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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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2
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Müller D, Trucks S, Schwalbe H, Hengesbach M. Genetic Code Expansion Facilitates Position-Selective Modification of Nucleic Acids and Proteins. Chempluschem 2020; 85:1233-1243. [PMID: 32515171 DOI: 10.1002/cplu.202000150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/11/2020] [Indexed: 12/12/2022]
Abstract
Transcription and translation obey to the genetic code of four nucleobases and 21 amino acids evolved over billions of years. Both these processes have been engineered to facilitate the use of non-natural building blocks in both nucleic acids and proteins, enabling researchers with a decent toolbox for structural and functional analyses. Here, we review the most common approaches for how labeling of both nucleic acids as well as proteins in a site-selective fashion with either modifiable building blocks or spectroscopic probes can be facilitated by genetic code expansion. We emphasize methodological approaches and how these can be adapted for specific modifications, both during as well as after biomolecule synthesis. These modifications can facilitate, for example, a number of different spectroscopic analysis techniques and can under specific circumstances even be used in combination.
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Affiliation(s)
- Diana Müller
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Sven Trucks
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
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3
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Lyon SE, Chen TH, Wallace AJ, Adib K, Gopalan V. An RNase P-Based Assay for Accurate Determination of the 5'-Deoxy-5'-azidoguanosine-Modified Fraction of in Vitro-Transcribed RNAs. Chembiochem 2018; 19:2353-2359. [PMID: 30194891 DOI: 10.1002/cbic.201800447] [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: 08/02/2018] [Indexed: 11/10/2022]
Abstract
Chemoenzymatic approaches are important for generating site-specific, chemically modified RNAs, a cornerstone for RNA structure-function correlation studies. T7 RNA polymerase (T7RNAP)-mediated in vitro transcription (IVT) of a DNA template containing the G-initiating class III Φ6.5 promoter is typically used to generate 5'-chemically modified RNAs by including a guanosine analogue (G analogue) initiator in the IVT. However, the yield of 5'-G analogue-initiated RNA is often poor and variable due to the high ratios of G analogue:GTP used in IVT. We recently reported that a T7RNAP P266L mutant afforded an approximately three-fold increase in fluorescent 5'-thienoguanosine-initiated pre-tRNACys compared to the wild type T7RNAP. We have further explored the use of T7RNAP P266L to generate 5'-deoxy-5'-azidoguanosine (az G)-initiated RNA and found that the mutant yielded approximately four times more az G-initiated pre-tRNACys than the wild type in an IVT containing a 10:1 ratio of az G:GTP. For accurate quantitation of the 5'-az G-initiated RNA fraction, we employed RNase P, an endonuclease that catalyzes the removal of the 5'-leader in pre-tRNAs. Importantly, we show herein how RNase P can be leveraged for assessing 5'-G analogue incorporation in any RNA by rendering the target RNA, upon its binding to a customized external guide sequence RNA, into an unnatural substrate of RNase P. Such an approach in conjunction with T7RNAP P266L-based IVT should aid chemoenzymatic methods that are designed to generate 5'-chemically modified RNAs.
