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Cornelissen NV, Mineikaitė R, Erguven M, Muthmann N, Peters A, Bartels A, Rentmeister A. Post-synthetic benzylation of the mRNA 5' cap via enzymatic cascade reactions. Chem Sci 2023; 14:10962-10970. [PMID: 37829022 PMCID: PMC10566477 DOI: 10.1039/d3sc03822j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 08/28/2023] [Indexed: 10/14/2023] Open
Abstract
mRNAs are emerging modalities for vaccination and protein replacement therapy. Increasing the amount of protein produced by stabilizing the transcript or enhancing translation without eliciting a strong immune response are major steps towards overcoming the present limitations and improving their therapeutic potential. The 5' cap is a hallmark of mRNAs and non-natural modifications can alter the properties of the entire transcript selectively. Here, we developed a versatile enzymatic cascade for regioselective benzylation of various biomolecules and applied it for post-synthetic modification of mRNA at the 5' cap to demonstrate its potential. Starting from six synthetic methionine analogues bearing (hetero-)benzyl groups, S-adenosyl-l-methionine analogues are formed and utilized for N7G-cap modification of mRNAs. This post-synthetic enzymatic modification exclusively modifies mRNAs at the terminal N7G, producing mRNAs with functional 5' caps. It avoids the wrong orientation of the 5' cap-a problem in common co-transcriptional capping. In the case of the 4-chlorobenzyl group, protein production was increased to 139% during in vitro translation and to 128-150% in four different cell lines. This 5' cap modification did not activate cytosolic pathogen recognition receptors TLR3, TLR7 or TLR8 significantly more than control mRNAs, underlining its potential to contribute to the development of future mRNA therapeutics.
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Affiliation(s)
- N V Cornelissen
- University of Münster, Department of Chemistry, Institute of Biochemistry Corrensstr. 36 48149 Münster Germany
| | - R Mineikaitė
- University of Münster, Department of Chemistry, Institute of Biochemistry Corrensstr. 36 48149 Münster Germany
| | - M Erguven
- University of Münster, Department of Chemistry, Institute of Biochemistry Corrensstr. 36 48149 Münster Germany
- University of Münster, Cells in Motion Interfaculty Centre Waldeyerstr. 15 48149 Münster Germany
| | - N Muthmann
- University of Münster, Department of Chemistry, Institute of Biochemistry Corrensstr. 36 48149 Münster Germany
| | - A Peters
- University of Münster, Department of Chemistry, Institute of Biochemistry Corrensstr. 36 48149 Münster Germany
| | - A Bartels
- University of Münster, Department of Chemistry, Institute of Biochemistry Corrensstr. 36 48149 Münster Germany
| | - A Rentmeister
- University of Münster, Department of Chemistry, Institute of Biochemistry Corrensstr. 36 48149 Münster Germany
- University of Münster, Cells in Motion Interfaculty Centre Waldeyerstr. 15 48149 Münster Germany
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2
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Malikėnas M, Masevičius V, Klimašauskas S. Synthesis of S-Adenosyl-L-Methionine Analogs with Extended Transferable Groups for Methyltransferase-Directed Labeling of DNA and RNA. Curr Protoc 2023; 3:e799. [PMID: 37327316 DOI: 10.1002/cpz1.799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
S-Adenosyl-L-methionine (AdoMet) is a ubiquitous methyl donor for a variety of biological methylation reactions catalyzed by methyltransferases (MTases). AdoMet analogs with extended propargylic chains replacing the sulfonium-bound methyl group can serve as surrogate cofactors for many DNA and RNA MTases, enabling covalent derivatization and subsequent labeling of their cognate target sites in DNA or RNA. Although AdoMet analogs with saturated aliphatic chains are less popular than propargylic ones, they can be useful for dedicated studies that require certain chemical derivatization. Here we describe synthetic procedures for the preparation of two AdoMet analogs, one with a transferable 6-azidohex-2-ynyl group (carrying an activating C≡C triple bond and a terminal azide functionality), and the other one with a transferable ethyl-2,2,2-d3 group (an isotope-labeled aliphatic moiety). Our synthetic approach is based on direct chemoselective alkylation of S-adenosyl-L-homocysteine at sulfur with a corresponding nosylate or triflate, respectively, under acidic conditions. We also describe synthetic routes to 6-azidohex-2-yn-1-ol and conversion of the alcohols to corresponding nosylate and triflate alkylators. Using these protocols, the synthetic AdoMet analogs can be prepared within 1 to 2 weeks. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of 6-azidohex-2-yn-1-ol Basic Protocol 2: Synthesis of 4-nitrobenzenesulfonate Basic Protocol 3: Synthesis of trifluoromethanesulfonates Basic Protocol 4: S-Alkylation of AdoHcy with sulfonates Basic Protocol 5: Purification and characterization of AdoMet analogs.
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Affiliation(s)
- Martynas Malikėnas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- Institute of Chemistry, Department of Chemistry and Geosciences, Vilnius University, Vilnius, Lithuania
| | - Viktoras Masevičius
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- Institute of Chemistry, Department of Chemistry and Geosciences, Vilnius University, Vilnius, Lithuania
| | - Saulius Klimašauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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3
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Brunderová M, Krömer M, Vlková M, Hocek M. Chloroacetamide-Modified Nucleotide and RNA for Bioconjugations and Cross-Linking with RNA-Binding Proteins. Angew Chem Int Ed Engl 2023; 62:e202213764. [PMID: 36533569 PMCID: PMC10107093 DOI: 10.1002/anie.202213764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 12/04/2022] [Accepted: 12/19/2022] [Indexed: 12/23/2022]
Abstract
Reactive RNA probes are useful for studying and identifying RNA-binding proteins. To that end, we designed and synthesized chloroacetamide-linked 7-deaza-ATP which was a good substrate for T7 RNA polymerase in in vitro transcription assay to synthesize reactive RNA probes bearing one or several reactive modifications. Modified RNA probes reacted with thiol-containing molecules as well as with cysteine- or histidine-containing peptides to form stable covalent products. They also reacted selectively with RNA-binding proteins to form cross-linked conjugates in high conversions thanks to proximity effect. Our modified nucleotide and RNA probes are promising tools for applications in RNA (bio)conjugations or RNA proteomics.
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Affiliation(s)
- Mária Brunderová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 12843, Prague 2, Czech Republic
| | - Matouš Krömer
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 12843, Prague 2, Czech Republic
| | - Marta Vlková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 12843, Prague 2, Czech Republic
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4
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Tota EM, Devaraj NK. Site-specific Covalent Labeling of DNA Substrates by an RNA Transglycosylase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.23.525207. [PMID: 36747847 PMCID: PMC9900779 DOI: 10.1101/2023.01.23.525207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Bacterial tRNA guanine transglycosylases (TGTs) catalyze the exchange of guanine for the 7-deazaguanine queuine precursor, prequeuosine1 (preQ1). While the native nucleic acid substrate for bacterial TGTs is the anticodon loop of queuine-cognate tRNAs, the minimum recognition sequence for the enzyme is a structured hairpin containing the target G nucleobase in a "UGU" loop motif. Previous work has established an RNA modification system, RNA-TAG, in which E. coli TGT exchanges the target G on an RNA of interest for chemically modified preQ1 substrates linked to a small molecule reporter such as biotin or a fluorophore. While extending the substrate scope of RNA transglycosylases to include DNA would enable numerous applications, it has been previously reported that TGT is incapable of modifying native DNA. Here we demonstrate that TGT can in fact recognize and label specific DNA substrates. Through iterative testing of rationally mutated DNA hairpin sequences, we determined the minimal sequence requirements for transglycosylation of unmodified DNA by E. coli TGT. Controlling steric constraint in the DNA hairpin dramatically affects labeling efficiency, and, when optimized, can lead to near quantitative site-specific modification. We demonstrate the utility of our newly developed DNA-TAG system by rapidly synthesizing probes for fluorescent Northern blotting of spliceosomal U6 RNA and RNA FISH visualization of the long noncoding RNA, MALAT1. The ease and convenience of the DNA-TAG system will provide researchers with a tool for accessing a wide variety of affordable modified DNA substrates.
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Klöcker N, Anhäuser L, Rentmeister A. Enzymatic Modification of the 5' Cap with Photocleavable ONB-Derivatives Using GlaTgs V34A. Chembiochem 2023; 24:e202200522. [PMID: 36408753 PMCID: PMC10108117 DOI: 10.1002/cbic.202200522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 11/22/2022]
Abstract
The 5' cap of mRNA plays a critical role in mRNA processing, quality control and turnover. Enzymatic availability of the 5' cap governs translation and could be a tool to investigate cell fate decisions and protein functions or develop protein replacement therapies. We have previously reported on the chemical synthesis of 5' cap analogues with photocleavable groups for this purpose. However, the synthesis is complex and post-synthetic enzymatic installation may make the technique more applicable to biological researchers. Common 5' cap analogues, like the cap 0, are commercially available and routinely used for in vitro transcription. Here, we report a facile enzymatic approach to attach photocleavable groups site-specifically to the N2 position of m7 G of the 5' cap. By expanding the substrate scope of the methyltransferase variant GlaTgs V34A and using synthetic co-substrate analogues, we could enzymatically photocage the 5' cap and recover it after irradiation.
