1
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Du J, Dartawan R, Rice W, Gao F, Zhou JH, Sheng J. Fluorescent Platforms for RNA Chemical Biology Research. Genes (Basel) 2022; 13:1348. [PMID: 36011259 PMCID: PMC9407474 DOI: 10.3390/genes13081348] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 12/03/2022] Open
Abstract
Efficient detection and observation of dynamic RNA changes remain a tremendous challenge. However, the continuous development of fluorescence applications in recent years enhances the efficacy of RNA imaging. Here we summarize some of these developments from different aspects. For example, single-molecule fluorescence in situ hybridization (smFISH) can detect low abundance RNA at the subcellular level. A relatively new aptamer, Mango, is widely applied to label and track RNA activities in living cells. Molecular beacons (MBs) are valid for quantifying both endogenous and exogenous mRNA and microRNA (miRNA). Covalent binding enzyme labeling fluorescent group with RNA of interest (ROI) partially overcomes the RNA length limitation associated with oligonucleotide synthesis. Forced intercalation (FIT) probes are resistant to nuclease degradation upon binding to target RNA and are used to visualize mRNA and messenger ribonucleoprotein (mRNP) activities. We also summarize the importance of some fluorescence spectroscopic techniques in exploring the function and movement of RNA. Single-molecule fluorescence resonance energy transfer (smFRET) has been employed to investigate the dynamic changes of biomolecules by covalently linking biotin to RNA, and a focus on dye selection increases FRET efficiency. Furthermore, the applications of fluorescence assays in drug discovery and drug delivery have been discussed. Fluorescence imaging can also combine with RNA nanotechnology to target tumors. The invention of novel antibacterial drugs targeting non-coding RNAs (ncRNAs) is also possible with steady-state fluorescence-monitored ligand-binding assay and the T-box riboswitch fluorescence anisotropy assay. More recently, COVID-19 tests using fluorescent clustered regularly interspaced short palindromic repeat (CRISPR) technology have been demonstrated to be efficient and clinically useful. In summary, fluorescence assays have significant applications in both fundamental and clinical research and will facilitate the process of RNA-targeted new drug discovery, therefore deserving further development and updating.
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Affiliation(s)
| | | | | | | | | | - Jia Sheng
- Department of Chemistry, The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (J.D.); (R.D.); (W.R.); (F.G.); (J.H.Z.)
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2
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Müggenburg F, Müller S. Azide-modified Nucleosides as Versatile Tools for Bioorthogonal Labeling and Functionalization. CHEM REC 2022; 22:e202100322. [PMID: 35189013 DOI: 10.1002/tcr.202100322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 02/06/2023]
Abstract
Azide-modified nucleosides are important building blocks for RNA and DNA functionalization by click chemistry based on azide-alkyne cycloaddition. This has put demand on synthetic chemistry to develop approaches for the preparation of azide-modified nucleoside derivatives. We review here the available methods for the synthesis of various nucleosides decorated with azido groups at the sugar residue or nucleobase, their incorporation into oligonucleotides and cellular RNAs, and their application in azide-alkyne cycloadditions for labelling and functionalization.
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Affiliation(s)
- Frederik Müggenburg
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Straße 4, 17487, Greifswald, Germany
| | - Sabine Müller
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Straße 4, 17487, Greifswald, Germany
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3
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Xiao L, Jun YW, Kool ET. DNA Tiling Enables Precise Acylation‐Based Labeling and Control of mRNA. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202112106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Lu Xiao
- Department of Chemistry Stanford University Stanford CA 94305 USA
| | - Yong Woong Jun
- Department of Chemistry Stanford University Stanford CA 94305 USA
| | - Eric T. Kool
- Department of Chemistry Stanford University Stanford CA 94305 USA
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4
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Xiao L, Jun YW, Kool ET. DNA Tiling Enables Precise Acylation-Based Labeling and Control of mRNA. Angew Chem Int Ed Engl 2021; 60:26798-26805. [PMID: 34624169 PMCID: PMC8649056 DOI: 10.1002/anie.202112106] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/04/2021] [Indexed: 12/15/2022]
Abstract
Methods for the site-selective labeling of long, native RNAs are needed for studying mRNA biology and future therapies. Current approaches involve engineering RNA sequences, which may alter folding, or are limited to specific sequences or bases. Here, we describe a versatile strategy for mRNA conjugation via a novel DNA-tiling approach. The method, TRAIL, exploits a pool of "protector" oligodeoxynucleotides to hybridize and block the mRNA, combined with an "inducer" DNA that extrudes a reactive RNA loop for acylation at a predetermined site. Using TRAIL, an azido-acylimidazole reagent was employed for labeling and controlling RNA for multiple applications in vitro and in cells, including analysis of RNA-binding proteins, imaging mRNA in cells, and analysis and control of translation. The TRAIL approach offers an efficient and accessible way to label and manipulate RNAs of virtually any length or origin without altering native sequence.