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Affiliation(s)
- Seth E Lyon
- Department of Chemistry and Biochemistry and, Center for RNA Biology, The Ohio State University, 774 Biological Sciences Building, 484 West 12th Avenue, Columbus, OH, 43210, USA.,Present address: Biological and Biomedical Sciences Graduate Program, Yale University, New Haven, CT, 06520, USA
| | - Tien-Hao Chen
- Department of Chemistry and Biochemistry and, Center for RNA Biology, The Ohio State University, 774 Biological Sciences Building, 484 West 12th Avenue, Columbus, OH, 43210, USA.,Present address: Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Andrew J Wallace
- Department of Chemistry and Biochemistry and, Center for RNA Biology, The Ohio State University, 774 Biological Sciences Building, 484 West 12th Avenue, Columbus, OH, 43210, USA.,Present address: Department of Chemistry, University of California, Santa Cruz, CA, 95094, USA
| | - Katie Adib
- Department of Chemistry and Biochemistry and, Center for RNA Biology, The Ohio State University, 774 Biological Sciences Building, 484 West 12th Avenue, Columbus, OH, 43210, USA.,Present address: Wright State University Boonshoft School of Medicine, Dayton, OH, 45435, USA
| | - Venkat Gopalan
- Department of Chemistry and Biochemistry and, Center for RNA Biology, The Ohio State University, 774 Biological Sciences Building, 484 West 12th Avenue, Columbus, OH, 43210, USA
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Keyhani S, Goldau T, Blümler A, Heckel A, Schwalbe H. Chemo-Enzymatic Synthesis of Position-Specifically Modified RNA for Biophysical Studies including Light Control and NMR Spectroscopy. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sara Keyhani
- Institute for Organic Chemistry and Chemical Biology; Center for Biomolecular Magnetic Resonance; Goethe University Frankfurt am Main; Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
- Institute for Organic Chemistry and Chemical Biology; Goethe University Frankfurt am Main; Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
| | - Thomas Goldau
- Institute for Organic Chemistry and Chemical Biology; Goethe University Frankfurt am Main; Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
| | - Anja Blümler
- Institute for Organic Chemistry and Chemical Biology; Goethe University Frankfurt am Main; Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology; Goethe University Frankfurt am Main; Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology; Center for Biomolecular Magnetic Resonance; Goethe University Frankfurt am Main; Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
- Institute for Organic Chemistry and Chemical Biology; Goethe University Frankfurt am Main; Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
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Keyhani S, Goldau T, Blümler A, Heckel A, Schwalbe H. Chemo-Enzymatic Synthesis of Position-Specifically Modified RNA for Biophysical Studies including Light Control and NMR Spectroscopy. Angew Chem Int Ed Engl 2018; 57:12017-12021. [PMID: 30007102 DOI: 10.1002/anie.201807125] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Indexed: 02/04/2023]
Abstract
The investigation of non-coding RNAs requires RNAs containing modifications at every possible position within the oligonucleotide. Here, we present the chemo-enzymatic RNA synthesis containing photoactivatable or 13 C,15 N-labelled nucleosides. All four ribonucleotides containing ortho-nitrophenylethyl (NPE) photocages, photoswitchable azobenzene C-nucleotides and 13 C,15 N-labelled nucleotides were incorporated position-specifically in high yields. We applied this approach for the synthesis of light-inducible 2'dG-sensing riboswitch variants and detected ligand-induced structural reorganization upon irradiation by NMR spectroscopy. This chemo-enzymatic method opens the possibility to incorporate a wide range of modifications at any desired position of RNAs of any lengths beyond the limits of solid-phase synthesis.
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Affiliation(s)
- Sara Keyhani
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany.,Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany
| | - Thomas Goldau
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany
| | - Anja Blümler
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany.,Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany
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6
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Winz ML, Linder EC, Becker J, Jäschke A. Site-specific one-pot triple click labeling for DNA and RNA. Chem Commun (Camb) 2018; 54:11781-11784. [DOI: 10.1039/c8cc04520h] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We report site-specific triple click labeling for DNA and RNA in a one-pot setup by performing inverse electron demand Diels–Alder reaction and strain-promoted and copper catalyzed click reactions sequentially.
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Affiliation(s)
- Marie-Luise Winz
- Heidelberg University
- Institute of Pharmacy and Molecular Biotechnology
- D-69120 Heidelberg
- Germany
| | - Eva Christina Linder
- Heidelberg University
- Institute of Pharmacy and Molecular Biotechnology
- D-69120 Heidelberg
- Germany
| | - Juliane Becker
- Heidelberg University
- Institute of Pharmacy and Molecular Biotechnology
- D-69120 Heidelberg
- Germany
| | - Andres Jäschke
- Heidelberg University
- Institute of Pharmacy and Molecular Biotechnology
- D-69120 Heidelberg
- Germany
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7
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Walczak S, Nowicka A, Kubacka D, Fac K, Wanat P, Mroczek S, Kowalska J, Jemielity J. A novel route for preparing 5' cap mimics and capped RNAs: phosphate-modified cap analogues obtained via click chemistry. Chem Sci 2017; 8:260-267. [PMID: 28451173 PMCID: PMC5355871 DOI: 10.1039/c6sc02437h] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/10/2016] [Indexed: 01/29/2023] Open
Abstract
The significant biological role of the mRNA 5' cap in translation initiation makes it an interesting subject for chemical modifications aimed at producing useful tools for the selective modulation of intercellular processes and development of novel therapeutic interventions. However, traditional approaches to the chemical synthesis of cap analogues are time-consuming and labour-intensive, which impedes the development of novel compounds and their applications. Here, we explore a different approach for synthesizing 5' cap mimics, making use of click chemistry (CuAAC) to combine two mononucleotide units and yield a novel class of dinucleotide cap analogues containing a triazole ring within the oligophosphate chain. As a result, we synthesized a library of 36 mRNA cap analogues differing in the location of the triazole ring, the polyphosphate chain length, and the type of linkers joining the phosphate and the triazole moieties. After biochemical evaluation, we identified two analogues that, when incorporated into mRNA, produced transcripts translated with efficiency similar to compounds unmodified in the oligophosphate bridge obtained by traditional synthesis. Moreover, we demonstrated that the triazole-modified cap structures can be generated at the RNA 5' end using two alternative capping strategies: either the typical co-transcriptional approach, or a new post-transcriptional approach based on CuAAC. Our findings open new possibilities for developing chemically modified mRNAs for research and therapeutic applications, including RNA-based vaccinations.