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Affiliation(s)
- Nils Klöcker
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, Münster, Germany
| | - Lea Anhäuser
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, Münster, Germany
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6
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Gupta M, Levine SR, Spitale RC. Probing Nascent RNA with Metabolic Incorporation of Modified Nucleosides. Acc Chem Res 2022; 55:2647-2659. [PMID: 36073807 DOI: 10.1021/acs.accounts.2c00347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The discovery of previously unknown functional roles of RNA in biological systems has led to increased interest in revealing novel RNA molecules as therapeutic targets and the development of tools to better understand the role of RNA in cells. RNA metabolic labeling broadens the scope of studying RNA by incorporating of unnatural nucleobases and nucleosides with bioorthogonal handles that can be utilized for chemical modification of newly synthesized cellular RNA. Such labeling of RNA provides access to applications including measurement of the rates of synthesis and decay of RNA, cellular imaging for RNA localization, and selective enrichment of nascent RNA from the total RNA pool. Several unnatural nucleosides and nucleobases have been shown to be incorporated into RNA by endogenous RNA synthesis machinery of the cells. RNA metabolic labeling can also be performed in a cell-specific manner, where only cells expressing an essential enzyme incorporate the unnatural nucleobase into their RNA. Although several discoveries have been enabled by the current RNA metabolic labeling methods, some key challenges still exist: (i) toxicity of unnatural analogues, (ii) lack of RNA-compatible conjugation chemistries, and (iii) background incorporation of modified analogues in cell-specific RNA metabolic labeling. In this Account, we showcase work done in our laboratory to overcome these challenges faced by RNA metabolic labeling.To begin, we discuss the cellular pathways that have been utilized to perform RNA metabolic labeling and study the interaction between nucleosides and nucleoside kinases. Then we discuss the use of vinyl nucleosides for metabolic labeling and demonstrate the low toxicity of 5-vinyluridine (5-VUrd) compared to other widely used nucleosides. Next, we discuss cell-specific RNA metabolic labeling with unnatural nucleobases, which requires the expression of a specific phosphoribosyl transferase (PRT) enzyme for incorporation of the nucleobase into RNA. In the course of this work, we discovered the enzyme uridine monophosphate synthase (UMPS), which is responsible for nonspecific labeling with modified uracil nucleobases. We were able to overcome this background labeling by discovering a mutant uracil PRT (UPRT) that demonstrates highly specific RNA metabolic labeling with 5-vinyluracil (5-VU). Furthermore, we discuss the optimization of inverse-electron-demand Diels-Alder (IEDDA) reactions for performing chemical modification of vinyl nucleosides to achieve covalent conjugation of RNA without transcript degradation. Finally, we highlight our latest endeavor: the development of mutually orthogonal chemical reactions for selective labeling of 5-VUrd and 2-vinyladenosine (2-VAdo), which allows for potential use of multiple vinyl nucleosides for simultaneous investigation of multiple cellular processes involving RNA. We hope that our methods and discoveries encourage scientists studying biological systems to include RNA metabolic labeling in their toolkit for studying RNA and its role in biological systems.
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Bollu A, Peters A, Rentmeister A. Chemo-Enzymatic Modification of the 5' Cap To Study mRNAs. Acc Chem Res 2022; 55:1249-1261. [PMID: 35420432 DOI: 10.1021/acs.accounts.2c00059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The central dogma of molecular biology hinges on messenger RNA (mRNA), which presents a blueprint of the genetic information encoded in the DNA and serves as a template for translation into proteins. In addition to its fundamental importance in basic research, this class of biomolecules has recently become the first approved Covid vaccine, underscoring its utility in medical applications.Eukaryotic mRNA is heavily processed, including the 5' cap as the primary hallmark. This 5' cap protects mRNA from degradation by exoribonucleases but also interacts specifically with several proteins and enzymes to ensure mRNA turnover and processing, like splicing, export from the nucleus to the cytoplasm, and initiation of translation. The absence of a 5' cap leads to a strong immune response, and the methylation status contributes to distinguishing self from non-self RNA.Non-natural modifications of the 5' cap provide an avenue to label mRNAs and make them accessible to analyses, which is important to study their cellular localization, trafficking, and binding partners. They bear potential to engineer mRNAs, e.g., more stable or immunogenic mRNAs that are still translated, by impacting select interactions in a distinct manner. The modification of the 5' cap itself is powerful as it can be applied to make long mRNAs (∼1000 nt, not directly accessible by solid-phase synthesis) by in vitro transcription.This Account describes our contribution to the field of chemo-enzymatic modification of mRNA at the 5' cap. Our approach relies on RNA methyltransferases (MTases) with promiscuous activity on analogues of their natural cosubstrate S-adenosyl-L-methionine (AdoMet). We will describe how RNA MTases in combination with non-natural cosubstrates provide access to site-specific modification of different positions of the 5' cap, namely, the N2 and N7 position of guanosine and the N6 position of adenosine as the transcription start nucleotide (TSN) and exemplify strategies to make long mRNAs with modified 5' caps.We will compare the chemical and enzymatic synthesis of the AdoMet analogues used for this purpose. We could overcome previous limitations in methionine adenosyltransferase (MAT) substrate scope by engineering variants (termed PC-MATs) with the ability to convert methionine analogues with benzylic and photocaging groups at the sulfonium ion.The final part of this Account will highlight applications of the modified mRNAs. Like in many chemo-enzymatic approaches, a versatile strategy is to install small functional groups enzymatically and use them as handles in subsequent bioorthogonal reactions. We showed fluorescent labeling of mRNAs via different types of click chemistry in vitro and in cells. In a second line of applications, we used the handles to make mRNAs amenable for analyses, most notably next-generation sequencing. In the case of extremely promiscuous enzymes, the direct installation of photo-cross-linking groups was successful also and provided a way to covalently bind protein-interaction partners. Finally, the non-natural modifications of mRNAs can also modulate the properties of mRNAs. Propargylation of Am as the transcription start nucleotide at its N6 position maintained the translation of mRNAs but increased their immunogenicity. The installation of photocaging groups provides a way to revert these effects and control interactions by light.
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Affiliation(s)
- Amarnath Bollu
- Department of Chemistry and Pharmacy, Institute of Biochemistry Westfälische Wilhelms-Universität Münster, University of Münster, Corrensstrasse 36, 48149 Münster, Germany
| | - Aileen Peters
- Department of Chemistry and Pharmacy, Institute of Biochemistry Westfälische Wilhelms-Universität Münster, University of Münster, Corrensstrasse 36, 48149 Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry and Pharmacy, Institute of Biochemistry Westfälische Wilhelms-Universität Münster, University of Münster, Corrensstrasse 36, 48149 Münster, Germany
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8
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Fischer TR, Meidner L, Schwickert M, Weber M, Zimmermann RA, Kersten C, Schirmeister T, Helm M. Chemical biology and medicinal chemistry of RNA methyltransferases. Nucleic Acids Res 2022; 50:4216-4245. [PMID: 35412633 PMCID: PMC9071492 DOI: 10.1093/nar/gkac224] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/17/2022] [Accepted: 04/08/2022] [Indexed: 12/24/2022] Open
Abstract
RNA methyltransferases (MTases) are ubiquitous enzymes whose hitherto low profile in medicinal chemistry, contrasts with the surging interest in RNA methylation, the arguably most important aspect of the new field of epitranscriptomics. As MTases become validated as drug targets in all major fields of biomedicine, the development of small molecule compounds as tools and inhibitors is picking up considerable momentum, in academia as well as in biotech. Here we discuss the development of small molecules for two related aspects of chemical biology. Firstly, derivates of the ubiquitous cofactor S-adenosyl-l-methionine (SAM) are being developed as bioconjugation tools for targeted transfer of functional groups and labels to increasingly visible targets. Secondly, SAM-derived compounds are being investigated for their ability to act as inhibitors of RNA MTases. Drug development is moving from derivatives of cosubstrates towards higher generation compounds that may address allosteric sites in addition to the catalytic centre. Progress in assay development and screening techniques from medicinal chemistry have led to recent breakthroughs, e.g. in addressing human enzymes targeted for their role in cancer. Spurred by the current pandemic, new inhibitors against coronaviral MTases have emerged at a spectacular rate, including a repurposed drug which is now in clinical trial.
