1
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Hartstock K, Kueck NA, Spacek P, Ovcharenko A, Hüwel S, Cornelissen NV, Bollu A, Dieterich C, Rentmeister A. MePMe-seq: antibody-free simultaneous m 6A and m 5C mapping in mRNA by metabolic propargyl labeling and sequencing. Nat Commun 2023; 14:7154. [PMID: 37935679 PMCID: PMC10630376 DOI: 10.1038/s41467-023-42832-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 10/23/2023] [Indexed: 11/09/2023] Open
Abstract
Internal modifications of mRNA have emerged as widespread and versatile regulatory mechanism to control gene expression at the post-transcriptional level. Most of these modifications are methyl groups, making S-adenosyl-L-methionine (SAM) a central metabolic hub. Here we show that metabolic labeling with a clickable metabolic precursor of SAM, propargyl-selenohomocysteine (PSH), enables detection and identification of various methylation sites. Propargylated A, C, and G nucleosides form at detectable amounts via intracellular generation of the corresponding SAM analogue. Integration into next generation sequencing enables mapping of N6-methyladenosine (m6A) and 5-methylcytidine (m5C) sites in mRNA with single nucleotide precision (MePMe-seq). Analysis of the termination profiles can be used to distinguish m6A from 2'-O-methyladenosine (Am) and N1-methyladenosine (m1A) sites. MePMe-seq overcomes the problems of antibodies for enrichment and sequence-motifs for evaluation, which was limiting previous methodologies. Metabolic labeling via clickable SAM facilitates the joint evaluation of methylation sites in RNA and potentially DNA and proteins.
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Affiliation(s)
- Katja Hartstock
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Nadine A Kueck
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Petr Spacek
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Anna Ovcharenko
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Sabine Hüwel
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Nicolas V Cornelissen
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Amarnath Bollu
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Berlin, Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany.
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2
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Cornelissen NV, Rentmeister A. Ribozyme for stabilized SAM analogue modifies RNA in cells. Nat Chem 2023; 15:1486-1487. [PMID: 37907605 DOI: 10.1038/s41557-023-01354-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
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3
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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4
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Mohr MKF, Saleem-Batcha R, Cornelissen NV, Andexer JN. Enzymatic Synthesis of l-Methionine Analogues and Application in a Methyltransferase Catalysed Alkylation Cascade. Chemistry 2023; 29:e202301503. [PMID: 37235813 DOI: 10.1002/chem.202301503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 05/28/2023]
Abstract
Chemical modification of small molecules is a key step for the development of pharmaceuticals. S-adenosyl-l-methionine (SAM) analogues are used by methyltransferases (MTs) to transfer alkyl, allyl and benzyl moieties chemo-, stereo- and regioselectively onto nucleophilic substrates, enabling an enzymatic way for specific derivatisation of a wide range of molecules. l-Methionine analogues are required for the synthesis of SAM analogues. Most of these are not commercially available. In nature, O-acetyl-l-homoserine sulfhydrolases (OAHS) catalyse the synthesis of l-methionine from O-acetyl-l-homoserine or l-homocysteine, and methyl mercaptan. Here, we investigated the substrate scope of ScOAHS from Saccharomyces cerevisiae for the production of l-methionine analogues from l-homocysteine and organic thiols. The promiscuous enzyme was used to synthesise nine different l-methionine analogues with modifications on the thioether residue up to a conversion of 75 %. ScOAHS was combined with an established MT dependent three-enzyme alkylation cascade, allowing transfer of in total seven moieties onto two MT substrates. For ethylation, conversion was nearly doubled with the new four-enzyme cascade, indicating a beneficial effect of the in situ production of l-methionine analogues with ScOAHS.
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Affiliation(s)
- Michael K F Mohr
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr. 25, 79104, Freiburg, Germany
| | - Raspudin Saleem-Batcha
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr. 25, 79104, Freiburg, Germany
| | | | - Jennifer N Andexer
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr. 25, 79104, Freiburg, Germany
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5
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Hoffmann A, Schülke KH, Hammer SC, Rentmeister A, Cornelissen NV. Comparative S-adenosyl-L-methionine analogue generation for selective biocatalytic Friedel-Crafts alkylation. Chem Commun (Camb) 2023; 59:5463-5466. [PMID: 37070635 DOI: 10.1039/d3cc01036h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
Methyltransferases provide excellent specificity in late-stage alkylation of biomolecules. Their dependence on S-adenosyl-L-methionine (SAM) mandates efficient access to SAM analogues for biocatalytic applications. We directly compared halide methyltransferase (HMT) and methionine adenosyltransferase (MAT) to access SAM analogues and explored their utility in cascade reactions with NovO for regioselective, late-stage Friedel-Crafts alkylation of a coumarin. The HMT cascade efficiently provided SAM for methylation, while the MAT cascade also supplied high levels of SAM analogues for alkylation reactions.