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Affiliation(s)
- Sylwia Walczak
- Centre of New Technologies , University of Warsaw , Banacha 2c , 02-097 , Warsaw , Poland .
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences , University of Warsaw , Banacha 2c , 02-097 , Warsaw , Poland
| | - Anna Nowicka
- Centre of New Technologies , University of Warsaw , Banacha 2c , 02-097 , Warsaw , Poland .
- Division of Biophysics , Institute of Experimental Physics , Faculty of Physics , University of Warsaw , Zwirki i Wigury 93 , 02-089 , Warsaw , Poland
| | - Dorota Kubacka
- Division of Biophysics , Institute of Experimental Physics , Faculty of Physics , University of Warsaw , Zwirki i Wigury 93 , 02-089 , Warsaw , Poland
| | - Kaja Fac
- Centre of New Technologies , University of Warsaw , Banacha 2c , 02-097 , Warsaw , Poland .
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences , University of Warsaw , Banacha 2c , 02-097 , Warsaw , Poland
| | - Przemyslaw Wanat
- Division of Biophysics , Institute of Experimental Physics , Faculty of Physics , University of Warsaw , Zwirki i Wigury 93 , 02-089 , Warsaw , Poland
| | - Seweryn Mroczek
- Department of Genetics and Biotechnology , Faculty of Biology , University of Warsaw , 02-106 Warsaw , Poland
- Institute of Biochemistry and Biophysics , Polish Academy of Sciences , 02-106 Warsaw , Poland
| | - 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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8
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Holstein JM, Rentmeister A. Current covalent modification methods for detecting RNA in fixed and living cells. Methods 2015; 98:18-25. [PMID: 26615954 DOI: 10.1016/j.ymeth.2015.11.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/20/2015] [Accepted: 11/22/2015] [Indexed: 12/13/2022] Open
Abstract
Labeling RNAs is of particular interest for elucidating localization, transport, and regulation of specific transcripts, ideally in living cells. Numerous methods have been developed ranging from hybridizing probes to genetically encoded reporters and chemo-enzymatic approaches. This review focuses on covalent labeling approaches that rely on the introduction of a small reactive group into the nascent or completed transcript followed by bioorthogonal click chemistry. State of the approaches for labeling RNA in fixed and living cells will be presented and emerging strategies with great potential for application in the complex cellular environment will be discussed.
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Affiliation(s)
- Josephin M Holstein
- Westfälische Wilhelms-Universität Münster, Institute of Biochemistry, 48149 Muenster, Germany
| | - Andrea Rentmeister
- Westfälische Wilhelms-Universität Münster, Institute of Biochemistry, 48149 Muenster, Germany; Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Muenster, 48149 Muenster, Germany.
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9
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Pradère U, Brunschweiger A, Gebert LFR, Lucic M, Roos M, Hall J. Chemical Synthesis of Mono- and Bis-Labeled Pre-MicroRNAs. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201304986] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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10
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Pradère U, Brunschweiger A, Gebert LFR, Lucic M, Roos M, Hall J. Chemical synthesis of mono- and bis-labeled pre-microRNAs. Angew Chem Int Ed Engl 2013; 52:12028-32. [PMID: 24115636 DOI: 10.1002/anie.201304986] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 07/26/2013] [Indexed: 12/21/2022]
Affiliation(s)
- Ugo Pradère
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich (Switzerland)
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