2
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Stroppel AS, Lappalainen R, Stafforst T. Controlling Site-Directed RNA Editing by Chemically Induced Dimerization. Chemistry 2021; 27:12300-12304. [PMID: 34169589 PMCID: PMC8456898 DOI: 10.1002/chem.202101985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Indexed: 11/24/2022]
Abstract
Various RNA‐targeting approaches have been engineered to modify specific sites on endogenous transcripts, breaking new ground for a variety of basic research tools and promising clinical applications in the future. Here, we combine site‐directed adenosine‐to‐inosine RNA editing with chemically induced dimerization. Specifically, we achieve tight and dose‐dependent control of the editing reaction with gibberellic acid, and obtain editing yields up to 20 % and 44 % in the endogenous STAT1 and GAPDH transcript in cell culture. Furthermore, the disease‐relevant MECP2 R106Q mutation was repaired with editing yields up to 42 %. The introduced principle will enable new applications where temporal or spatiotemporal control of an RNA‐targeting mechanism is desired.
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Affiliation(s)
- Anna S Stroppel
- Interfaculty Institute of Biochemistry, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Ruth Lappalainen
- Interfaculty Institute of Biochemistry, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Thorsten Stafforst
- Interfaculty Institute of Biochemistry, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
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4
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Ankenbruck N, Courtney T, Naro Y, Deiters A. Optochemical Control of Biological Processes in Cells and Animals. Angew Chem Int Ed Engl 2018; 57:2768-2798. [PMID: 28521066 PMCID: PMC6026863 DOI: 10.1002/anie.201700171] [Citation(s) in RCA: 320] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 05/06/2017] [Indexed: 12/13/2022]
Abstract
Biological processes are naturally regulated with high spatial and temporal control, as is perhaps most evident in metazoan embryogenesis. Chemical tools have been extensively utilized in cell and developmental biology to investigate cellular processes, and conditional control methods have expanded applications of these technologies toward resolving complex biological questions. Light represents an excellent external trigger since it can be controlled with very high spatial and temporal precision. To this end, several optically regulated tools have been developed and applied to living systems. In this review we discuss recent developments of optochemical tools, including small molecules, peptides, proteins, and nucleic acids that can be irreversibly or reversibly controlled through light irradiation, with a focus on applications in cells and animals.
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Affiliation(s)
- Nicholas Ankenbruck
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Taylor Courtney
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Yuta Naro
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
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6
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Schelkle KM, Schmid C, Yserentant K, Bender M, Wacker I, Petzoldt M, Hamburger M, Herten DP, Wombacher R, Schröder RR, Bunz UHF. Cell Fixation by Light-Triggered Release of Glutaraldehyde. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201612112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Korwin M. Schelkle
- Organisch-Chemisches Institut; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 270 69120 Heidelberg Germany
- InnovationLab GmbH; Speyerer Strasse 4 69115 Heidelberg Germany
| | - Christopher Schmid
- Center of Advanced Materials; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 225 69120 Heidelberg Germany
| | - Klaus Yserentant
- Center of Advanced Materials; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 225 69120 Heidelberg Germany
- Physikalisch-Chemisches Institut; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 229 69120 Heidelberg Germany
- CellNetworks; Single Molecule Spectroscopy; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 267 69120 Heidelberg Germany
| | - Markus Bender
- Organisch-Chemisches Institut; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Irene Wacker
- Center of Advanced Materials; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 225 69120 Heidelberg Germany
| | - Martin Petzoldt
- Organisch-Chemisches Institut; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 270 69120 Heidelberg Germany
- InnovationLab GmbH; Speyerer Strasse 4 69115 Heidelberg Germany
| | - Manuel Hamburger
- Organisch-Chemisches Institut; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 270 69120 Heidelberg Germany
- InnovationLab GmbH; Speyerer Strasse 4 69115 Heidelberg Germany
| | - Dirk-Peter Herten
- Physikalisch-Chemisches Institut; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 229 69120 Heidelberg Germany
- CellNetworks; Single Molecule Spectroscopy; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 267 69120 Heidelberg Germany
| | - Richard Wombacher
- Institut für Pharmazie und Molekulare Biotechnologie; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Rasmus R. Schröder
- Center of Advanced Materials; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 225 69120 Heidelberg Germany
- CellNetworks; Cryo Electron Microscopy; Universitätsklinikum Heidelberg; Im Neuenheimer Feld 267 69120 Heidelberg Germany
| | - Uwe H. F. Bunz
- Organisch-Chemisches Institut; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 270 69120 Heidelberg Germany