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Affiliation(s)
- Arne Hoffmann
- University of Muenster, Institute of Biochemistry, Corrensstr. 36, Muenster D-48149, Germany.
| | - Kai H Schülke
- Bielefeld University, Faculty of Chemistry, Organic Chemistry and Biocatalysis Universitätsstraße 25, Bielefeld D-33615, Germany.
| | - Stephan C Hammer
- Bielefeld University, Faculty of Chemistry, Organic Chemistry and Biocatalysis Universitätsstraße 25, Bielefeld D-33615, Germany.
| | - Andrea Rentmeister
- University of Muenster, Institute of Biochemistry, Corrensstr. 36, Muenster D-48149, Germany.
| | - Nicolas V Cornelissen
- University of Muenster, Institute of Biochemistry, Corrensstr. 36, Muenster D-48149, Germany.
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6
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Gericke L, Mhaindarkar D, Karst LC, Jahn S, Kuge M, Mohr MKF, Gagsteiger J, Cornelissen NV, Wen X, Mordhorst S, Jessen HJ, Rentmeister A, Seebeck FP, Layer G, Loenarz C, Andexer JN. Biomimetic S-Adenosylmethionine Regeneration Starting from Multiple Byproducts Enables Biocatalytic Alkylation with Radical SAM Enzymes. Chembiochem 2023; 24:e202300133. [PMID: 36942622 DOI: 10.1002/cbic.202300133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/17/2023] [Accepted: 03/19/2023] [Indexed: 03/23/2023]
Abstract
S-Adenosylmethionine (SAM) is an enzyme cofactor involved in methylation, aminopropyl transfer, and radical reactions. This versatility renders SAM-dependent enzymes of great interest in biocatalysis. The usage of SAM analogues adds to this diversity. However, high cost and instability of the cofactor impedes the investigation and usage of these enzymes. While SAM regeneration protocols from the methyltransferase (MT) byproduct S-adenosylhomocysteine are available, aminopropyl transferases and radical SAM enzymes are not covered. Here, we report a set of efficient one-pot systems to supply or regenerate SAM and SAM analogues for all three enzyme classes. The systems' flexibility is showcased by the transfer of an ethyl group with a cobalamin-dependent radical SAM MT using S-adenosylethionine as a cofactor. This shows the potential of SAM (analogue) supply and regeneration for the application of diverse chemistry, as well as for mechanistic studies using cofactor analogues.
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Affiliation(s)
- Lukas Gericke
- University of Freiburg: Albert-Ludwigs-Universitat Freiburg, Institute of Pharmaceutical Sciences, GERMANY
| | - Dipali Mhaindarkar
- University of Freiburg: Albert-Ludwigs-Universitat Freiburg, Institute of Pharmaceutical Sciences, GERMANY
| | - Lukas C Karst
- University of Freiburg: Albert-Ludwigs-Universitat Freiburg, Institute of Pharmaceutical Sciences, GERMANY
| | - Sören Jahn
- University of Freiburg: Albert-Ludwigs-Universitat Freiburg, Institute of Pharmaceutical Sciences, GERMANY
| | - Marco Kuge
- University of Freiburg: Albert-Ludwigs-Universitat Freiburg, Institute of Pharmaceutical Sciences, GERMANY
| | - Michael K F Mohr
- University of Freiburg: Albert-Ludwigs-Universitat Freiburg, Institute of Pharmaceutical Sciences, GERMANY
| | - Jana Gagsteiger
- University of Freiburg: Albert-Ludwigs-Universitat Freiburg, Institute of Pharmaceutical Sciences, GERMANY
| | - Nicolas V Cornelissen
- University of Münster: Westfalische Wilhelms-Universitat Munster, Institute of Biochemistry, GERMANY
| | - Xiaojin Wen
- University of Basel: Universitat Basel, Department of Chemistry, SWITZERLAND
| | - Silja Mordhorst
- University of Freiburg: Albert-Ludwigs-Universitat Freiburg, Institute of Pharmaceutical Sciences, GERMANY
| | - Henning J Jessen
- University of Freiburg: Albert-Ludwigs-Universitat Freiburg, Institute of Organic Chemistry, GERMANY
| | - Andrea Rentmeister
- University of Munster: Westfalische Wilhelms-Universitat Munster, Institute of Biochemistry, GERMANY
| | - Florian P Seebeck
- University of Basel: Universitat Basel, Department of Chemistry, SWITZERLAND
| | - Gunhild Layer
- University of Freiburg: Albert-Ludwigs-Universitat Freiburg, Institute of Pharmaceutical Sciences, GERMANY
| | - Christoph Loenarz
- University of Freiburg: Albert-Ludwigs-Universitat Freiburg, Institute of Pharmaceutical Sciences, GERMANY
| | - Jennifer Nina Andexer
- University of Freiburg: Albert-Ludwigs-Universitat Freiburg, Institute of Pharmaceutical Sciences, Albertstr. 25, 79104, Freiburg, GERMANY