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Affiliation(s)
- Tim R Fischer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Laurenz Meidner
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Marvin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Marlies Weber
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Robert A Zimmermann
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
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9
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Zhou H, Li Y, Gan Y, Wang R. Total RNA Synthesis and its Covalent Labeling Innovation. Top Curr Chem (Cham) 2022; 380:16. [PMID: 35218412 DOI: 10.1007/s41061-022-00371-z] [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: 09/27/2021] [Accepted: 01/24/2022] [Indexed: 12/16/2022]
Abstract
RNA plays critical roles in a wide range of physiological processes. For example, it is well known that RNA plays an important role in regulating gene expression, cell proliferation, and differentiation, and many other chemical and biological processes. However, the research community still suffers from limited approaches that can be applied to readily visualize a specific RNA-of-interest (ROI). Several methods can be used to track RNAs; these rely mainly on biological properties, namely, hybridization, aptamer, reporter protein, and protein binding. With respect to covalent approaches, very few cases have been reported. Happily, several new methods for efficient labeling studies of ROIs have been demonstrated successfully in recent years. Additionally, methods employed for the detection of ROIs by RNA modifying enzymes have also proved feasible. Several approaches, namely, phosphoramidite chemistry, in vitro transcription reactions, co-transcription reactions, chemical post-modification, RNA modifying enzymes, ligation, and other methods targeted at RNA labeling have been revealed in the past decades. To illustrate the most recent achievements, this review aims to summarize the most recent research in the field of synthesis of RNAs-of-interest bearing a variety of unnatural nucleosides, the subsequent RNA labeling research via biocompatible ligation, and beyond.
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Affiliation(s)
- Hongling Zhou
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yuanyuan Li
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Youfang Gan
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Rui Wang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China. .,Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China. .,Key Laboratory of Natural Product and Resource, Shanghai Institute of Organic Chemistry, Shanghai, 230030, China.
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10
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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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11
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DNA Labeling Using DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:535-562. [DOI: 10.1007/978-3-031-11454-0_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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12
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Darrah KE, Deiters A. Translational control of gene function through optically regulated nucleic acids. Chem Soc Rev 2021; 50:13253-13267. [PMID: 34739027 DOI: 10.1039/d1cs00257k] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Translation of mRNA into protein is one of the most fundamental processes within biological systems. Gene expression is tightly regulated both in space and time, often involving complex signaling or gene regulatory networks, as most prominently observed in embryo development. Thus, studies of gene function require tools with a matching level of external control. Light is an excellent conditional trigger as it is minimally invasive, can be easily tuned in wavelength and amplitude, and can be applied with excellent spatial and temporal resolution. To this end, modification of established oligonucleotide-based technologies with optical control elements, in the form of photocaging groups and photoswitches, has rendered these tools capable of navigating the dynamic regulatory pathways of mRNA translation in cellular and in vivo models. In this review, we discuss the different optochemical approaches used to generate photoresponsive nucleic acids that activate and deactivate gene expression and function at the translational level.
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Affiliation(s)
- Kristie E Darrah
- 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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13
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Peters A, Herrmann E, Cornelissen NV, Klöcker N, Kümmel D, Rentmeister A. Visible-Light Removable Photocaging Groups Accepted by MjMAT Variant: Structural Basis and Compatibility with DNA and RNA Methyltransferases. Chembiochem 2021; 23:e202100437. [PMID: 34606675 PMCID: PMC9298006 DOI: 10.1002/cbic.202100437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/01/2021] [Indexed: 12/20/2022]
Abstract
Methylation and demethylation of DNA, RNA and proteins constitutes a major regulatory mechanism in epigenetic processes. Investigations would benefit from the ability to install photo‐cleavable groups at methyltransferase target sites that block interactions with reader proteins until removed by non‐damaging light in the visible spectrum. Engineered methionine adenosyltransferases (MATs) have been exploited in cascade reactions with methyltransferases (MTases) to modify biomolecules with non‐natural groups, including first evidence for accepting photo‐cleavable groups. We show that an engineered MAT from Methanocaldococcus jannaschii (PC‐MjMAT) is 308‐fold more efficient at converting ortho‐nitrobenzyl‐(ONB)‐homocysteine than the wildtype enzyme. PC‐MjMAT is active over a broad range of temperatures and compatible with MTases from mesophilic organisms. We solved the crystal structures of wildtype and PC‐MjMAT in complex with AdoONB and a red‐shifted derivative thereof. These structures reveal that aromatic stacking interactions within the ligands are key to accommodating the photocaging groups in PC‐MjMAT. The enlargement of the binding pocket eliminates steric clashes to enable AdoMet analogue binding. Importantly, PC‐MjMAT exhibits remarkable activity on methionine analogues with red‐shifted ONB‐derivatives enabling photo‐deprotection of modified DNA by visible light.
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Affiliation(s)
- Aileen Peters
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Eric Herrmann
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Nicolas V Cornelissen
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Nils Klöcker
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Daniel Kümmel
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
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14
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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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15
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Jalali E, Thorson JS. Enzyme-mediated bioorthogonal technologies: catalysts, chemoselective reactions and recent methyltransferase applications. Curr Opin Biotechnol 2021; 69:290-298. [PMID: 33901763 DOI: 10.1016/j.copbio.2021.02.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/28/2022]
Abstract
Transferases have emerged as among the best catalysts for enzyme-mediated bioorthogonal functional group installation to advance innovative in vitro, cell-based and in vivo chemical biology applications. This review introduces the key considerations for selecting enzyme catalysts and chemoselective reactions most amenable to bioorthogonal platform development and highlights relevant key technology development and applications for one ubiquitous transferase subclass - methyltransferases (MTs). Within this context, recent advances in MT-enabled bioorthogonal labeling/conjugation relevant to DNA, RNA, protein, and natural products (i.e. complex small molecule metabolites) are highlighted.
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Affiliation(s)
- Elnaz Jalali
- Department of Pharmaceutical Sciences, University of Kentucky College of Pharmacy, Lexington, KY 40536, United States
| | - Jon S Thorson
- Department of Pharmaceutical Sciences, University of Kentucky College of Pharmacy, Lexington, KY 40536, United States; Center for Pharmaceutical Research and Innovation, University of Kentucky College of Pharmacy, Lexington, KY 40536, United States.
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16
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Englert D, Matveeva R, Sunbul M, Wombacher R, Jäschke A. Aptamer-based proximity labeling guides covalent RNA modification. Chem Commun (Camb) 2021; 57:3480-3483. [PMID: 33688891 DOI: 10.1039/d1cc00786f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe the development of a proximity-induced bio-orthogonal inverse electron demand Diels-Alder reaction that exploits the high-affinity interaction between a dienophile-modified RhoBAST aptamer and its tetramethyl rhodamine methyltetrazine substrate. We applied this concept for covalent RNA labeling in proof-of-principle experiments.
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Affiliation(s)
- Daniel Englert
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany.
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17
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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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18
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Fantoni NZ, El-Sagheer AH, Brown T. A Hitchhiker's Guide to Click-Chemistry with Nucleic Acids. Chem Rev 2021; 121:7122-7154. [PMID: 33443411 DOI: 10.1021/acs.chemrev.0c00928] [Citation(s) in RCA: 143] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Click chemistry is an immensely powerful technique for the fast and efficient covalent conjugation of molecular entities. Its broad scope has positively impacted on multiple scientific disciplines, and its implementation within the nucleic acid field has enabled researchers to generate a wide variety of tools with application in biology, biochemistry, and biotechnology. Azide-alkyne cycloadditions (AAC) are still the leading technology among click reactions due to the facile modification and incorporation of azide and alkyne groups within biological scaffolds. Application of AAC chemistry to nucleic acids allows labeling, ligation, and cyclization of oligonucleotides efficiently and cost-effectively relative to previously used chemical and enzymatic techniques. In this review, we provide a guide to inexperienced and knowledgeable researchers approaching the field of click chemistry with nucleic acids. We discuss in detail the chemistry, the available modified-nucleosides, and applications of AAC reactions in nucleic acid chemistry and provide a critical view of the advantages, limitations, and open-questions within the field.
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Affiliation(s)
- Nicolò Zuin Fantoni
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K.,Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K
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19
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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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20
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Abstract
Labeling of nucleic acids is required for many studies aiming to elucidate their functions and dynamics in vitro and in cells. Out of the numerous labeling concepts that have been devised, covalent labeling provides the most stable linkage, an unrivaled choice of small and highly fluorescent labels and - thanks to recent advances in click chemistry - an incredible versatility. Depending on the approach, site-, sequence- and cell-specificity can be achieved. DNA and RNA labeling are rapidly developing fields that bring together multiple areas of research: on the one hand, synthetic and biophysical chemists develop new fluorescent labels and isomorphic nucleobases as well as faster and more selective bioorthogonal reactions. On the other hand, the number of enzymes that can be harnessed for post-synthetic and site-specific labeling of nucleic acids has increased significantly. Together with protein engineering and genetic manipulation of cells, intracellular and cell-specific labeling has become possible. In this review, we provide a structured overview of covalent labeling approaches for nucleic acids and highlight notable developments, in particular recent examples. The majority of this review will focus on fluorescent labeling; however, the principles can often be readily applied to other labels. We will start with entirely chemical approaches, followed by chemo-enzymatic strategies and ribozymes, and finish with metabolic labeling of nucleic acids. Each section is subdivided into direct (or one-step) and two-step labeling approaches and will start with DNA before treating RNA.