- Center of Advanced Materials; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 225 69120 Heidelberg Germany
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7
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Chen X, Venkatachalapathy M, Kamps D, Weigel S, Kumar R, Orlich M, Garrecht R, Hirtz M, Niemeyer CM, Wu YW, Dehmelt L. “Molecular Activity Painting”: Switch-like, Light-Controlled Perturbations inside Living Cells. Angew Chem Int Ed Engl 2017; 56:5916-5920. [DOI: 10.1002/anie.201611432] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/10/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Xi Chen
- Chemical Genomics Centre of the Max-Planck Society; Dortmund Germany
| | - Muthukumaran Venkatachalapathy
- Department for Systemic Cell Biology; Max Planck Institute of Molecular Physiology and Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Germany
| | - Dominic Kamps
- Department for Systemic Cell Biology; Max Planck Institute of Molecular Physiology and Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Germany
| | - Simone Weigel
- Institute for Biological Interfaces; Karlsruhe Institute of Technology (KIT); Karlsruhe Germany
| | - Ravi Kumar
- Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF); Karlsruhe Institute of Technology (KIT); Karlsruhe Germany
| | - Michael Orlich
- Department for Systemic Cell Biology; Max Planck Institute of Molecular Physiology and Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Germany
| | - Ruben Garrecht
- Institute for Biological Interfaces; Karlsruhe Institute of Technology (KIT); Karlsruhe Germany
| | - Michael Hirtz
- Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF); Karlsruhe Institute of Technology (KIT); Karlsruhe Germany
| | - Christof M. Niemeyer
- Institute for Biological Interfaces; Karlsruhe Institute of Technology (KIT); Karlsruhe Germany
| | - Yao-Wen Wu
- Chemical Genomics Centre of the Max-Planck Society; Dortmund Germany
| | - Leif Dehmelt
- Department for Systemic Cell Biology; Max Planck Institute of Molecular Physiology and Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Germany
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8
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Chen X, Venkatachalapathy M, Kamps D, Weigel S, Kumar R, Orlich M, Garrecht R, Hirtz M, Niemeyer CM, Wu YW, Dehmelt L. “Molecular Activity Painting”: schaltbare, lichtgesteuerte Manipulation in lebenden Zellen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611432] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xi Chen
- Chemical Genomics Centre der Max-Planck-Gesellschaft; Dortmund Deutschland
| | - Muthukumaran Venkatachalapathy
- Abteilung für Systemische Zellbiologie; Max-Planck-Institut für Molekulare Physiologie und Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Deutschland
| | - Dominic Kamps
- Abteilung für Systemische Zellbiologie; Max-Planck-Institut für Molekulare Physiologie und Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Deutschland
| | - Simone Weigel
- Institut für Biologische Grenzflächen; Karlsruher Institut für Technologie (KIT); Karlsruhe Deutschland
| | - Ravi Kumar
- Institut für Nanotechnologie (INT) und Karlsruhe Nano Micro Facility (KNMF); Karlsruher Institut für Technologie (KIT); Karlsruhe Deutschland
| | - Michael Orlich
- Abteilung für Systemische Zellbiologie; Max-Planck-Institut für Molekulare Physiologie und Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Deutschland
| | - Ruben Garrecht
- Institut für Biologische Grenzflächen; Karlsruher Institut für Technologie (KIT); Karlsruhe Deutschland
| | - Michael Hirtz
- Institut für Nanotechnologie (INT) und Karlsruhe Nano Micro Facility (KNMF); Karlsruher Institut für Technologie (KIT); Karlsruhe Deutschland
| | - Christof M. Niemeyer
- Institut für Biologische Grenzflächen; Karlsruher Institut für Technologie (KIT); Karlsruhe Deutschland
| | - Yao-Wen Wu
- Chemical Genomics Centre der Max-Planck-Gesellschaft; Dortmund Deutschland
| | - Leif Dehmelt
- Abteilung für Systemische Zellbiologie; Max-Planck-Institut für Molekulare Physiologie und Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Dortmund Deutschland
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9
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Schelkle KM, Schmid C, Yserentant K, Bender M, Wacker I, Petzoldt M, Hamburger M, Herten DP, Wombacher R, Schröder RR, Bunz UHF. Cell Fixation by Light-Triggered Release of Glutaraldehyde. Angew Chem Int Ed Engl 2017; 56:4724-4728. [PMID: 28328078 DOI: 10.1002/anie.201612112] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/23/2017] [Indexed: 01/13/2023]
Abstract
Chemical fixation of living cells for microscopy is commonly achieved by crosslinking of intracellular proteins with dialdehydes prior to examination. We herein report a photocleavable protecting group for glutaraldehyde that results in a light-triggered and membrane-permeable fixative, which is nontoxic prior to photocleavage. Lipophilic ester groups allow for diffusion across the cell membrane and intracellular accumulation after enzymatic hydrolysis. Irradiation with UV light releases glutaraldehyde. The in situ generated fixative crosslinks intracellular proteins and preserves and stabilizes the cell so that it is ready for microscopy. In contrast to conventional glutaraldehyde fixation, tissue autofluorescence does not increase after fixation. Caged glutaraldehyde may in future enable functional experiments on living cells under a light microscope in which events of interest can be stopped in spatially confined volumes at defined time points. Samples with individually stopped events could then later be analyzed in ultrastructural studies.