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7
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Cornelissen NV, Hoffmann A, Rentmeister A. DNA‐Methyltransferasen und AdoMet‐Analoga als Werkzeuge für die Molekularbiologie und Biotechnologie. CHEM-ING-TECH 2023. [DOI: 10.1002/cite.202200174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Affiliation(s)
- Nicolas V. Cornelissen
- Westfälische Wilhelms-Universität Münster Institut für Biochemie, Fachbereich Chemie und Pharmazie Corrensstraße 36 48149 Münster Deutschland
| | - Arne Hoffmann
- Westfälische Wilhelms-Universität Münster Institut für Biochemie, Fachbereich Chemie und Pharmazie Corrensstraße 36 48149 Münster Deutschland
| | - Andrea Rentmeister
- Westfälische Wilhelms-Universität Münster Institut für Biochemie, Fachbereich Chemie und Pharmazie Corrensstraße 36 48149 Münster Deutschland
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8
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Erguven M, Cornelissen NV, Peters A, Karaca E, Rentmeister A. Enzymatic Generation of Double-Modified AdoMet Analogues and Their Application in Cascade Reactions with Different Methyltransferases. Chembiochem 2022; 23:e202200511. [PMID: 36288101 PMCID: PMC10100234 DOI: 10.1002/cbic.202200511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/26/2022] [Indexed: 01/25/2023]
Abstract
Methyltransferases (MTases) have become an important tool for site-specific alkylation and biomolecular labelling. In biocatalytic cascades with methionine adenosyltransferases (MATs), transfer of functional moieties has been realized starting from methionine analogues and ATP. However, the widespread use of S-adenosyl-l-methionine (AdoMet) and the abundance of MTases accepting sulfonium centre modifications limit selective modification in mixtures. AdoMet analogues with additional modifications at the nucleoside moiety bear potential for acceptance by specific MTases. Here, we explored the generation of double-modified AdoMets by an engineered Methanocaldococcus jannaschii MAT (PC-MjMAT), using 19 ATP analogues in combination with two methionine analogues. This substrate screening was extended to cascade reactions and to MTase competition assays. Our results show that MTase targeting selectivity can be improved by using bulky substituents at the N6 of adenine. The facile access to >10 new AdoMet analogues provides the groundwork for developing MAT-MTase cascades for orthogonal biomolecular labelling.
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Affiliation(s)
- Mehmet Erguven
- Department of Chemistry and PharmacyInstitute of BiochemistryUniversity of MünsterCorrensstr. 36, 48149MünsterGermany
- Cells in Motion Interfaculty CentreUniversity of MünsterWaldeyerstraße 1548149MünsterGermany
| | - Nicolas V. Cornelissen
- Department of Chemistry and PharmacyInstitute of BiochemistryUniversity of MünsterCorrensstr. 36, 48149MünsterGermany
| | - Aileen Peters
- Department of Chemistry and PharmacyInstitute of BiochemistryUniversity of MünsterCorrensstr. 36, 48149MünsterGermany
| | - Ezgi Karaca
- Izmir Biomedicine and Genome Center35330IzmirTurkey
- Izmir International Biomedicine and Genome InstituteDokuz Eylul University, 35340 Izmir (Turkey)
| | - Andrea Rentmeister
- Department of Chemistry and PharmacyInstitute of BiochemistryUniversity of MünsterCorrensstr. 36, 48149MünsterGermany
- Cells in Motion Interfaculty CentreUniversity of MünsterWaldeyerstraße 1548149MünsterGermany
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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Rickhoff J, Cornelissen NV, Beuse T, Rentmeister A, Jan Ravoo B. Multiresponsive hydrogels and organogels based on photocaged cysteine. Chem Commun (Camb) 2021; 57:5913-5916. [PMID: 34008646 DOI: 10.1039/d1cc01363g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Here we present the readily accessible amino acid 4,5-dimethoxy-2-nitrobenzyl-l-cysteine (DNC), as an ultra-low molecular weight gelator (MW = 316 g mol-1). Sonication of DNC in water or organic solvents as well as pH adjustment in water trigger gelation. A diverse set of stimuli (UV irradiation, oxidation, heat or pH change) induce a gel-sol transition. Moreover, the photo-triggered gel-sol transition was used to obtain a controlled cysteine release from the hydrogel.