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Affiliation(s)
- Nils Klöcker
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, D-48149 Münster, Germany.
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21
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George JT, Srivatsan SG. Bioorthogonal chemistry-based RNA labeling technologies: evolution and current state. Chem Commun (Camb) 2020; 56:12307-12318. [PMID: 33026365 PMCID: PMC7611129 DOI: 10.1039/d0cc05228k] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
To understand the structure and ensuing function of RNA in various cellular processes, researchers greatly rely on traditional as well as contemporary labeling technologies to devise efficient biochemical and biophysical platforms. In this context, bioorthogonal chemistry based on chemoselective reactions that work under biologically benign conditions has emerged as a state-of-the-art labeling technology for functionalizing biopolymers. Implementation of this technology on sugar, protein, lipid and DNA is fairly well established. However, its use in labeling RNA has posed challenges due to the fragile nature of RNA. In this feature article, we provide an account of bioorthogonal chemistry-based RNA labeling techniques developed in our lab along with a detailed discussion on other technologies put forward recently. In particular, we focus on the development and applications of covalent methods to label RNA by transcription and posttranscription chemo-enzymatic approaches. It is expected that existing as well as new bioorthogonal functionalization methods will immensely advance our understanding of RNA and support the development of RNA-based diagnostic and therapeutic tools.
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Affiliation(s)
- Jerrin Thomas George
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr Homi Bhabha Road, Pune 411008, India.
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22
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Busby KN, Fulzele A, Zhang D, Bennett EJ, Devaraj NK. Enzymatic RNA Biotinylation for Affinity Purification and Identification of RNA-Protein Interactions. ACS Chem Biol 2020; 15:2247-2258. [PMID: 32706237 DOI: 10.1021/acschembio.0c00445] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Throughout their cellular lifetime, RNA transcripts are bound to proteins, playing crucial roles in RNA metabolism, trafficking, and function. Despite the importance of these interactions, identifying the proteins that interact with an RNA of interest in mammalian cells represents a major challenge in RNA biology. Leveraging the ability to site-specifically and covalently label an RNA of interest using E. coli tRNA guanine transglycosylase and an unnatural nucleobase substrate, we establish the identification of RNA-protein interactions and the selective enrichment of cellular RNA in mammalian systems. We demonstrate the utility of this approach through the identification of known binding partners of 7SK snRNA via mass spectrometry. Through a minimal 4-nucleotide mutation of the long noncoding RNA HOTAIR, enzymatic biotinylation enables identification of putative HOTAIR binding partners in MCF7 breast cancer cells that suggest new potential pathways for oncogenic function. Furthermore, using RNA sequencing and qPCR, we establish that an engineered enzyme variant achieves high levels of labeling selectivity against the human transcriptome allowing for 145-fold enrichment of cellular RNA directly from mammalian cell lysates. The flexibility and breadth of this approach suggests that this system could be routinely applied to the functional characterization of RNA, greatly expanding the toolbox available for studying mammalian RNA biology.
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Affiliation(s)
- Kayla N Busby
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Amitkumar Fulzele
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Dongyang Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Eric J Bennett
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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23
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Krell K, Harijan D, Ganz D, Doll L, Wagenknecht HA. Postsynthetic Modifications of DNA and RNA by Means of Copper-Free Cycloadditions as Bioorthogonal Reactions. Bioconjug Chem 2020; 31:990-1011. [DOI: 10.1021/acs.bioconjchem.0c00072] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Katja Krell
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Dennis Harijan
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Dorothée Ganz
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Larissa Doll
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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24
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Westerich KJ, Chandrasekaran KS, Gross-Thebing T, Kueck N, Raz E, Rentmeister A. Bioorthogonal mRNA labeling at the poly(A) tail for imaging localization and dynamics in live zebrafish embryos. Chem Sci 2020; 11:3089-3095. [PMID: 33623655 PMCID: PMC7879197 DOI: 10.1039/c9sc05981d] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/21/2020] [Indexed: 12/14/2022] Open
Abstract
Live imaging of mRNA in cells and organisms is important for understanding the dynamic aspects underlying its function.
Live imaging of mRNA in cells and organisms is important for understanding the dynamic aspects underlying its function. Ideally, labeling of mRNA should not alter its structure or function, nor affect the biological system. However, most methods applied in vivo make use of genetically encoded tags and reporters that significantly enhance the size of the mRNA of interest. Alternately, we utilize the 3′ poly(A) tail as a non-coding repetitive hallmark to covalently label mRNAs via bioorthogonal chemistry with different fluorophores from a wide range of spectra without significantly changing the size. We demonstrate that the labeled mRNAs can be visualized in cells and zebrafish embryos, and that they are efficiently translated. Importantly, the labeled mRNAs acquired the proper subcellular localization in developing zebrafish embryos and their dynamics could be tracked in vivo.
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Affiliation(s)
- Kim J Westerich
- Institute of Cell Biology Center for Molecular Biology of Inflammation , University of Münster , D-48149 Münster , Germany .
| | - Karthik S Chandrasekaran
- Institut für Biochemie , Westfälische Wilhelms-Universität Münster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
| | - Theresa Gross-Thebing
- Institute of Cell Biology Center for Molecular Biology of Inflammation , University of Münster , D-48149 Münster , Germany .
| | - Nadine Kueck
- Institut für Biochemie , Westfälische Wilhelms-Universität Münster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
| | - Erez Raz
- Cells in Motion Interfaculty Centre (CiMIC) , Waldeyerstraße 15 , D-48149 Münster , Germany.,Institute of Cell Biology Center for Molecular Biology of Inflammation , University of Münster , D-48149 Münster , Germany .
| | - Andrea Rentmeister
- Cells in Motion Interfaculty Centre (CiMIC) , Waldeyerstraße 15 , D-48149 Münster , Germany.,Institut für Biochemie , Westfälische Wilhelms-Universität Münster , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
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25
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Cornelissen NV, Michailidou F, Muttach F, Rau K, Rentmeister A. Nucleoside-modified AdoMet analogues for differential methyltransferase targeting. Chem Commun (Camb) 2020; 56:2115-2118. [PMID: 31970375 PMCID: PMC7030947 DOI: 10.1039/c9cc07807j] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Methyltransferases (MTases) modify a wide range of biomolecules using S-adenosyl-l-methionine (AdoMet) as the cosubstrate. Synthetic AdoMet analogues are powerful tools to site-specifically introduce a variety of functional groups and exhibit potential to be converted only by distinct MTases. Extending the size of the substituent at the sulfur/selenium atom provides selectivity among MTases but is insufficient to discriminate between promiscuous MTases. We present a panel of AdoMet analogues differing in the nucleoside moiety (NM-AdoMets). These NM-AdoMets were efficiently produced by a previously uncharacterized methionine adenosyltransferase (MAT) from methionine and ATP analogues, such as ITP and N6-propargyl-ATP. The N6-modification changed the relative activity of three representative MTases up to 13-fold resulting in discrimination of substrates for the methyl transfer and could also be combined with transfer of allyl and propargyl groups.
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Affiliation(s)
- Nicolas V Cornelissen
- Department of Chemistry, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Straße 2, D-48149 Muenster, Germany.
| | - Freideriki Michailidou
- Department of Chemistry, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Straße 2, D-48149 Muenster, Germany.
| | - Fabian Muttach
- Department of Chemistry, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Straße 2, D-48149 Muenster, Germany.
| | - Kristina Rau
- Department of Chemistry, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Straße 2, D-48149 Muenster, Germany.
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Straße 2, D-48149 Muenster, Germany.
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26
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Ghaem Maghami M, Scheitl CPM, Höbartner C. Direct in Vitro Selection of Trans-Acting Ribozymes for Posttranscriptional, Site-Specific, and Covalent Fluorescent Labeling of RNA. J Am Chem Soc 2019; 141:19546-19549. [PMID: 31778306 DOI: 10.1021/jacs.9b10531] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
General and efficient tools for site-specific fluorescent or bioorthogonal labeling of RNA are in high demand. Here, we report direct in vitro selection, characterization, and application of versatile trans-acting 2'-5' adenylyl transferase ribozymes for covalent and site-specific RNA labeling. The design of our partially structured RNA pool allowed for in vitro evolution of ribozymes that modify a predetermined nucleotide in cis (i.e., intramolecular reaction) and can then be easily engineered for applications in trans (i.e., in an intermolecular setup). The resulting ribozymes are readily designed for specific target sites in small and large RNAs and accept a wide variety of N6-modified ATP analogues as small-molecule substrates. The most efficient new ribozyme (FH14) shows excellent specificity toward its target sequence also in the context of total cellular RNA.