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Affiliation(s)
- Lu Xiao
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Yong Woong Jun
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
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5
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Depmeier H, Hoffmann E, Bornewasser L, Kath‐Schorr S. Strategies for Covalent Labeling of Long RNAs. Chembiochem 2021; 22:2826-2847. [PMID: 34043861 PMCID: PMC8518768 DOI: 10.1002/cbic.202100161] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/26/2021] [Indexed: 12/17/2022]
Abstract
The introduction of chemical modifications into long RNA molecules at specific positions for visualization, biophysical investigations, diagnostic and therapeutic applications still remains challenging. In this review, we present recent approaches for covalent internal labeling of long RNAs. Topics included are the assembly of large modified RNAs via enzymatic ligation of short synthetic oligonucleotides and synthetic biology approaches preparing site-specifically modified RNAs via in vitro transcription using an expanded genetic alphabet. Moreover, recent approaches to employ deoxyribozymes (DNAzymes) and ribozymes for RNA labeling and RNA methyltransferase based labeling strategies are presented. We discuss the potentials and limits of the individual methods, their applicability for RNAs with several hundred to thousands of nucleotides in length and indicate future directions in the field.
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Affiliation(s)
- Hannah Depmeier
- University of CologneDepartment of ChemistryGreinstr. 450939CologneGermany
| | - Eva Hoffmann
- University of CologneDepartment of ChemistryGreinstr. 450939CologneGermany
| | - Lisa Bornewasser
- University of CologneDepartment of ChemistryGreinstr. 450939CologneGermany
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6
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Ovcharenko A, Weissenboeck FP, Rentmeister A. Tag-Free Internal RNA Labeling and Photocaging Based on mRNA Methyltransferases. Angew Chem Int Ed Engl 2021; 60:4098-4103. [PMID: 33095964 PMCID: PMC7898847 DOI: 10.1002/anie.202013936] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Indexed: 12/19/2022]
Abstract
The mRNA modification N6 -methyladenosine (m6 A) is associated with multiple roles in cell function and disease. The methyltransferases METTL3-METTL14 and METTL16 act as "writers" for different target transcripts and sequence motifs. The modification is perceived by dedicated "reader" and "eraser" proteins, but not by polymerases. We report that METTL3-14 shows remarkable cosubstrate promiscuity, enabling sequence-specific internal labeling of RNA without additional guide RNAs. The transfer of ortho-nitrobenzyl and 6-nitropiperonyl groups allowed enzymatic photocaging of RNA in the consensus motif, which impaired polymerase-catalyzed primer extension in a reversible manner. METTL16 was less promiscuous but suitable for chemo-enzymatic labeling using different types of click chemistry. Since both enzymes act on distinct sequence motifs, their combination allowed orthogonal chemo-enzymatic modification of different sites in a single RNA.
