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Muthmann N, Muttach F, Rentmeister A. Enzymatic Transfer of Photo-Cross-Linkers for RNA-Protein Photo-Cross-Linking at the mRNA 5'-Cap. Methods Mol Biol 2019; 2008:131-146. [PMID: 31124094 DOI: 10.1007/978-1-4939-9537-0_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Photo-cross-linking moieties have proven invaluable for elucidating interactions of biomolecules. While methods for site-specific incorporation of those moieties into proteins have been developed, comparable methods for nucleic acids are lacking. Utilizing the inherent specificity of enzymes, methyltransferases (MTase) exhibiting relaxed cosubstrate specificity in combination with synthetic analogs of S-adenosyl-L-methionine (AdoMet) allow for the precise installation of reporter molecules or affinity tags in various biomolecules. In this chapter, we describe AdoMet analogs with photo-cross-linking moieties that-in combination with an MTase-are ideal for site-specific installation. The workflow for chemo-enzymatic installation of photo-cross-linking moieties at the mRNA cap based on AdoMet analogs is given in detail.
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Affiliation(s)
- Nils Muthmann
- Westfälische Wilhelms-Universität Münster, Institute of Biochemistry, Münster, Germany
| | - Fabian Muttach
- Westfälische Wilhelms-Universität Münster, Institute of Biochemistry, Münster, Germany
| | - Andrea Rentmeister
- Westfälische Wilhelms-Universität Münster, Institute of Biochemistry, Münster, Germany. .,Cells-in-Motion Cluster of Excellence (EXC 1003-CiM), University of Muenster, Münster, Germany.
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2
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Suter SR, Ball-Jones A, Mumbleau MM, Valenzuela R, Ibarra-Soza J, Owens H, Fisher AJ, Beal PA. Controlling miRNA-like off-target effects of an siRNA with nucleobase modifications. Org Biomol Chem 2018; 15:10029-10036. [PMID: 29164215 DOI: 10.1039/c7ob02654d] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
SiRNAs can cause unintended gene silencing due to miRNA-like effects because of the similarity in function of an siRNA guide strand and a miRNA. Here we evaluate the effect on miRNA-like off targeting of introducing the adenosine derivative 7-EAA and triazoles prepared from 7-EAA at different positions in an siRNA guide strand. We find that a sterically demanding triazole placed in the RNA duplex major groove at position six of the guide strand dramatically reduces miRNA-like off targeting potency. A high-resolution structure of an RNA duplex bearing a novel, major-groove localized triazole is reported, which suggests that modified triazoles could be disrupting the hAgo2-guide-target RNA ternary complex. Five different triazole modifications were tested at the guide strand 6-position for effects on on-target and miRNA-like off target knockdown potency. A 7-EAA triazole bearing a benzylamine substituent displayed on-target knockdown activity as potent as the native siRNA, while having an IC50 against a miRNA-like off target >100-fold higher. Melting temperature studies revealed no obvious correlation between potency in knockdown assays and a modification's effect on duplex stability. These results, along with known structures of hAgo2-guide-target ternary complexes, are used to rationalize the effect of 7-EAA triazoles on miRNA-like off target effects.
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Affiliation(s)
- Scott R Suter
- Department of Chemistry, University of California, Davis, One Shields Ave, Davis, California, 95616 USA.
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3
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Muttach F, Mäsing F, Studer A, Rentmeister A. New AdoMet Analogues as Tools for Enzymatic Transfer of Photo-Cross-Linkers and Capturing RNA-Protein Interactions. Chemistry 2017; 23:5988-5993. [PMID: 28042932 DOI: 10.1002/chem.201605663] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Indexed: 11/06/2022]
Abstract
Elucidation of biomolecular interactions is of utmost importance in biochemistry. Photo-cross-linking offers the possibility to precisely determine RNA-protein interactions. However, despite the inherent specificity of enzymes, approaches for site-specific introduction of photo-cross-linking moieties into nucleic acids are scarce. Methyltransferases in combination with synthetic analogues of their natural cosubstrate S-adenosyl-l-methionine (AdoMet) allow for the post-synthetic site-specific modification of biomolecules. We report on three novel AdoMet analogues bearing the most widespread photo-cross-linking moieties (aryl azide, diazirine, and benzophenone). We show that these photo-cross-linkers can be enzymatically transferred to the methyltransferase target, that is, the mRNA cap, with high efficiency. Photo-cross-linking of the resulting modified mRNAs with the cap interacting protein eIF4E was successful with aryl azide and diazirine but not benzophenone, reflecting the affinity of the modified 5' caps.