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Affiliation(s)
- Mohammad Ghaem Maghami
- Institute of Organic Chemistry , University of Würzburg , Am Hubland , 97074 Würzburg , Germany.,International Max Planck Research School for Molecular Biology , University Göttingen , 37077 Göttingen , Germany
| | - Carolin P M Scheitl
- Institute of Organic Chemistry , University of Würzburg , Am Hubland , 97074 Würzburg , Germany
| | - Claudia Höbartner
- Institute of Organic Chemistry , University of Würzburg , Am Hubland , 97074 Würzburg , Germany.,International Max Planck Research School for Molecular Biology , University Göttingen , 37077 Göttingen , Germany
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27
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Anhäuser L, Hüwel S, Zobel T, Rentmeister A. Multiple covalent fluorescence labeling of eukaryotic mRNA at the poly(A) tail enhances translation and can be performed in living cells. Nucleic Acids Res 2019; 47:e42. [PMID: 30726958 PMCID: PMC6468298 DOI: 10.1093/nar/gkz084] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 01/24/2019] [Accepted: 01/31/2019] [Indexed: 12/22/2022] Open
Abstract
Post-transcriptional regulation of gene expression occurs by multiple mechanisms, including subcellular localization of mRNA and alteration of the poly(A) tail length. These mechanisms play crucial roles in the dynamics of cell polarization and embryonic development. Furthermore, mRNAs are emerging therapeutics and chemical alterations to increase their translational efficiency are highly sought after. We show that yeast poly(A) polymerase can be used to install multiple azido-modified adenosine nucleotides to luciferase and eGFP-mRNAs. These mRNAs can be efficiently reacted in a bioorthogonal click reaction with fluorescent reporters without degradation and without sequence alterations in their coding or untranslated regions. Importantly, the modifications in the poly(A) tail impact positively on the translational efficiency of reporter-mRNAs in vitro and in cells. Therefore, covalent fluorescent labeling at the poly(A) tail presents a new way to increase the amount of reporter protein from exogenous mRNA and to label genetically unaltered and translationally active mRNAs.
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Affiliation(s)
- Lea Anhäuser
- Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Straße 2, 48149 Münster, Germany
| | - Sabine Hüwel
- Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Straße 2, 48149 Münster, Germany
| | - Thomas Zobel
- Cells-in-Motion Cluster of Excellence (EXC1003-CiM), University of Münster, Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Straße 2, 48149 Münster, Germany.,Cells-in-Motion Cluster of Excellence (EXC1003-CiM), University of Münster, Germany
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28
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Muthmann N, Hartstock K, Rentmeister A. Chemo-enzymatic treatment of RNA to facilitate analyses. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1561. [PMID: 31392842 DOI: 10.1002/wrna.1561] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/17/2019] [Accepted: 07/04/2019] [Indexed: 12/11/2022]
Abstract
Labeling RNA is a recurring problem to make RNA compatible with state-of-the-art methodology and comes in many flavors. Considering only cellular applications, the spectrum still ranges from site-specific labeling of individual transcripts, for example, for live-cell imaging of mRNA trafficking, to metabolic labeling in combination with next generation sequencing to capture dynamic aspects of RNA metabolism on a transcriptome-wide scale. Combining the specificity of RNA-modifying enzymes with non-natural substrates has emerged as a valuable strategy to modify RNA site- or sequence-specifically with functional groups suitable for subsequent bioorthogonal reactions and thus label RNA with reporter moieties such as affinity or fluorescent tags. In this review article, we will cover chemo-enzymatic approaches (a) for in vitro labeling of RNA for application in cells, (b) for treatment of total RNA, and (c) for metabolic labeling of RNA. This article is categorized under: RNA Processing < RNA Editing and Modification RNA Methods < RNA Analyses in vitro and In Silico RNA Methods < RNA Analyses in Cells.
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Affiliation(s)
- Nils Muthmann
- Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Katja Hartstock
- Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Münster, Germany
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29
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Cheng MSQ, Su MXX, Wang MXN, Sun MZY, Ou TM. Probes and drugs that interfere with protein translation via targeting to the RNAs or RNA-protein interactions. Methods 2019; 167:124-133. [PMID: 31185274 DOI: 10.1016/j.ymeth.2019.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/08/2019] [Accepted: 06/05/2019] [Indexed: 11/18/2022] Open
Abstract
Protein synthesis is critical to cell survival and translation regulation is essential to post-transcriptional gene expression regulation. Disorders of this process, particularly through RNA-binding proteins, is associated with the development and progression of a number of diseases, including cancers. However, the molecular mechanisms underlying the initiation of protein synthesis are intricate, making it difficult to find a drug that interferes with this process. Chemical probes are useful in elucidating the structures of RNA-protein complex and molecular mechanism of biological events. Moreover, some of these chemical probes show certain therapeutic benefits and can be further developed as leading compounds. Here, we will briefly review the general process and mechanism of protein synthesis, and emphasis on chemical probes in examples of probing the RNA structural changes and RNA-protein interactions. Moreover, the therapeutic potential of these probes is also discussed to give a comprehensive understanding.
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Affiliation(s)
- Miss Sui-Qi Cheng
- Sun Yat-Sen University, School of Pharmaceutical Sciences, Guangzhou, Guangdong 510006, China
| | - Miss Xiao-Xuan Su
- Sun Yat-Sen University, School of Pharmaceutical Sciences, Guangzhou, Guangdong 510006, China.
| | - Miss Xiao-Na Wang
- Sun Yat-Sen University, School of Pharmaceutical Sciences, Guangzhou, Guangdong 510006, China
| | - Miss Zhi-Yin Sun
- Sun Yat-Sen University, School of Pharmaceutical Sciences, Guangzhou, Guangdong 510006, China
| | - Tian-Miao Ou
- Sun Yat-Sen University, School of Pharmaceutical Sciences, 132 Waihuan East Road, Guangzhou University City, Guangzhou, Guangdong, China.
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30
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Kopcial M, Wojtczak BA, Kasprzyk R, Kowalska J, Jemielity J. N1-Propargylguanosine Modified mRNA Cap Analogs: Synthesis, Reactivity, and Applications to the Study of Cap-Binding Proteins. Molecules 2019; 24:molecules24101899. [PMID: 31108861 PMCID: PMC6572376 DOI: 10.3390/molecules24101899] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/14/2019] [Accepted: 05/15/2019] [Indexed: 01/07/2023] Open
Abstract
The mRNA 5′ cap consists of N7-methylguanosine bound by a 5′,5′-triphosphate bridge to the first nucleotide of the transcript. The cap interacts with various specific proteins and participates in all key mRNA-related processes, which may be of therapeutic relevance. There is a growing demand for new biophysical and biochemical methods to study cap–protein interactions and identify the factors which inhibit them. The development of such methods can be aided by the use of properly designed fluorescent molecular probes. Herein, we synthesized a new class of m7Gp3G cap derivatives modified with an alkyne handle at the N1-position of guanosine and, using alkyne-azide cycloaddition, we functionalized them with fluorescent tags to obtain potential probes. The cap derivatives and probes were evaluated in the context of two cap-binding proteins, eukaryotic translation initiation factor (eIF4E) and decapping scavenger (DcpS). Biochemical and biophysical studies revealed that N1-propargyl moiety did not significantly disturb cap–protein interaction. The fluorescent properties of the probes turned out to be in line with microscale thermophoresis (MST)-based binding assays.
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Affiliation(s)
- Michal Kopcial
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland.
- Centre of New Technologies, University of Warsaw; S. Banacha 2c, 02-097 Warsaw, Poland.
- Faculty of Physics, University of Warsaw; L. Pasteura 5, 02-093 Warsaw, Poland.
| | - Blazej A Wojtczak
- Centre of New Technologies, University of Warsaw; S. Banacha 2c, 02-097 Warsaw, Poland.
| | - Renata Kasprzyk
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland.
- Centre of New Technologies, University of Warsaw; S. Banacha 2c, 02-097 Warsaw, Poland.
- Faculty of Physics, University of Warsaw; L. Pasteura 5, 02-093 Warsaw, Poland.
| | - Joanna Kowalska
- Faculty of Physics, University of Warsaw; L. Pasteura 5, 02-093 Warsaw, Poland.
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw; S. Banacha 2c, 02-097 Warsaw, Poland.