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Affiliation(s)
- Anna Ovcharenko
- Department of ChemistryInstitute of BiochemistryUniversity of Münster, Corrensstrasse 3648149MünsterGermany
- Cells in Motion Interfaculty CenterUniversity of MünsterWaldeyerstraße 1548149MünsterGermany
| | - Florian P. Weissenboeck
- Department of ChemistryInstitute of BiochemistryUniversity of Münster, Corrensstrasse 3648149MünsterGermany
- Cells in Motion Interfaculty CenterUniversity of MünsterWaldeyerstraße 1548149MünsterGermany
| | - Andrea Rentmeister
- Department of ChemistryInstitute of BiochemistryUniversity of Münster, Corrensstrasse 3648149MünsterGermany
- Cells in Motion Interfaculty CenterUniversity of MünsterWaldeyerstraße 1548149MünsterGermany
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7
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Ovcharenko A, Weissenboeck FP, Rentmeister A. Tag‐Free Internal RNA Labeling and Photocaging Based on mRNA Methyltransferases. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202013936] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Anna Ovcharenko
- Department of Chemistry Institute of Biochemistry University of Münster, Corrensstrasse 36 48149 Münster Germany
- Cells in Motion Interfaculty Center University of Münster Waldeyerstraße 15 48149 Münster Germany
| | - Florian P. Weissenboeck
- Department of Chemistry Institute of Biochemistry University of Münster, Corrensstrasse 36 48149 Münster Germany
- Cells in Motion Interfaculty Center University of Münster Waldeyerstraße 15 48149 Münster Germany
| | - Andrea Rentmeister
- Department of Chemistry Institute of Biochemistry University of Münster, Corrensstrasse 36 48149 Münster Germany
- Cells in Motion Interfaculty Center University of Münster Waldeyerstraße 15 48149 Münster Germany
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8
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Velema WA, Park HS, Kadina A, Orbai L, Kool ET. Trapping Transient RNA Complexes by Chemically Reversible Acylation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202010861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Willem A. Velema
- Institute for Molecules and Materials Radboud University Nijmegen 6525 AJ The Netherlands
| | - Hyun Shin Park
- Department of Chemistry Stanford University Stanford CA 94305 USA
| | - Anastasia Kadina
- Department of Chemistry Stanford University Stanford CA 94305 USA
| | - Lucian Orbai
- Cell Data Sciences 46127 Landing Pkwy Fremont CA 94538 USA
| | - Eric T. Kool
- Department of Chemistry Stanford University Stanford CA 94305 USA
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9
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Velema WA, Park HS, Kadina A, Orbai L, Kool ET. Trapping Transient RNA Complexes by Chemically Reversible Acylation. Angew Chem Int Ed Engl 2020; 59:22017-22022. [PMID: 32845055 DOI: 10.1002/anie.202010861] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Indexed: 01/01/2023]
Abstract
RNA-RNA interactions are essential for biology, but they can be difficult to study due to their transient nature. While crosslinking strategies can in principle be used to trap such interactions, virtually all existing strategies for crosslinking are poorly reversible, chemically modifying the RNA and hindering molecular analysis. We describe a soluble crosslinker design (BINARI) that reacts with RNA through acylation. We show that it efficiently crosslinks noncovalent RNA complexes with mimimal sequence bias and establish that the crosslink can be reversed by phosphine reduction of azide trigger groups, thereby liberating the individual RNA components for further analysis. The utility of the new approach is demonstrated by reversible protection against nuclease degradation and trapping transient RNA complexes of E. coli DsrA-rpoS derived bulge-loop interactions, which underlines the potential of BINARI crosslinkers to probe RNA regulatory networks.
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Affiliation(s)
- Willem A Velema
- Institute for Molecules and Materials, Radboud University, Nijmegen, 6525, AJ, The Netherlands
| | - Hyun Shin Park
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Anastasia Kadina
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Lucian Orbai
- Cell Data Sciences, 46127 Landing Pkwy, Fremont, CA, 94538, USA
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
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10
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Ghaem Maghami M, Dey S, Lenz AK, Höbartner C. Repurposing Antiviral Drugs for Orthogonal RNA-Catalyzed Labeling of RNA. Angew Chem Int Ed Engl 2020; 59:9335-9339. [PMID: 32162405 PMCID: PMC7318677 DOI: 10.1002/anie.202001300] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/29/2020] [Indexed: 12/16/2022]
Abstract
In vitro selected ribozymes are promising tools for site-specific labeling of RNA. Previously known nucleic acid catalysts attached fluorescently labeled adenosine or guanosine derivatives through 2',5'-branched phosphodiester bonds to the RNA of interest. Herein, we report new ribozymes that use orthogonal substrates, derived from the antiviral drug tenofovir, and attach bioorthogonal functional groups, as well as affinity handles and fluorescent reporter units through a hydrolytically more stable phosphonate ester linkage. The tenofovir transferase ribozymes were identified by in vitro selection and are orthogonal to nucleotide transferase ribozymes. As genetically encodable functional RNAs, these ribozymes may be developed for potential cellular applications. The orthogonal ribozymes addressed desired target sites in large RNAs in vitro, as shown by fluorescent labeling of E. coli 16S and 23S rRNAs in total cellular RNA.