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Affiliation(s)
- Korwin M Schelkle
- Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany.,InnovationLab GmbH, Speyerer Strasse 4, 69115, Heidelberg, Germany
| | - Christopher Schmid
- Center of Advanced Materials, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 225, 69120, Heidelberg, Germany
| | - Klaus Yserentant
- Center of Advanced Materials, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 225, 69120, Heidelberg, Germany.,Physikalisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 229, 69120, Heidelberg, Germany.,CellNetworks, Single Molecule Spectroscopy, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany
| | - Markus Bender
- Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Irene Wacker
- Center of Advanced Materials, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 225, 69120, Heidelberg, Germany
| | - Martin Petzoldt
- Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany.,InnovationLab GmbH, Speyerer Strasse 4, 69115, Heidelberg, Germany
| | - Manuel Hamburger
- Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany.,InnovationLab GmbH, Speyerer Strasse 4, 69115, Heidelberg, Germany
| | - Dirk-Peter Herten
- Physikalisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 229, 69120, Heidelberg, Germany.,CellNetworks, Single Molecule Spectroscopy, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany
| | - Richard Wombacher
- Institut für Pharmazie und Molekulare Biotechnologie, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Rasmus R Schröder
- Center of Advanced Materials, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 225, 69120, Heidelberg, Germany.,CellNetworks, Cryo Electron Microscopy, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany
| | - Uwe H F Bunz
- Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany.,Center of Advanced Materials, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 225, 69120, Heidelberg, Germany
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10
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Fichte MAH, Weyel XMM, Junek S, Schäfer F, Herbivo C, Goeldner M, Specht A, Wachtveitl J, Heckel A. Three-Dimensional Control of DNA Hybridization by Orthogonal Two-Color Two-Photon Uncaging. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603281] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Manuela A. H. Fichte
- Institute of Organic Chemistry and Chemical Biology; Goethe-University Frankfurt; Max-von-Laue-Strasse 9 60438 Frankfurt am Main Germany
| | - Xenia M. M. Weyel
- Institute of Organic Chemistry and Chemical Biology; Goethe-University Frankfurt; Max-von-Laue-Strasse 9 60438 Frankfurt am Main Germany
| | - Stephan Junek
- Imaging Facility; Max Planck Institute for Brain Research; Max-von-Laue-Strasse 4 60438 Frankfurt am Main Germany
| | - Florian Schäfer
- Institute of Organic Chemistry and Chemical Biology; Goethe-University Frankfurt; Max-von-Laue-Strasse 9 60438 Frankfurt am Main Germany
| | - Cyril Herbivo
- Centre National de la Recherche Scientifique; Université de Strasbourg, Unité Mixte de Recherche 7199, Laboratoire de Conception et Application de Molécules Bioactives, Équipe de Chimie et Neurobiologie Moléculaire; 67400 Illkirch France
| | - Maurice Goeldner
- Centre National de la Recherche Scientifique; Université de Strasbourg, Unité Mixte de Recherche 7199, Laboratoire de Conception et Application de Molécules Bioactives, Équipe de Chimie et Neurobiologie Moléculaire; 67400 Illkirch France
| | - Alexandre Specht
- Centre National de la Recherche Scientifique; Université de Strasbourg, Unité Mixte de Recherche 7199, Laboratoire de Conception et Application de Molécules Bioactives, Équipe de Chimie et Neurobiologie Moléculaire; 67400 Illkirch France
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry; Goethe University Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Alexander Heckel
- Institute of Organic Chemistry and Chemical Biology; Goethe-University Frankfurt; Max-von-Laue-Strasse 9 60438 Frankfurt am Main Germany
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