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Affiliation(s)
- Jonas Rickhoff
- Organic Chemistry Institute, University of Muenster, Corrensstr. 36, D-48149 Muenster, Germany.
| | - Nicolas V Cornelissen
- Institute of Biochemistry, University of Muenster, Corrensstr. 36, D-48149 Muenster, Germany.
| | - Thomas Beuse
- MEET Battery Research Center, Institute of Physical Chemistry, University of Muenster, Corrensstr. 46, D-48149 Muenster, Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, University of Muenster, Corrensstr. 36, D-48149 Muenster, Germany.
| | - Bart Jan Ravoo
- Organic Chemistry Institute, University of Muenster, Corrensstr. 36, D-48149 Muenster, Germany.
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11
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Kueck NA, Ovcharenko A, Hartstock K, Cornelissen NV, Rentmeister A. Chemoenzymatic labeling of RNA to enrich, detect and identify methyltransferase-target sites. Methods Enzymol 2021; 658:161-190. [PMID: 34517946 DOI: 10.1016/bs.mie.2021.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The RNA methyltransferase (MTase) complex METTL3-METTL14 transfers methyl groups from S-adenosyl-l-methionine (AdoMet) to the N6-position of adenosines within its consensus sequence, the DRACH motif (D=A, G, U; R=A, G; H=A, C, U). Interestingly, this MTase complex shows remarkable promiscuity regarding the cosubstrate. This can be exploited to install nonnatural modifications, like clickable or photocaging groups. Clickable groups are widely used for subsequent functionalization and open a broad range of possibilities for downstream applications. Here, we elaborate on click chemistry for coupling of RNA to biotin to enrich MTase targets via streptavidin-coated magnetic beads. Importantly, after clicking and coupling to beads the modification becomes sterically demanding and stalls reverse transcriptases, leading to termination adjacent to the MTase target site. Using radioactively labeled primers in the reverse transcription, the modified position can be precisely identified on a sequencing gel via phosphor imaging.
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Affiliation(s)
- Nadine A Kueck
- Department of Chemistry, Institute of Biochemistry, University of Münster, Münster, Germany
| | - Anna Ovcharenko
- Department of Chemistry, Institute of Biochemistry, University of Münster, Münster, Germany
| | - Katja Hartstock
- Department of Chemistry, Institute of Biochemistry, University of Münster, Münster, Germany
| | - Nicolas V Cornelissen
- Department of Chemistry, Institute of Biochemistry, University of Münster, Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, University of Münster, Münster, Germany; Cells in Motion Interfaculty Center, University of Münster, Münster, Germany.
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12
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Michailidou F, Klöcker N, Cornelissen NV, Singh RK, Peters A, Ovcharenko A, Kümmel D, Rentmeister A. Cover Picture: Engineered SAM Synthetases for Enzymatic Generation of AdoMet Analogs with Photocaging Groups and Reversible DNA Modification in Cascade Reactions (Angew. Chem. Int. Ed. 1/2021). Angew Chem Int Ed Engl 2020. [DOI: 10.1002/anie.202015604] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Freideriki Michailidou
- Department of Chemistry Institute of Biochemistry University of Münster Corrensstr. 36 48149 Münster Germany
- Current address: ETH Zürich Department of Chemistry and Applied Biosciences Laboratory of Organic Chemistry Vladimir-Prelog-Weg 1–5/10 8093 Zürich Switzerland
| | - Nils Klöcker
- Department of Chemistry Institute of Biochemistry University of Münster Corrensstr. 36 48149 Münster Germany
| | - Nicolas V. Cornelissen
- Department of Chemistry Institute of Biochemistry University of Münster Corrensstr. 36 48149 Münster Germany
| | - Rohit K. Singh
- Department of Chemistry Institute of Biochemistry University of Münster Corrensstr. 36 48149 Münster Germany
| | - Aileen Peters
- Department of Chemistry Institute of Biochemistry University of Münster Corrensstr. 36 48149 Münster Germany
| | - Anna Ovcharenko
- Department of Chemistry Institute of Biochemistry University of Münster Corrensstr. 36 48149 Münster Germany
| | - Daniel Kümmel
- Department of Chemistry Institute of Biochemistry University of Münster Corrensstr. 36 48149 Münster Germany
| | - Andrea Rentmeister
- Department of Chemistry Institute of Biochemistry University of Münster Corrensstr. 36 48149 Münster Germany
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13
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Michailidou F, Klöcker N, Cornelissen NV, Singh RK, Peters A, Ovcharenko A, Kümmel D, Rentmeister A. Titelbild: Maßgeschneiderte SAM‐Synthetasen zur enzymatischen Herstellung von AdoMet‐Analoga mit Photoschutzgruppen und zur reversiblen DNA‐Modifizierung in Kaskadenreaktionen (Angew. Chem. 1/2021). Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202015604] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Freideriki Michailidou
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
- Derzeitige Adresse: ETH Zürich Fachbereich Chemie und angewandte Biowissenschaften Laboratorium für Organische Chemie Vladimir-Prelog-Weg 1–5/10 8093 Zürich Schweiz