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31
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Tera M, Harati Taji Z, Luedtke NW. Intercalation‐enhanced “Click” Crosslinking of DNA. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201808054] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Masayuki Tera
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
- Bioorganic Research InstituteSuntory Foundation for Life Sciences (SUNBOR) 8-1-1 Seikadai, Seika, Soraku Kyoto 619-0284 Japan
| | - Zahra Harati Taji
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Nathan W. Luedtke
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
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32
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Bednarek S, Madan V, Sikorski PJ, Bartenschlager R, Kowalska J, Jemielity J. mRNAs biotinylated within the 5' cap and protected against decapping: new tools to capture RNA-protein complexes. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0167. [PMID: 30397103 DOI: 10.1098/rstb.2018.0167] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2018] [Indexed: 01/09/2023] Open
Abstract
The 5'-terminus of eukaryotic mRNAs comprises a 7-methylguanosine cap linked to the first transcribed nucleotide via a 5'-5' triphosphate bond. This cap structure facilitates numerous interactions with molecules participating in mRNA processing, turnover and RNA translation. Here, we report the synthesis and biochemical properties of a set of biotin-labelled cap analogues modified within the triphosphate bridge and increasing mRNA stability while retaining biological activity. Successful co-transcriptional incorporation of the cap analogues allowed for the quantification of cap-dependent translation efficiency, capping efficiency and the susceptibility to decapping by Dcp2. The utility of such cap-biotinylated RNAs as molecular tool was demonstrated by ultraviolet-cross-linking and affinity capture of protein-RNA complexes. In conclusion, RNAs labelled with biotin via the 5' cap structure can be applied to a variety of biological experiments based on biotin-avidin interaction or by means of biotin-specific antibodies, including protein affinity purification, pull-down assays, in vivo visualization, cellular delivery and many others.This article is part of the theme issue '5' and 3' modifications controlling RNA degradation'.
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Affiliation(s)
- Sylwia Bednarek
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland.,Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Vanesa Madan
- Department of Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| | - Pawel J Sikorski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Ralf Bartenschlager
- Department of Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
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33
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Tera M, Harati Taji Z, Luedtke NW. Intercalation-enhanced "Click" Crosslinking of DNA. Angew Chem Int Ed Engl 2018; 57:15405-15409. [PMID: 30240107 DOI: 10.1002/anie.201808054] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 08/22/2018] [Indexed: 01/05/2023]
Abstract
DNA-DNA cross-linking agents constitute an important family of chemotherapeutics that non-specifically react with endogenous nucleophiles and therefore exhibit undesirable side effects. Here we report a cationic Sondheimer diyne derivative "DiMOC" that exhibits weak, reversible intercalation into duplex DNA (Kd =15 μm) where it undergoes tandem strain-promoted cross-linking of azide-containing DNA to give DNA-DNA interstrand crosslinks (ICLs) with an exceptionally high apparent rate constant kapp =2.1×105 m-1 s-1 . This represents a 21 000-fold rate enhancement as compared the reaction between DIMOC and 5-(azidomethyl)-2'-deoxyuridine (AmdU) nucleoside. As single agents, 5'-bispivaloyloxymethyl (POM)-AmdU and DiMOC exhibited low cytotoxicity, but highly toxic DNA-DNA ICLs were generated by metabolic incorporation of AmdU groups into cellular DNA, followed by treatment of the cells with DiMOC. These results provide the first examples of intercalation-enhanced bioorthogonal chemical reactions on DNA, and furthermore, the first strain-promoted double click (SPDC) reactions inside of living cells.
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Affiliation(s)
- Masayuki Tera
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Bioorganic Research Institute, Suntory Foundation for Life Sciences (SUNBOR), 8-1-1 Seikadai, Seika, Soraku, Kyoto, 619-0284, Japan
| | - Zahra Harati Taji
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Nathan W Luedtke
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
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34
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Tomkuvienė M, Mickutė M, Vilkaitis G, Klimašauskas S. Repurposing enzymatic transferase reactions for targeted labeling and analysis of DNA and RNA. Curr Opin Biotechnol 2018; 55:114-123. [PMID: 30296696 DOI: 10.1016/j.copbio.2018.09.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/14/2018] [Accepted: 09/19/2018] [Indexed: 12/16/2022]
Abstract
Produced as linear biopolymers from four major types of building blocks, DNA and RNA are further furnished with a range of covalent modifications. Despite the impressive specificity of natural enzymes, the transferred groups are often poor reporters and not amenable to further derivatization. Therefore, strategies based on repurposing some of these enzymatic reactions to accept derivatized versions of the transferrable groups have been exploited. By far the most widely used are S-adenosylmethionine-dependent methyltransferases, which along with several other nucleic acids modifying enzymes offer a broad selection of tagging chemistries and molecular features on DNA and RNA that can be targeted in vitro and in vivo. Engineered enzymatic reactions have been implemented in validated DNA sequencing-based protocols for epigenome analysis. The utility of chemo-enzymatic labeling is further enhanced with recent advances in physical detection of individual reporter groups on DNA using super resolution microscopy and nanopore sensing enabling single-molecule multiplex analysis of genetic and epigenetic marks in minute samples. Altogether, a number of new powerful techniques are currently in use or on the verge of real benchtop applications as research tools or next generation diagnostics.
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Affiliation(s)
- Miglė Tomkuvienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius LT-10257, Lithuania
| | - Milda Mickutė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius LT-10257, Lithuania
| | - Giedrius Vilkaitis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius LT-10257, Lithuania
| | - Saulius Klimašauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius LT-10257, Lithuania.
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35
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Rasale D, Patil K, Sauter B, Geigle S, Zhanybekova S, Gillingham D. A new water soluble copper N-heterocyclic carbene complex delivers mild O 6G-selective RNA alkylation. Chem Commun (Camb) 2018; 54:9174-9177. [PMID: 30062331 DOI: 10.1039/c8cc04476g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We show here that copper carbenes generated from diazo acetamides alkylate single RNAs, mRNAs, or pools of total transcriptome RNA, delivering exclusively alkylation at the O6 position in guanine (O6G). Although the reaction is effective with free copper some RNA fragmentation occurs, a problem we resolve by developing a novel water-stable copper N-heterocyclic carbene complex. Carboxymethyl adducts at O6G are known mutagenic lesions in DNA but their relevance in RNA biochemistry is unknown. As a case-in-point we re-examine an old controversy regarding whether O6G damage in RNA is susceptible to direct RNA repair.
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Affiliation(s)
- Dnyaneshwar Rasale
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056, Basel, Switzerland.
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36
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Anhäuser L, Muttach F, Rentmeister A. Reversible modification of DNA by methyltransferase-catalyzed transfer and light-triggered removal of photo-caging groups. Chem Commun (Camb) 2018; 54:449-451. [PMID: 29184954 DOI: 10.1039/c7cc08300a] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Methyltransferases are powerful tools for site-specific transfer of non-natural functional groups from synthetic analogs of their cosubstrate S-adenosyl-l-methionine (AdoMet). We present a new class of AdoMet analogs containing photo-caging (PC) groups in their side chain, enzymatic transfer of PC groups by a promiscuous DNA MTase as well as light-triggered removal from the target DNA. This strategy provides a new avenue to reversibly modulate the functionality of DNA at MTase target sites.
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Affiliation(s)
- Lea Anhäuser
- University of Münster, Department of Chemistry, Institute of Biochemistry, Wilhelm-Klemm-Str. 2, 48149 Münster, Germany.
| | - Fabian Muttach
- University of Münster, Department of Chemistry, Institute of Biochemistry, Wilhelm-Klemm-Str. 2, 48149 Münster, Germany.
| | - Andrea Rentmeister
- University of Münster, Department of Chemistry, Institute of Biochemistry, Wilhelm-Klemm-Str. 2, 48149 Münster, Germany. and Cells-in-Motion Cluster of Excellence (EXC1003-CiM), University of Münster, Germany
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37
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Hartstock K, Nilges BS, Ovcharenko A, Cornelissen NV, Püllen N, Lawrence-Dörner AM, Leidel SA, Rentmeister A. Enzymatic or In Vivo Installation of Propargyl Groups in Combination with Click Chemistry for the Enrichment and Detection of Methyltransferase Target Sites in RNA. Angew Chem Int Ed Engl 2018; 57:6342-6346. [PMID: 29461645 DOI: 10.1002/anie.201800188] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Indexed: 12/14/2022]
Abstract
m6 A is the most abundant internal modification in eukaryotic mRNA. It is introduced by METTL3-METTL14 and tunes mRNA metabolism, impacting cell differentiation and development. Precise transcriptome-wide assignment of m6 A sites is of utmost importance. However, m6 A does not interfere with Watson-Crick base pairing, making polymerase-based detection challenging. We developed a chemical biology approach for the precise mapping of methyltransferase (MTase) target sites based on the introduction of a bioorthogonal propargyl group in vitro and in cells. We show that propargyl groups can be introduced enzymatically by wild-type METTL3-METTL14. Reverse transcription terminated up to 65 % at m6 A sites after bioconjugation and purification, hence enabling detection of METTL3-METTL14 target sites by next generation sequencing. Importantly, we implemented metabolic propargyl labeling of RNA MTase target sites in vivo based on propargyl-l-selenohomocysteine and validated different types of known rRNA methylation sites.