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Affiliation(s)
- Fabian Muttach
- University of Münster, Department of Chemistry, Institute of Biochemistry, Wilhelm-Klemm-Str. 2, 48149, Münster, Germany
| | - Florian Mäsing
- University of Münster, Department of Chemistry, Institute of Organic Chemistry, Corrensstr. 40, 48149, Münster, Germany
| | - Armido Studer
- University of Münster, Department of Chemistry, Institute of Organic Chemistry, Corrensstr. 40, 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 (EXC 1003-CiM), University of Münster, Germany
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4
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Li W, Fedosov SN, Tan T, Xu X, Guo Z. Kinetic Insights of DNA/RNA Segment Salts Catalyzed Knoevenagel Condensation Reaction. ACS Catal 2014. [DOI: 10.1021/cs500882r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Weina Li
- Department
of Engineering, Faculty of Science and Technology, Aarhus University, Gustav
Wied Vej 10, Aarhus 8000, Denmark
- College of Life Science and Technology, Beijing University of Chemical Technology, Beisanhuan East Road 15, Beijing 100029, China
| | - Sergey N. Fedosov
- Department
of Engineering, Faculty of Science and Technology, Aarhus University, Gustav
Wied Vej 10, Aarhus 8000, Denmark
| | - Tianwei Tan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beisanhuan East Road 15, Beijing 100029, China
| | - Xuebing Xu
- Department
of Engineering, Faculty of Science and Technology, Aarhus University, Gustav
Wied Vej 10, Aarhus 8000, Denmark
| | - Zheng Guo
- Department
of Engineering, Faculty of Science and Technology, Aarhus University, Gustav
Wied Vej 10, Aarhus 8000, Denmark
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5
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Agopcan Cinar S, Ercan S, Erol Gunal S, Dogan I, Aviyente V. The origin of exo-stereoselectivity of norbornene in hetero Diels–Alder reactions. Org Biomol Chem 2014; 12:8079-86. [DOI: 10.1039/c4ob01217h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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6
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Nierth A, Jäschke A. Radioactive phosphorylation of alcohols to monitor biocatalytic Diels-Alder reactions. PLoS One 2011; 6:e21391. [PMID: 21731729 PMCID: PMC3120863 DOI: 10.1371/journal.pone.0021391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Accepted: 05/26/2011] [Indexed: 11/17/2022] Open
Abstract
Nature has efficiently adopted phosphorylation for numerous biological key processes, spanning from cell signaling to energy storage and transmission. For the bioorganic chemist the number of possible ways to attach a single phosphate for radioactive labeling is surprisingly small. Here we describe a very simple and fast one-pot synthesis to phosphorylate an alcohol with phosphoric acid using trichloroacetonitrile as activating agent. Using this procedure, we efficiently attached the radioactive phosphorus isotope (32)P to an anthracene diene, which is a substrate for the Diels-Alderase ribozyme-an RNA sequence that catalyzes the eponymous reaction. We used the (32)P-substrate for the measurement of RNA-catalyzed reaction kinetics of several dye-labeled ribozyme variants for which precise optical activity determination (UV/vis, fluorescence) failed due to interference of the attached dyes. The reaction kinetics were analyzed by thin-layer chromatographic separation of the (32)P-labeled reaction components and densitometric analysis of the substrate and product radioactivities, thereby allowing iterative optimization of the dye positions for future single-molecule studies. The phosphorylation strategy with trichloroacetonitrile may be applicable for labeling numerous other compounds that contain alcoholic hydroxyl groups.
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Affiliation(s)
- Alexander Nierth
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
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Kellner S, Seidu-Larry S, Burhenne J, Motorin Y, Helm M. A multifunctional bioconjugate module for versatile photoaffinity labeling and click chemistry of RNA. Nucleic Acids Res 2011; 39:7348-60. [PMID: 21646334 PMCID: PMC3167637 DOI: 10.1093/nar/gkr449] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A multifunctional reagent based on a coumarin scaffold was developed for derivatization of naive RNA. The alkylating agent N3BC [7-azido-4-(bromomethyl)coumarin], obtained by Pechmann condensation, is selective for uridine. N3BC and its RNA conjugates are pre-fluorophores which permits controlled modular and stepwise RNA derivatization. The success of RNA alkylation by N3BC can be monitored by photolysis of the azido moiety, which generates a coumarin fluorophore that can be excited with UV light of 320 nm. The azidocoumarin-modified RNA can be flexibly employed in structure-function studies. Versatile applications include direct use in photo-crosslinking studies to cognate proteins, as demonstrated with tRNA and RNA fragments from the MS2 phage and the HIV genome. Alternatively, the azide function can be used for further derivatization by click-chemistry. This allows e.g. the introduction of an additional fluorophore for excitation with visible light.