| | - Nils Klöcker
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Nicolas V. Cornelissen
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Rohit K. Singh
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Aileen Peters
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Anna Ovcharenko
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Daniel Kümmel
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Andrea Rentmeister
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
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14
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Michailidou F, Klöcker N, Cornelissen NV, Singh RK, Peters A, Ovcharenko A, Kümmel D, Rentmeister A. Maßgeschneiderte SAM‐Synthetasen zur enzymatischen Herstellung von AdoMet‐Analoga mit Photoschutzgruppen und zur reversiblen DNA‐Modifizierung in Kaskadenreaktionen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202012623] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Freideriki Michailidou
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
- Derzeitige Adresse: ETH Zürich Fachbereich Chemie und angewandte Biowissenschaften Laboratorium für Organische Chemie Vladimir-Prelog-Weg 1–5/10 8093 Zürich Schweiz
| | - Nils Klöcker
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Nicolas V. Cornelissen
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Rohit K. Singh
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Aileen Peters
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Anna Ovcharenko
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Daniel Kümmel
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Andrea Rentmeister
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
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15
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Michailidou F, Klöcker N, Cornelissen NV, Singh RK, Peters A, Ovcharenko A, Kümmel D, Rentmeister A. Engineered SAM Synthetases for Enzymatic Generation of AdoMet Analogs with Photocaging Groups and Reversible DNA Modification in Cascade Reactions. Angew Chem Int Ed Engl 2020; 60:480-485. [PMID: 33017502 PMCID: PMC7839696 DOI: 10.1002/anie.202012623] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Indexed: 12/17/2022]
Abstract
Methylation and demethylation of DNA, RNA and proteins has emerged as a major regulatory mechanism. Studying the function of these modifications would benefit from tools for their site‐specific inhibition and timed removal. S‐Adenosyl‐L‐methionine (AdoMet) analogs in combination with methyltransferases (MTases) have proven useful to map or block and release MTase target sites, however their enzymatic generation has been limited to aliphatic groups at the sulfur atom. We engineered a SAM synthetase from Cryptosporidium hominis (PC‐ChMAT) for efficient generation of AdoMet analogs with photocaging groups that are not accepted by any WT MAT reported to date. The crystal structure of PC‐ChMAT at 1.87 Å revealed how the photocaged AdoMet analog is accommodated and guided engineering of a thermostable MAT from Methanocaldococcus jannaschii. PC‐MATs were compatible with DNA‐ and RNA‐MTases, enabling sequence‐specific modification (“writing”) of plasmid DNA and light‐triggered removal (“erasing”).
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Affiliation(s)
- Freideriki Michailidou
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany.,Current address: ETH Zürich, Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | - Nils Klöcker
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Nicolas V Cornelissen
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Rohit K Singh
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Aileen Peters
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Anna Ovcharenko
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Daniel Kümmel
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
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16
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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17
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Hartstock K, Nilges BS, Ovcharenko A, Cornelissen NV, Püllen N, Lawrence‐Dörner A, Leidel SA, Rentmeister A. Inside Cover: 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. 21/2018). Angew Chem Int Ed Engl 2018. [DOI: 10.1002/anie.201803995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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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18
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Hartstock K, Nilges BS, Ovcharenko A, Cornelissen NV, Püllen N, Lawrence‐Dörner A, Leidel SA, Rentmeister A. Innentitelbild: Enzymatischer oder In‐vivo‐Einbau von Propargylgruppen in Kombination mit Klick‐Chemie zur Anreicherung und Detektion von Methyltransferase‐Zielsequenzen in RNA (Angew. Chem. 21/2018). Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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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19
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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