been recently used to improve the fluorescence quantum yield of several classes of fluorophores. Herein, we demonstrate that other useful photochemical processes can be modulated using this strategy. In particular, we prepared and measured the quantum yield of photorelease of a series of 7-azetidinyl-4-methyl coumarin esters and compared it to their 7-diethylamino and julolidine-fused analogues. The efficiency of the photorelease reactions of the azetidinyl-substituted compounds was 2- to 5-fold higher than the corresponding diethylamino coumarins. We investigated the origin of this effect in model fluorophores and in the photoactivatable esters, and found that H-bonding with the solvent seems to be the prominent deactivation channel inhibited upon substitution with an azetidinyl ring. We anticipate that this substitution strategy could be used to modulate other photochemical processes with applications in chemical biology, catalysis and materials science.
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Affiliation(s)
- Giovanni Bassolino
- Laboratorium für Organische Chemie , ETH Zürich , HCI G329, Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland .
| | - Christoph Nançoz
- Department of Physical Chemistry , University of Geneva , 30 Quai Ernest-Ansermet , 1211 Geneva 4 , Switzerland .
| | - Zacharias Thiel
- Laboratorium für Organische Chemie , ETH Zürich , HCI G329, Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland .
| | - Estelle Bois
- Department of Physical Chemistry , University of Geneva , 30 Quai Ernest-Ansermet , 1211 Geneva 4 , Switzerland .
| | - Eric Vauthey
- Department of Physical Chemistry , University of Geneva , 30 Quai Ernest-Ansermet , 1211 Geneva 4 , Switzerland .
| | - Pablo Rivera-Fuentes
- Laboratorium für Organische Chemie , ETH Zürich , HCI G329, Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland .
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24
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Bassolino G, Rivera-Fuentes P. Intracellular Photoactivation and Quantification Using Fluorescence Microscopy: Chemical Tools and Imaging Approaches. Chimia (Aarau) 2017; 70:796-799. [PMID: 28661340 DOI: 10.2533/chimia.2016.796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Recent advances in optical microscopy enable the visualization and quantification of biological processes within live cells. To a great extent, these imaging techniques remain limited by the physical properties of the chemical probes that are used as fluorescent tags, detectors and actuators. At the same time, the quantification of concentrations in the intracellular medium is not trivial, but a few approaches that employ optical microscopy have been developed. Herein, we highlight a few examples of how a combination of novel chemical probes and microscopy methods could be used to bring a much-needed quantitative dimension to the field of biological imaging.
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Affiliation(s)
- Giovanni Bassolino
- Laboratorium für Organische Chemie, ETH Zürich, HCI G329, Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland
| | - Pablo Rivera-Fuentes
- Laboratorium für Organische Chemie, ETH Zürich, HCI G329, Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland.
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25
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Halabi EA, Thiel Z, Trapp N, Pinotsi D, Rivera-Fuentes P. A Photoactivatable Probe for Super-Resolution Imaging of Enzymatic Activity in Live Cells. J Am Chem Soc 2017; 139:13200-13207. [DOI: 10.1021/jacs.7b07748] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Elias A. Halabi
- Laboratory
of Organic Chemistry, ETH Zurich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
| | - Zacharias Thiel
- Laboratory
of Organic Chemistry, ETH Zurich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
| | - Nils Trapp
- Laboratory
of Organic Chemistry, ETH Zurich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
| | - Dorothea Pinotsi
- Scientific
Center for Optical and Electron Microscopy, ETH Zurich, Otto-Stern-Weg
3, CH-8093 Zurich, Switzerland
| | - Pablo Rivera-Fuentes
- Laboratory
of Organic Chemistry, ETH Zurich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
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26
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Rivera-Fuentes P, Weiss M. The 52nd EUCHEMS Conference on Stereochemistry: Bürgenstock Conference 2017, Brunnen, April 30th–May 4th, 2017. Chimia (Aarau) 2017; 71:387-389. [DOI: 10.2533/chimia.2017.387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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27
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Tirla A, Rivera-Fuentes P. Development of a Photoactivatable Phosphine Probe for Induction of Intracellular Reductive Stress with Single-Cell Precision. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608779] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Alina Tirla
- Laboratorium für Organische Chemie; ETH Zürich; HCI G329; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Pablo Rivera-Fuentes
- Laboratorium für Organische Chemie; ETH Zürich; HCI G329; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
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28
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Abstract
The synthesis of a small-molecule dyad consisting of a far-red-emitting silicon rhodamine dye that is covalently linked to a photochromic spironaphthothiopyran unit, which serves as a photoswitchable quencher, is reported. This system can be switched reversibly between the fluorescent and nonfluorescent states using visible light at wavelengths of 405 and 630 nm, respectively, and it works effectively in aqueous solution. Live-cell imaging demonstrates that this dyad has several desirable features, including excellent membrane permeability, fast and reversible modulation of fluorescence by visible light, and good contrast between the bright and dark states.