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Affiliation(s)
- Stefanie Kellner
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
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Affiliation(s)
- Jose M. Palomo
- Departamento de Biocatálisis, Instituto de Catálisis (CSIC), c/ Marie Curie 2, Cantoblanco Campus UAM, 28049 Madrid, Spain, Fax: +34‐91‐585‐4760
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Schoch J, Wiessler M, Jäschke A. Post-synthetic modification of DNA by inverse-electron-demand Diels-Alder reaction. J Am Chem Soc 2010; 132:8846-7. [PMID: 20550120 DOI: 10.1021/ja102871p] [Citation(s) in RCA: 157] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
There is currently a tremendous interest in developing bioorthogonal "click chemistry" methods for the modification of biopolymers. Very recently, inverse-electron-demand Diels-Alder reactions have received attention, but to date they have not been applied to nucleic acids. Here we describe the first example of DNA modification by inverse-electron-demand Diels-Alder reaction. We synthesized four different building blocks for 3'-terminal, 5'-terminal, and internal incorporation of norbornene dienophiles into oligonucleotides. These DNA strands were either directly reacted with suitably derivatized tetrazine dienes or first subjected to enzymatic manipulations. We demonstrate that the inverse-electron-demand Diels-Alder reaction allows efficient site-specific post-synthetic conjugation, often at a 1:1 stoichiometry, without any side reaction. The reaction works in aqueous media at room temperature, and no transition metals are required. Both short chemically synthesized oligonucleotides and long enzymatically amplified DNA strands were successfully conjugated.
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Affiliation(s)
- Juliane Schoch
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany
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10
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Nierth A, Kobitski AY, Nienhaus GU, Jäschke A. Anthracene−BODIPY Dyads as Fluorescent Sensors for Biocatalytic Diels−Alder Reactions. J Am Chem Soc 2010; 132:2646-54. [DOI: 10.1021/ja9084397] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexander Nierth
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany, Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe Institute of Technology, Wolfgang-Gaede-Strasse 1, 76131 Karlsruhe, Germany, and Department of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Andrei Yu. Kobitski
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany, Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe Institute of Technology, Wolfgang-Gaede-Strasse 1, 76131 Karlsruhe, Germany, and Department of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - G. Ulrich Nienhaus
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany, Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe Institute of Technology, Wolfgang-Gaede-Strasse 1, 76131 Karlsruhe, Germany, and Department of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany, Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe Institute of Technology, Wolfgang-Gaede-Strasse 1, 76131 Karlsruhe, Germany, and Department of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
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11
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Gagnon KT, Ju SY, Goshe MB, Maxwell ES, Franzen S. A role for hydrophobicity in a Diels-Alder reaction catalyzed by pyridyl-modified RNA. Nucleic Acids Res 2009; 37:3074-82. [PMID: 19304744 PMCID: PMC2685102 DOI: 10.1093/nar/gkp177] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
New classes of RNA enzymes or ribozymes have been obtained by in vitro evolution and selection of RNA molecules. Incorporation of modified nucleotides into the RNA sequence has been proposed to enhance function. DA22 is a modified RNA containing 5-(4-pyridylmethyl) carboxamide uridines, which has been selected for its ability to promote a Diels–Alder cycloaddition reaction. Here, we show that DA_TR96, the most active member of the DA22 RNA sequence family, which was selected with pyridyl-modified nucleotides, accelerates a cycloaddition reaction between anthracene and maleimide derivatives with high turnover. These widely used reactants were not used in the original selection for DA22 and yet here they provide the first demonstration of DA_TR96 as a true multiple-turnover catalyst. In addition, the absence of a structural or essential kinetic role for Cu2+, as initially postulated, and nonsequence-specific hydrophobic interactions with the anthracene substrate have led to a reevaluation of the pyridine modification's role. These findings broaden the catalytic repertoire of the DA22 family of pyridyl-modified RNAs and suggest a key role for the hydrophobic effect in the catalytic mechanism.
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Affiliation(s)
- Keith T Gagnon
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
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12
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Qiu Z, Lu L, Jian X, He C. A diazirine-based nucleoside analogue for efficient DNA interstrand photocross-linking. J Am Chem Soc 2008; 130:14398-9. [PMID: 18842048 DOI: 10.1021/ja805445j] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A diazirine-based nucleoside analogue (DBN) efficiently forms DNA interstand cross-linking under near-UV irradiation. This new base analogue may find broad applications in biotechnology and phototherapy.
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Affiliation(s)
- Zhihai Qiu
- Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
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