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Affiliation(s)
- Mohammad Ghaem Maghami
- Universität Würzburg, Institut für Organische Chemie, Am Hubland, 97074, Würzburg, Germany.,International Max Planck Research School Molecular Biology, University of Göttingen, Germany
| | - Surjendu Dey
- Universität Würzburg, Institut für Organische Chemie, Am Hubland, 97074, Würzburg, Germany
| | - Ann-Kathrin Lenz
- Universität Würzburg, Institut für Organische Chemie, Am Hubland, 97074, Würzburg, Germany
| | - Claudia Höbartner
- Universität Würzburg, Institut für Organische Chemie, Am Hubland, 97074, Würzburg, Germany.,International Max Planck Research School Molecular Biology, University of Göttingen, Germany
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11
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Ghaem Maghami M, Dey S, Lenz A, Höbartner C. Repurposing Antiviral Drugs for Orthogonal RNA‐Catalyzed Labeling of RNA. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001300] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mohammad Ghaem Maghami
- Universität WürzburgInstitut für Organische Chemie Am Hubland 97074 Würzburg Germany
- International Max Planck Research School Molecular BiologyUniversity of Göttingen Germany
| | - Surjendu Dey
- Universität WürzburgInstitut für Organische Chemie Am Hubland 97074 Würzburg Germany
| | - Ann‐Kathrin Lenz
- Universität WürzburgInstitut für Organische Chemie Am Hubland 97074 Würzburg Germany
| | - Claudia Höbartner
- Universität WürzburgInstitut für Organische Chemie Am Hubland 97074 Würzburg Germany
- International Max Planck Research School Molecular BiologyUniversity of Göttingen Germany
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12
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Jain PK, Friedman SH. The ULTIMATE Reagent: A Universal Photocleavable and Clickable Reagent for the Regiospecific and Reversible End Labeling of Any Nucleic Acid. Chembiochem 2018. [PMID: 29516677 DOI: 10.1002/cbic.201800028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
There is a need for methods to chemically incorporate photocleavable labels into synthetic and biologically sourced nucleic acids in a chemically defined and reversible manner. We have previously demonstrated that the light-cleaved diazo di-methoxy nitro phenyl ethyl (diazo-DMNPE) group has a remarkable regiospecificity for modifying terminally phosphorylated siRNA. Building on this observation, we have identified conditions under which a diazo-DMNPE reagent that we designed (diazo-DMNPE-azide or DDA) is able to singly modify any nucleic acid (RNA, DNA, single-stranded, double-stranded, 3' or 5' phosphate). It can then be modified with any clickable reagent to incorporate arbitrary labels such as fluorophores into the nucleic acid. Finally, native nucleic acid can be regenerated directly through photolysis of the reagent. Use of the described approach should allow for the tagging of any nucleic acid, from any source-natural or unnatural-while allowing for the light-induced regeneration of native nucleic acid.
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Affiliation(s)
- Piyush K Jain
- University of Missouri-Kansas City, Department of Pharmaceutical Sciences, 2464 Charlotte Street, Kansas City, MO, 64108, USA
| | - Simon H Friedman
- University of Missouri-Kansas City, Department of Pharmaceutical Sciences, 2464 Charlotte Street, Kansas City, MO, 64108, USA
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13
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Fonvielle M, Sakkas N, Iannazzo L, Le Fournis C, Patin D, Mengin-Lecreulx D, El-Sagheer A, Braud E, Cardon S, Brown T, Arthur M, Etheve-Quelquejeu M. Electrophilic RNA for Peptidyl-RNA Synthesis and Site-Specific Cross-Linking with tRNA-Binding Enzymes. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606843] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Matthieu Fonvielle