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Affiliation(s)
- Katja Hartstock
- Institute of Biochemistry, Department of Chemistry, University of Münster, Wilhelm-Klemm-Straße 2, 48149, Münster, Germany
| | - Benedikt S Nilges
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany
| | - Anna Ovcharenko
- Institute of Biochemistry, Department of Chemistry, University of Münster, Wilhelm-Klemm-Straße 2, 48149, Münster, Germany
| | - Nicolas V Cornelissen
- Institute of Biochemistry, Department of Chemistry, University of Münster, Wilhelm-Klemm-Straße 2, 48149, Münster, Germany
| | - Nikolai Püllen
- Institute of Biochemistry, Department of Chemistry, University of Münster, Wilhelm-Klemm-Straße 2, 48149, Münster, Germany
| | - Ann-Marie Lawrence-Dörner
- Institute of Biochemistry, Department of Chemistry, University of Münster, Wilhelm-Klemm-Straße 2, 48149, Münster, Germany
| | - Sebastian A Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, Department of Chemistry, University of Münster, Wilhelm-Klemm-Straße 2, 48149, Münster, Germany
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38
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Hartstock K, Nilges BS, Ovcharenko A, Cornelissen NV, Püllen N, Lawrence‐Dörner A, Leidel SA, Rentmeister A. Enzymatischer oder In‐vivo‐Einbau von Propargylgruppen in Kombination mit Klick‐Chemie zur Anreicherung und Detektion von Methyltransferase‐Zielsequenzen in RNA. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201800188] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Katja Hartstock
- Institut für Biochemie Fachbereich Chemie und Pharmazie Universität Münster Wilhelm-Klemm-Straße 2 48149 Münster Deutschland
| | - Benedikt S. Nilges
- Max-Planck-Forschungsgruppe für RNA Biologie – Max-Planck-Institut für molekulare Biomedizin Röntgenstraße 20 48149 Münster Deutschland
| | - Anna Ovcharenko
- Institut für Biochemie Fachbereich Chemie und Pharmazie Universität Münster Wilhelm-Klemm-Straße 2 48149 Münster Deutschland
| | - Nicolas V. Cornelissen
- Institut für Biochemie Fachbereich Chemie und Pharmazie Universität Münster Wilhelm-Klemm-Straße 2 48149 Münster Deutschland
| | - Nikolai Püllen
- Institut für Biochemie Fachbereich Chemie und Pharmazie Universität Münster Wilhelm-Klemm-Straße 2 48149 Münster Deutschland
| | - Ann‐Marie Lawrence‐Dörner
- Institut für Biochemie Fachbereich Chemie und Pharmazie Universität Münster Wilhelm-Klemm-Straße 2 48149 Münster Deutschland
| | - Sebastian A. Leidel
- Max-Planck-Forschungsgruppe für RNA Biologie – Max-Planck-Institut für molekulare Biomedizin Röntgenstraße 20 48149 Münster Deutschland
| | - Andrea Rentmeister
- Institut für Biochemie Fachbereich Chemie und Pharmazie Universität Münster Wilhelm-Klemm-Straße 2 48149 Münster Deutschland
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39
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Muttach F, Muthmann N, Rentmeister A. Synthetic mRNA capping. Beilstein J Org Chem 2017; 13:2819-2832. [PMID: 30018667 PMCID: PMC5753152 DOI: 10.3762/bjoc.13.274] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 12/04/2017] [Indexed: 12/25/2022] Open
Abstract
Eukaryotic mRNA with its 5'-cap is of central importance for the cell. Many studies involving mRNA require reliable preparation and modification of 5'-capped RNAs. Depending on the length of the desired capped RNA, chemical or enzymatic preparation - or a combination of both - can be advantageous. We review state-of-the art methods and give directions for choosing the appropriate approach. We also discuss the preparation and properties of mRNAs with non-natural caps providing novel features such as improved stability or enhanced translational efficiency.
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Affiliation(s)
- Fabian Muttach
- University of Münster, Department of Chemistry, Institute of Biochemistry, Wilhelm-Klemm-Str. 2, 48149 Münster, Germany
| | - Nils Muthmann
- University of Münster, Department of Chemistry, Institute of Biochemistry, Wilhelm-Klemm-Str. 2, 48149 Münster, Germany
| | - Andrea Rentmeister
- University of Münster, Department of Chemistry, Institute of Biochemistry, Wilhelm-Klemm-Str. 2, 48149 Münster, Germany
- Cells-in-Motion Cluster of Excellence (EXC1003-CiM), University of Münster, Germany
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40
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Enzymatic Modification of 5'-Capped RNA and Subsequent Labeling by Click Chemistry. Methods Mol Biol 2017; 1428:45-60. [PMID: 27236791 DOI: 10.1007/978-1-4939-3625-0_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The combination of enzymatic modification and bioorthogonal click chemistry provides a powerful approach for site-specific labeling of different classes of biomolecules in vitro and even in cellular environments. Herein, we describe a chemoenzymatic method to site specifically label 5'-capped model mRNAs independent of their sequence. A trimethylguanosine synthase was engineered to introduce alkyne, azido, or 4-vinylbenzyl moieties to the 5'-cap. These functional groups were then used for labeling using typical click reactions, such as the azide-alkyne cycloaddition or the tetrazine ligation.
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41
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Anhäuser L, Rentmeister A. Enzyme-mediated tagging of RNA. Curr Opin Biotechnol 2017; 48:69-76. [DOI: 10.1016/j.copbio.2017.03.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/10/2017] [Indexed: 12/24/2022]
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42
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Muttach F, Muthmann N, Reichert D, Anhäuser L, Rentmeister A. A benzylic linker promotes methyltransferase catalyzed norbornene transfer for rapid bioorthogonal tetrazine ligation. Chem Sci 2017; 8:7947-7953. [PMID: 29619168 PMCID: PMC5858020 DOI: 10.1039/c7sc03631k] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/09/2017] [Indexed: 01/21/2023] Open
Abstract
Site-specific alkylation of complex biomolecules is critical for late-stage product diversification as well as post-synthetic labeling and manipulation of proteins and nucleic acids. Promiscuous methyltransferases in combination with analogs of S-adenosyl-l-methionine (AdoMet) can functionalize all major classes of biomolecules. We show that benzylic moieties are transferred by Ecm1 with higher catalytic efficiency than the natural AdoMet. A relative specificity of up to 80% is achieved when a norbornene moiety is placed in para-position, enabling for the first time enzymatic norbornene transfer to specific positions in DNA and RNA- even in cell lysate. Subsequent tetrazine ligation of the stable norbornene moiety is fast, efficient, biocompatible and - in combination with an appropriate tetrazine - fluorogenic.
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Affiliation(s)
- F Muttach
- University of Münster , Department of Chemistry , Institute of Biochemistry , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
| | - N Muthmann
- University of Münster , Department of Chemistry , Institute of Biochemistry , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
| | - D Reichert
- University of Münster , Department of Chemistry , Institute of Biochemistry , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
- Cells-in-Motion Cluster of Excellence (EXC1003-CiM) , University of Münster , Germany .
| | - L Anhäuser
- University of Münster , Department of Chemistry , Institute of Biochemistry , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
| | - A Rentmeister
- University of Münster , Department of Chemistry , Institute of Biochemistry , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
- Cells-in-Motion Cluster of Excellence (EXC1003-CiM) , University of Münster , Germany .