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Affiliation(s)
- Yaoyao Xiong
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Oxford OX1 3TA, U.K
| | - Pablo Rivera-Fuentes
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Oxford OX1 3TA, U.K
| | - Erdinc Sezgin
- MRC Human Immunology Unit and Wolfson Imaging Centre Oxford, Weatherall Institute of Molecular Medicine, University of Oxford , Oxford OX3 9DS, U.K
| | - Andreas Vargas Jentzsch
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Oxford OX1 3TA, U.K
| | - Christian Eggeling
- MRC Human Immunology Unit and Wolfson Imaging Centre Oxford, Weatherall Institute of Molecular Medicine, University of Oxford , Oxford OX3 9DS, U.K
| | - Harry L Anderson
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Oxford OX1 3TA, U.K
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29
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Abstract
Nitroxyl (HNO) is a biological signaling agent that displays distinctive reactivity compared to nitric oxide (NO). As a consequence, these two reactive nitrogen species trigger different physiological responses. Selective detection of HNO over NO has been a challenge for chemists, and several fluorogenic molecular probes have been recently developed with that goal in mind. Common constructs take advantage of the HNO-induced reduction of Cu(II) to Cu(I). The sensing mechanism of such probes relies on the ability of the unpaired electron in a d orbital of the Cu(II) center to quench the fluorescence of a photoemissive ligand by either an electron or energy transfer mechanism. Experimental and theoretical mechanistic studies suggest that proton-coupled electron transfer mediates this process, and careful tuning of the copper coordination environment has led to sensors with optimized selectivity and kinetics. The current optical probes cover the visible and near-infrared regions of the spectrum. This palette of sensors comprises structurally and functionally diverse fluorophores such as coumarin (blue/green emission), boron dipyrromethane (BODIPY, green emission), benzoresorufin (red emission), and dihydroxanthenes (near-infrared emission). Many of these sensors have been successfully applied to detect HNO production in live cells. For example, copper-based optical probes have been used to detect HNO production in live mammalian cells that have been treated with H2S and various nitrosating agents. These studies have established a link between HSNO, the smallest S-nitrosothiol, and HNO. In addition, a near-infrared HNO sensor has been used to perform multicolor/multianalyte microscopy, revealing that exogenously applied HNO elevates the concentration of intracellular mobile zinc. This mobilization of zinc ions is presumably a consequence of nitrosation of cysteine residues in zinc-chelating proteins such as metallothionein. Future challenges for the optical imaging of HNO include devising probes that can detect HNO reversibly, especially because ratiometric imaging can only report equilibrium concentrations when the sensing event is reversible. Another important aspect that needs to be addressed is the creation of probes that can sense HNO in specific subcellular locations. These tools would be useful to identify the organelles in which HNO is produced in mammalian cells and probe the intracellular signaling networks in which this reactive nitrogen species is involved. In addition, near-infrared emitting probes might be applied to detect HNO in thicker specimens, such as acute tissue slices and even live animals, enabling the investigation of the roles of HNO in physiological or pathological conditions in multicellular systems.