- Laboratoire de Recherche Moléculaire sur les Antibiotiques Centre de Recherche des Cordeliers, Equipe 12, UMR S 1138; INSERM; Université Pierre et Marie Curie-Paris 6, Université Paris Descartes; 15 rue de L'Ecole de Médecine Paris F-75006 France
| | - Nicolas Sakkas
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques; Université Paris Descartes, UMR 8601; Paris F-75006 France
- CNRS UMR 8601; Paris F-75006 France
| | - Laura Iannazzo
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques; Université Paris Descartes, UMR 8601; Paris F-75006 France
- CNRS UMR 8601; Paris F-75006 France
| | - Chloé Le Fournis
- Laboratoire de Recherche Moléculaire sur les Antibiotiques Centre de Recherche des Cordeliers, Equipe 12, UMR S 1138; INSERM; Université Pierre et Marie Curie-Paris 6, Université Paris Descartes; 15 rue de L'Ecole de Médecine Paris F-75006 France
| | - Delphine Patin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud; Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Dominique Mengin-Lecreulx
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud; Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Afaf El-Sagheer
- Department of Chemistry; University of Oxford, Chemistry Research Laboratory; 12 Mansfield Road Oxford OX1 3TA UK
- Chemistry Branch, Dept. of Science and Mathematics, Faculty of Petroleum and Mining Engineering; Suez Canal University; Suez 43721 Egypt
| | - Emmanuelle Braud
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques; Université Paris Descartes, UMR 8601; Paris F-75006 France
- CNRS UMR 8601; Paris F-75006 France
| | - Sébastien Cardon
- Laboratoire de Recherche Moléculaire sur les Antibiotiques Centre de Recherche des Cordeliers, Equipe 12, UMR S 1138; INSERM; Université Pierre et Marie Curie-Paris 6, Université Paris Descartes; 15 rue de L'Ecole de Médecine Paris F-75006 France
| | - Tom Brown
- Department of Chemistry; University of Oxford, Chemistry Research Laboratory; 12 Mansfield Road Oxford OX1 3TA UK
| | - Michel Arthur
- Laboratoire de Recherche Moléculaire sur les Antibiotiques Centre de Recherche des Cordeliers, Equipe 12, UMR S 1138; INSERM; Université Pierre et Marie Curie-Paris 6, Université Paris Descartes; 15 rue de L'Ecole de Médecine Paris F-75006 France
| | - Mélanie Etheve-Quelquejeu
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques; Université Paris Descartes, UMR 8601; Paris F-75006 France
- CNRS UMR 8601; Paris F-75006 France
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14
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Fonvielle M, Sakkas N, Iannazzo L, Le Fournis C, Patin D, Mengin-Lecreulx D, El-Sagheer A, Braud E, Cardon S, Brown T, Arthur M, Etheve-Quelquejeu M. Electrophilic RNA for Peptidyl-RNA Synthesis and Site-Specific Cross-Linking with tRNA-Binding Enzymes. Angew Chem Int Ed Engl 2016; 55:13553-13557. [PMID: 27667506 DOI: 10.1002/anie.201606843] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 09/03/2016] [Indexed: 12/12/2022]
Abstract
RNA functionalization is challenging due to the instability of RNA and the limited range of available enzymatic reactions. We developed a strategy based on solid phase synthesis and post-functionalization to introduce an electrophilic site at the 3' end of tRNA analogues. The squarate diester used as an electrophile enabled sequential amidation and provided asymmetric squaramides with high selectivity. The squaramate-RNAs specifically reacted with the lysine of UDP-MurNAc-pentapeptide, a peptidoglycan precursor used by the aminoacyl-transferase FemXWv for synthesis of the bacterial cell wall. The peptidyl-RNA obtained with squaramate-RNA and unprotected UDP-MurNAc-pentapeptide efficiently inhibited FemXWv . The squaramate unit also promoted specific cross-linking of RNA to the catalytic Lys of FemXWv but not to related transferases recognizing different aminoacyl-tRNAs. Thus, squaramate-RNAs provide specificity for cross-linking with defined groups in complex biomolecules due to its unique reactivity.