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43
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Mamot A, Sikorski PJ, Warminski M, Kowalska J, Jemielity J. Azido-Functionalized 5′ Cap Analogues for the Preparation of Translationally Active mRNAs Suitable for Fluorescent Labeling in Living Cells. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201709052] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Adam Mamot
- University of Warsaw; Centre of New Technologies; Laboratory of Bioorganic Chemistry; Banacha 2c 02-097 Warsaw Poland
- University of Warsaw; Faculty of Chemistry; Pasteura 1 02-093 Warsaw Poland
| | - Pawel J. Sikorski
- University of Warsaw; Centre of New Technologies; Laboratory of Bioorganic Chemistry; Banacha 2c 02-097 Warsaw Poland
| | - Marcin Warminski
- University of Warsaw; Faculty of Physics; Institute of Experimental Physics, Division of Biophysics; Pasteura 5 02-093 Warsaw Poland
| | - Joanna Kowalska
- University of Warsaw; Faculty of Physics; Institute of Experimental Physics, Division of Biophysics; Pasteura 5 02-093 Warsaw Poland
| | - Jacek Jemielity
- University of Warsaw; Centre of New Technologies; Laboratory of Bioorganic Chemistry; Banacha 2c 02-097 Warsaw Poland
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44
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Mamot A, Sikorski PJ, Warminski M, Kowalska J, Jemielity J. Azido-Functionalized 5' Cap Analogues for the Preparation of Translationally Active mRNAs Suitable for Fluorescent Labeling in Living Cells. Angew Chem Int Ed Engl 2017; 56:15628-15632. [PMID: 29048718 DOI: 10.1002/anie.201709052] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Indexed: 12/18/2022]
Abstract
The 7-methylguanosine (m7 G) cap structure is a unique feature present at the 5' ends of messenger RNAs (mRNAs), and it can be subjected to extensive modifications, resulting in alterations to mRNA properties (e.g. translatability, susceptibility to degradation). It also can provide molecular tools to study mRNA metabolism. We developed new mRNA 5' cap analogues that enable the site-specific labeling of RNA at the 5' end using strain-promoted azide-alkyne cycloaddition (SPAAC) without disrupting the basic function of mRNA in protein biosynthesis. Some of these azide-functionalized compounds are equipped with additional modifications to augment mRNA properties. The application of these tools was demonstrated by labeling translationally active mRNAs in living cells.
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Affiliation(s)
- Adam Mamot
- University of Warsaw, Centre of New Technologies, Laboratory of Bioorganic Chemistry, Banacha 2c, 02-097, Warsaw, Poland.,University of Warsaw, Faculty of Chemistry, Pasteura 1, 02-093, Warsaw, Poland
| | - Pawel J Sikorski
- University of Warsaw, Centre of New Technologies, Laboratory of Bioorganic Chemistry, Banacha 2c, 02-097, Warsaw, Poland
| | - Marcin Warminski
- University of Warsaw, Faculty of Physics, Institute of Experimental Physics, Division of Biophysics, Pasteura 5, 02-093, Warsaw, Poland
| | - Joanna Kowalska
- University of Warsaw, Faculty of Physics, Institute of Experimental Physics, Division of Biophysics, Pasteura 5, 02-093, Warsaw, Poland
| | - Jacek Jemielity
- University of Warsaw, Centre of New Technologies, Laboratory of Bioorganic Chemistry, Banacha 2c, 02-097, Warsaw, Poland
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45
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Naik A, Alzeer J, Triemer T, Bujalska A, Luedtke NW. Chemoselective Modification of Vinyl DNA by Triazolinediones. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702554] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Anu Naik
- Department of Chemistry; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Jawad Alzeer
- Department of Chemistry; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Therese Triemer
- Department of Chemistry; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Anna Bujalska
- Department of Chemistry; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Nathan W. Luedtke
- Department of Chemistry; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
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Naik A, Alzeer J, Triemer T, Bujalska A, Luedtke NW. Chemoselective Modification of Vinyl DNA by Triazolinediones. Angew Chem Int Ed Engl 2017; 56:10850-10853. [PMID: 28561928 DOI: 10.1002/anie.201702554] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/09/2017] [Indexed: 11/10/2022]
Abstract
A new method for the post-synthetic modification of nucleic acids was developed that involves mixing a phenyl triazolinedione (PTAD) derivative with DNA containing a vinyl nucleobase. The resulting reactions proceeded through step-wise mechanisms, giving either a formal [4+2] cycloaddition product, or, depending on the context of nucleobase, PTAD addition along with solvent trapping to give a secondary alcohol in water. Catalyst-free addition between PTAD and the terminal alkene of 5-vinyl-2'-deoxyuridine (VdU) was exceptionally fast, with a second-order rate constant of 2×103 m-1 s-1 . PTAD derivatives selectively reacted with VdU-containing oligonucleotides in a conformation-selective manner, with higher yields observed for G-quadruplex versus duplex DNA. These results demonstrate a new strategy for copper-free bioconjugation of DNA that can potentially be used to probe nucleic acid conformations in cells.
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Affiliation(s)
- Anu Naik
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Jawad Alzeer
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Therese Triemer
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Anna Bujalska
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Nathan W Luedtke
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
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47
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Rau K, Rentmeister A. Making the Message Clear: Concepts for mRNA Imaging. ACS CENTRAL SCIENCE 2017; 3:701-707. [PMID: 28776011 PMCID: PMC5532709 DOI: 10.1021/acscentsci.7b00251] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Indexed: 05/13/2023]
Abstract
The transcriptome of each individual cell contains numerous RNA species, each of which can be controlled by multiple mechanisms during their lifetime. The standard transcriptome analysis focuses on the expression levels of the genes of interest. To gain additional insights into spatiotemporal RNA distribution and the underlying trafficking processes, RNA labeling and imaging are necessary-ideally in living cells. This perspective will summarize state-of-the-art RNA imaging methods including their strengths and weaknesses.
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Affiliation(s)
| | - Andrea Rentmeister
- Cells-in-Motion Cluster of Excellence
(EXC1003-CiM), University of Münster, Germany. E-mail:
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48
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Warminski M, Sikorski PJ, Warminska Z, Lukaszewicz M, Kropiwnicka A, Zuberek J, Darzynkiewicz E, Kowalska J, Jemielity J. Amino-Functionalized 5' Cap Analogs as Tools for Site-Specific Sequence-Independent Labeling of mRNA. Bioconjug Chem 2017; 28:1978-1992. [PMID: 28613834 DOI: 10.1021/acs.bioconjchem.7b00291] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
mRNA is a template for protein biosynthesis, and consequently mRNA transport, translation, and turnover are key elements in the overall regulation of gene expression. Along with growing interest in the mechanisms regulating mRNA decay and localization, there is an increasing need for tools enabling convenient fluorescent labeling or affinity tagging of mRNA. We report new mRNA 5' cap analog-based tools that enable site-specific labeling of RNA within the cap using N-hydroxysuccinimide (NHS) chemistry. We explored two complementary methods: a co-transcriptional labeling method, in which the label is first attached to a cap analog and then incorporated into RNA by in vitro transcription, and a post-transcriptional labeling method, in which an amino-functionalized cap analog is incorporated into RNA followed by chemical labeling of the resulting transcript. After testing the biochemical properties of RNAs carrying the novel modified cap structures, we demonstrated the utility of fluorescently labeled RNAs in decapping assays, RNA decay assays, and RNA visualization in cells. Finally, we also demonstrated that mRNAs labeled by the reported method are translationally active. We envisage that the novel analogs will provide an alternative to radiolabeling of mRNA caps for in vitro studies and open possibilities for new applications related to the study of mRNA fates in vivo.
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Affiliation(s)
- Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw , 02-093, Warsaw, Poland
| | - Pawel J Sikorski
- Centre of New Technologies, University of Warsaw , 02-097, Warsaw, Poland
| | - Zofia Warminska
- Centre of New Technologies, University of Warsaw , 02-097, Warsaw, Poland.,College of Interfaculty Individual Studies of Mathematics and Natural Sciences, University of Warsaw , 02-093, Warsaw, Poland
| | - Maciej Lukaszewicz
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw , 02-093, Warsaw, Poland
| | - Anna Kropiwnicka
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw , 02-093, Warsaw, Poland
| | - Joanna Zuberek
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw , 02-093, Warsaw, Poland
| | - Edward Darzynkiewicz
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw , 02-093, Warsaw, Poland.,Centre of New Technologies, University of Warsaw , 02-097, Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw , 02-093, Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw , 02-097, Warsaw, Poland
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49
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Gillingham D, Geigle S, Anatole von Lilienfeld O. Properties and reactivity of nucleic acids relevant to epigenomics, transcriptomics, and therapeutics. Chem Soc Rev 2017; 45:2637-55. [PMID: 26992131 DOI: 10.1039/c5cs00271k] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Developments in epigenomics, toxicology, and therapeutic nucleic acids all rely on a precise understanding of nucleic acid properties and chemical reactivity. In this review we discuss the properties and chemical reactivity of each nucleobase and attempt to provide some general principles for nucleic acid targeting or engineering. For adenine-thymine and guanine-cytosine base pairs, we review recent quantum chemical estimates of their Watson-Crick interaction energy, π-π stacking energies, as well as the nuclear quantum effects on tautomerism. Reactions that target nucleobases have been crucial in the development of new sequencing technologies and we believe further developments in nucleic acid chemistry will be required to deconstruct the enormously complex transcriptome.
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Affiliation(s)
- Dennis Gillingham
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, Basel, CH-4056, Switzerland.
| | - Stefanie Geigle
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, Basel, CH-4056, Switzerland.
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50
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Posttranscriptional chemical labeling of RNA by using bioorthogonal chemistry. Methods 2017; 120:28-38. [DOI: 10.1016/j.ymeth.2017.02.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 02/13/2017] [Accepted: 02/14/2017] [Indexed: 12/26/2022] Open
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