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Affiliation(s)
- Pablo Rivera-Fuentes
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Stephen J. Lippard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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30
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Mügge C, Marzo T, Massai L, Hildebrandt J, Ferraro G, Rivera-Fuentes P, Metzler-Nolte N, Merlino A, Messori L, Weigand W. Platinum(II) Complexes with O,S Bidentate Ligands: Biophysical Characterization, Antiproliferative Activity, and Crystallographic Evidence of Protein Binding. Inorg Chem 2015; 54:8560-70. [PMID: 26280387 DOI: 10.1021/acs.inorgchem.5b01238] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We recently characterized a series of novel platinum(II) compounds bearing a conserved O,S binding moiety as a bifunctional ligand and evaluated their solution behavior and antiproliferative properties in vitro against a representative cancer cell line. On the whole, those platinum compounds showed an appreciable stability in mixed dimethyl sulfoxide-aqueous buffers and promising in vitro cytotoxic effects; yet they manifested a rather limited solubility in aqueous media making them poorly suitable for further pharmaceutical development. To overcome this drawback, four new derivatives of this series were prepared and characterized based on a careful choice of substituents on the O,S bidentate ligand. The solubility and stability profile of these novel compounds in a reference buffer was determined, as well as the ligands' log P(o/w) value (P(o/w) = n-octanol-water partition coefficient) as an indirect measure for the complexes' lipophilicity. The antiproliferative properties were comparatively evaluated in a panel of three cancer cell lines. The protein binding properties of the four platinum compounds were assessed using the model protein hen egg white lysozyme (HEWL), and the molecular structures of two relevant HEWL-metallodrug adducts were solved. Overall, it is shown that a proper choice of the substituents leads to a higher solubility and enables a selective fine-tuning of the antiproliferative properties. The implications of these results are thoroughly discussed.
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Affiliation(s)
- Carolin Mügge
- Institute of Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena , Humboldtstraße 8, 07743 Jena, Germany.,Inorganic Chemistry I - Bioinorganic Chemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum , Universitaetsstrasse 150, 44801 Bochum, Germany
| | - Tiziano Marzo
- Laboratory of Metals in Medicine, Department of Chemistry, University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy
| | - Lara Massai
- Laboratory of Metals in Medicine, Department of Chemistry, University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy
| | - Jana Hildebrandt
- Institute of Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena , Humboldtstraße 8, 07743 Jena, Germany
| | - Giarita Ferraro
- Department of Chemical Sciences, University of Naples Federico II , via Cintia, Napoli I-80126, Italy
| | - Pablo Rivera-Fuentes
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Nils Metzler-Nolte
- Inorganic Chemistry I - Bioinorganic Chemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum , Universitaetsstrasse 150, 44801 Bochum, Germany
| | - Antonello Merlino
- Department of Chemical Sciences, University of Naples Federico II , via Cintia, Napoli I-80126, Italy.,CNR Institute of Biostructures and Bioimages , via Mezzocannone 16, Napoli I-80100, Italy
| | - Luigi Messori
- Laboratory of Metals in Medicine, Department of Chemistry, University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy
| | - Wolfgang Weigand
- Institute of Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena , Humboldtstraße 8, 07743 Jena, Germany.,Jena Center for Soft Matter (JCSM) , Philosophenweg 7, 07743 Jena, Germany
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31
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Rivera-Fuentes P, Wrobel AT, Zastrow ML, Khan M, Georgiou J, Luyben TT, Roder JC, Okamoto K, Lippard SJ. A Far-Red Emitting Probe for Unambiguous Detection of Mobile Zinc in Acidic Vesicles and Deep Tissue. Chem Sci 2015; 6:1944-1948. [PMID: 25815162 PMCID: PMC4372157 DOI: 10.1039/c4sc03388d] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 01/02/2015] [Indexed: 12/12/2022] Open
Abstract
Imaging mobile zinc in acidic environments remains challenging because most small-molecule optical probes display pH-dependent fluorescence. Here we report a reaction-based sensor that detects mobile zinc unambiguously at low pH. The sensor responds reversibly and with a large dynamic range to exogenously applied Zn2+ in lysosomes of HeLa cells, endogenous Zn2+ in insulin granules of MIN6 cells, and zinc-rich mossy fiber boutons in hippocampal tissue from mice. This long-wavelength probe is compatible with the green-fluorescent protein, enabling multicolor imaging, and facilitates visualization of mossy fiber boutons at depths of >100 µm, as demonstrated by studies in live tissue employing two-photon microscopy.