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Affiliation(s)
- Matthieu Fonvielle
- Laboratoire de Recherche Moléculaire sur les Antibiotiques Centre de Recherche des Cordeliers, Equipe 12, UMR S 1138; INSERM, Université Pierre et Marie Curie-Paris 6, Université Paris Descartes, 15 rue de L'Ecole de Médecine, Paris, F-75006, France
| | - Nicolas Sakkas
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601, Paris, F-75006, France.,CNRS UMR 8601, Paris, F-75006, France
| | - Laura Iannazzo
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601, Paris, F-75006, France.,CNRS UMR 8601, Paris, F-75006, France
| | - Chloé Le Fournis
- Laboratoire de Recherche Moléculaire sur les Antibiotiques Centre de Recherche des Cordeliers, Equipe 12, UMR S 1138; INSERM, Université Pierre et Marie Curie-Paris 6, Université Paris Descartes, 15 rue de L'Ecole de Médecine, Paris, F-75006, France
| | - Delphine Patin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Dominique Mengin-Lecreulx
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Afaf El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK.,Chemistry Branch, Dept. of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez Canal University, Suez, 43721, Egypt
| | - Emmanuelle Braud
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601, Paris, F-75006, France.,CNRS UMR 8601, Paris, F-75006, France
| | - Sébastien Cardon
- Laboratoire de Recherche Moléculaire sur les Antibiotiques Centre de Recherche des Cordeliers, Equipe 12, UMR S 1138; INSERM, Université Pierre et Marie Curie-Paris 6, Université Paris Descartes, 15 rue de L'Ecole de Médecine, Paris, F-75006, France
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Michel Arthur
- Laboratoire de Recherche Moléculaire sur les Antibiotiques Centre de Recherche des Cordeliers, Equipe 12, UMR S 1138; INSERM, Université Pierre et Marie Curie-Paris 6, Université Paris Descartes, 15 rue de L'Ecole de Médecine, Paris, F-75006, France.
| | - Mélanie Etheve-Quelquejeu
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601, Paris, F-75006, France. .,CNRS UMR 8601, Paris, F-75006, France.
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15
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Muttach F, Rentmeister A. One-pot modification of 5′-capped RNA based on methionine analogs. Methods 2016; 107:3-9. [DOI: 10.1016/j.ymeth.2016.02.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 02/12/2016] [Indexed: 12/29/2022] Open
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16
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Holstein JM, Anhäuser L, Rentmeister A. Modifying the 5'-Cap for Click Reactions of Eukaryotic mRNA and To Tune Translation Efficiency in Living Cells. Angew Chem Int Ed Engl 2016; 55:10899-903. [PMID: 27511141 DOI: 10.1002/anie.201604107] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 06/21/2016] [Indexed: 11/06/2022]
Abstract
The 5'-cap is a hallmark of eukaryotic mRNAs and plays fundamental roles in RNA metabolism, ranging from quality control to export and translation. Modifying the 5'-cap may thus enable modulation of the underlying processes and investigation or tuning of several biological functions. A straightforward approach is presented for the efficient production of a range of N7-modified caps based on the highly promiscuous methyltransferase Ecm1. We show that these, as well as N(2) -modified 5'-caps, can be used to tune translation of the respective mRNAs both in vitro and in cells. Appropriate modifications allow subsequent bioorthogonal chemistry, as demonstrated by intracellular live-cell labeling of a target mRNA. The efficient and versatile N7 manipulation of the mRNA cap makes mRNAs amenable to both modulation of their biological function and intracellular labeling, and represents a valuable addition to the chemical biology toolbox.
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Affiliation(s)
- Josephin M Holstein
- University of Muenster, Department of Chemistry, Institute of Biochemistry, Wilhelm-Klemm-Strasse 2, 48149, Muenster, Germany
| | - Lea Anhäuser
- University of Muenster, Department of Chemistry, Institute of Biochemistry, Wilhelm-Klemm-Strasse 2, 48149, Muenster, Germany
| | - Andrea Rentmeister
- University of Muenster, Department of Chemistry, Institute of Biochemistry, Wilhelm-Klemm-Strasse 2, 48149, Muenster, Germany. .,Cells-in-Motion Cluster of Excellence (EXC 1003-CiM), University of Muenster, Germany.
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Holstein JM, Anhäuser L, Rentmeister A. Modifizierung der 5′-Kappe eukaryotischer mRNA für Klick-Reaktionen und zur Beeinflussung der Translationseffizienz in lebenden Zellen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604107] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Josephin M. Holstein
- Westfälische Wilhelms-Universität Münster; Fachbereich Chemie und Pharmazie; Institut für Biochemie; Wilhelm-Klemm-Straße 2 48149 Münster Deutschland
| | - Lea Anhäuser
- Westfälische Wilhelms-Universität Münster; Fachbereich Chemie und Pharmazie; Institut für Biochemie; Wilhelm-Klemm-Straße 2 48149 Münster Deutschland
| | - Andrea Rentmeister
- Westfälische Wilhelms-Universität Münster; Fachbereich Chemie und Pharmazie; Institut für Biochemie; Wilhelm-Klemm-Straße 2 48149 Münster Deutschland
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM); Westfälische Wilhelms-Universität Münster; Deutschland
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