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Affiliation(s)
- Pablo Rivera-Fuentes
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , MA 02139 , USA .
| | - Alexandra T. Wrobel
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , MA 02139 , USA .
| | - Melissa L. Zastrow
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , MA 02139 , USA .
| | - Mustafa Khan
- Lunenfeld-Tanenbaum Research Institute , Mount Sinai Hospital , Toronto , ON M5G 1X5 , Canada
| | - John Georgiou
- Lunenfeld-Tanenbaum Research Institute , Mount Sinai Hospital , Toronto , ON M5G 1X5 , Canada
| | - Thomas T. Luyben
- Lunenfeld-Tanenbaum Research Institute , Mount Sinai Hospital , Toronto , ON M5G 1X5 , Canada
- Department of Molecular Genetics , Faculty of Medicine , University of Toronto , Toronto , ON M5S 1A8 , Canada
| | - John C. Roder
- Lunenfeld-Tanenbaum Research Institute , Mount Sinai Hospital , Toronto , ON M5G 1X5 , Canada
- Department of Molecular Genetics , Faculty of Medicine , University of Toronto , Toronto , ON M5S 1A8 , Canada
| | - Kenichi Okamoto
- Lunenfeld-Tanenbaum Research Institute , Mount Sinai Hospital , Toronto , ON M5G 1X5 , Canada
- Department of Molecular Genetics , Faculty of Medicine , University of Toronto , Toronto , ON M5S 1A8 , Canada
| | - Stephen J. Lippard
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , MA 02139 , USA .
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32
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Wrobel AT, Johnstone TC, Deliz Liang A, Lippard SJ, Rivera-Fuentes P. A fast and selective near-infrared fluorescent sensor for multicolor imaging of biological nitroxyl (HNO). J Am Chem Soc 2014; 136:4697-705. [PMID: 24564324 PMCID: PMC3985477 DOI: 10.1021/ja500315x] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
The
first near-infrared fluorescent turn-on sensor for the detection
of nitroxyl (HNO), the one-electron reduced form of nitric oxide (NO),
is reported. The new copper-based probe, CuDHX1, contains a dihydroxanthene
(DHX) fluorophore and a cyclam derivative as a Cu(II) binding site.
Upon reaction with HNO, CuDHX1 displays a five-fold fluorescence turn-on
in cuvettes and is selective for HNO over thiols and reactive nitrogen
and oxygen species. CuDHX1 can detect exogenously applied HNO in live
mammalian cells and in conjunction with the zinc-specific, green-fluorescent
sensor ZP1 can perform multicolor/multianalyte microscopic imaging.
These studies reveal that HNO treatment elicits an increase in the
concentration of intracellular mobile zinc.
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Affiliation(s)
- Alexandra T Wrobel
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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33
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Rivera-Fuentes P, Lippard SJ. SpiroZin1: a reversible and pH-Insensitive, reaction-based, red-fluorescent probe for imaging biological mobile zinc. ChemMedChem 2014; 9:1238-43. [PMID: 24616292 DOI: 10.1002/cmdc.201400014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Indexed: 11/06/2022]
Abstract
A reversible, reaction-based sensor for biological mobile zinc was designed, prepared, and characterized. The sensing mechanism of this probe is based on the zinc-induced, ring-opening reaction of spirobenzopyran to give a cyanine fluorophore that emits in the deep-red region of the electromagnetic spectrum. This probe is not activated by protons and operates efficiently in aqueous solution at pH 7 and high ionic strength. The mechanism of this reaction was studied by using a combination of kinetics experiments and DFT calculations. The biocompatibility of the probe was demonstrated in live HeLa cells.
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Affiliation(s)
- Pablo Rivera-Fuentes
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139 (USA) http://web.mit.edu/lippardlab/
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Rivera-Fuentes P, Rekowski MVW, Schweizer WB, Gisselbrecht JP, Boudon C, Diederich F. Cascade Carbopalladation Reaction between Alkynes and gem-Dibromoolefins: Facile Access to Monoannelated Pentalenes. Org Lett 2012; 14:4066-9. [DOI: 10.1021/ol301670d] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Pablo Rivera-Fuentes
- Laboratorium für Organische Chemie, ETH Zürich, Hönggerberg, HCI, 8093 Zürich, Switzerland, and Laboratoire d’Electrochimie et de Chimie Physique du Corps Solide, Institut de Chimie-UMR 7177, C.N.R.S., Universitè de Strasbourg, 4 rue Blaise Pascal, 67081 Strasbourg Cedex, France
| | - Margarete von Wantoch Rekowski
- Laboratorium für Organische Chemie, ETH Zürich, Hönggerberg, HCI, 8093 Zürich, Switzerland, and Laboratoire d’Electrochimie et de Chimie Physique du Corps Solide, Institut de Chimie-UMR 7177, C.N.R.S., Universitè de Strasbourg, 4 rue Blaise Pascal, 67081 Strasbourg Cedex, France
| | - W. Bernd Schweizer
- Laboratorium für Organische Chemie, ETH Zürich, Hönggerberg, HCI, 8093 Zürich, Switzerland, and Laboratoire d’Electrochimie et de Chimie Physique du Corps Solide, Institut de Chimie-UMR 7177, C.N.R.S., Universitè de Strasbourg, 4 rue Blaise Pascal, 67081 Strasbourg Cedex, France
| | - Jean-Paul Gisselbrecht
- Laboratorium für Organische Chemie, ETH Zürich, Hönggerberg, HCI, 8093 Zürich, Switzerland, and Laboratoire d’Electrochimie et de Chimie Physique du Corps Solide, Institut de Chimie-UMR 7177, C.N.R.S., Universitè de Strasbourg, 4 rue Blaise Pascal, 67081 Strasbourg Cedex, France
| | - Corinne Boudon
- Laboratorium für Organische Chemie, ETH Zürich, Hönggerberg, HCI, 8093 Zürich, Switzerland, and Laboratoire d’Electrochimie et de Chimie Physique du Corps Solide, Institut de Chimie-UMR 7177, C.N.R.S., Universitè de Strasbourg, 4 rue Blaise Pascal, 67081 Strasbourg Cedex, France
| | - François Diederich
- Laboratorium für Organische Chemie, ETH Zürich, Hönggerberg, HCI, 8093 Zürich, Switzerland, and Laboratoire d’Electrochimie et de Chimie Physique du Corps Solide, Institut de Chimie-UMR 7177, C.N.R.S., Universitè de Strasbourg, 4 rue Blaise Pascal, 67081 Strasbourg Cedex, France
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Ehmke V, Quinsaat JEQ, Rivera-Fuentes P, Heindl C, Freymond C, Rottmann M, Brun R, Schirmeister T, Diederich F. Tuning and predicting biological affinity: aryl nitriles as cysteine protease inhibitors. Org Biomol Chem 2012; 10:5764-8. [DOI: 10.1039/c2ob00034b] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Reisinger CM, Rivera-Fuentes P, Lampart S, Schweizer WB, Diederich F. Cascade Pericyclic Reactions of Alleno-Acetylenes: Facile Access to Highly Substituted Cyclobutene, Dendralene, Pentalene, and Indene Skeletons. Chemistry 2011; 17:12906-11. [DOI: 10.1002/chem.201102852] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Rivera-Fuentes P, Nieto-Ortega B, Schweizer WB, López Navarrete JT, Casado J, Diederich F. Enantiopure, Monodisperse Alleno-acetylenic Cyclooligomers: Effect of Symmetry and Conformational Flexibility on the Chiroptical Properties of Carbon-Rich Compounds. Chemistry 2011; 17:3876-85. [DOI: 10.1002/chem.201100131] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Indexed: 11/11/2022]
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Rivera-Fuentes P, Alonso-Gómez JL, Petrovic A, Seiler P, Santoro F, Harada N, Berova N, Rzepa H, Diederich F. Inside Cover: Enantiomerically Pure Alleno-Acetylenic Macrocycles: Synthesis, Solid-State Structures, Chiroptical Properties, and Electron Localization Function Analysis (Chem. Eur. J. 32/2010). Chemistry 2010. [DOI: 10.1002/chem.201090158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Rivera-Fuentes P, Alonso-Gómez JL, Petrovic A, Seiler P, Santoro F, Harada N, Berova N, Rzepa H, Diederich F. Enantiomerically Pure Alleno-Acetylenic Macrocycles: Synthesis, Solid-State Structures, Chiroptical Properties, and Electron Localization Function Analysis. Chemistry 2010; 16:9796-807. [DOI: 10.1002/chem.201001087] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Kraszewska A, Rivera-Fuentes P, Rapenne G, Crassous J, Petrovic AG, Alonso-Gómez JL, Huerta E, Diederich F, Thilgen C. Regioselectivity in Tether-Directed Remote Functionalization - The Addition of a Cyclotriveratrylene-Based Trimalonate to C60 Revisited. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000396] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Buschhaus B, Convertino V, Rivera-Fuentes P, Alonso-Gómez JL, Petrovic AG, Diederich F. Optically Active Trialkynyl(phenyl)methane: Synthesis and Determination of Its Absolute Configuration by Vibrational Circular Dichroism (VCD) and Optical Rotatory Dispersion (ORD). European J Org Chem 2010. [DOI: 10.1002/ejoc.201000076] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Yamada M, Rivera-Fuentes P, Schweizer W, Diederich F. Optische Stabilität axial-chiraler push-pull-substituierter Buta-1,3-diene: Effekt einer einzelnen Methylgruppe auf der Oberfläche von C60. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906853] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Yamada M, Rivera-Fuentes P, Schweizer W, Diederich F. Optical Stability of Axially Chiral Push-Pull-Substituted Buta-1,3-dienes: Effect of a Single Methyl Group on the C60 Surface. Angew Chem Int Ed Engl 2010; 49:3532-5. [DOI: 10.1002/anie.200906853] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Rivera-Fuentes P, Alonso-Gómez J, Petrovic A, Santoro F, Harada N, Berova N, Diederich F. Amplifikation der Chiralität in monodispersen, enantiomerenreinen Allen-Acetylen-Oligomeren. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906191] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Rivera-Fuentes P, Alonso-Gómez J, Petrovic A, Santoro F, Harada N, Berova N, Diederich F. Amplification of Chirality in Monodisperse, Enantiopure Alleno-Acetylenic Oligomers. Angew Chem Int Ed Engl 2010; 49:2247-50. [DOI: 10.1002/anie.200906191] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Alonso-Gómez JL, Petrovic A, Harada N, Rivera-Fuentes P, Berova N, Diederich F. Chiral Induction from Allenes into Twisted 1,1,4,4-Tetracyanobuta-1,3-dienes (TCBDs): Conformational Assignment by Circular Dichroism Spectroscopy. Chemistry 2009; 15:8396-8400. [DOI: 10.1002/chem.200900103] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Alonso-Gómez J, Rivera-Fuentes P, Harada N, Berova N, Diederich F. Cover Picture: An Enantiomerically Pure Alleno-Acetylenic Macrocycle: Synthesis and Rationalization of Its Outstanding Chiroptical Response (Angew. Chem. Int. Ed. 30/2009). Angew Chem Int Ed Engl 2009. [DOI: 10.1002/anie.200990154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Alonso-Gómez J, Rivera-Fuentes P, Harada N, Berova N, Diederich F. Titelbild: Ein enantiomerenreiner alleno-acetylenischer Makrocyclus: Synthese und Interpretation seiner herausragenden chiroptischen Eigenschaften (Angew. Chem. 30/2009). Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200990156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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