1
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Noël M, Guez T, Thillier Y, Vasseur JJ, Debart F. Access to High-Purity 7m G-cap RNA in Substantial Quantities by a Convenient All-Chemical Solid-Phase Method. Chembiochem 2023; 24:e202300544. [PMID: 37666794 DOI: 10.1002/cbic.202300544] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/24/2023] [Accepted: 09/04/2023] [Indexed: 09/06/2023]
Abstract
Given the importance of mRNA with 5'-cap, easy access to RNA substrates with different 7m G caps, of high quality and in large quantities is essential to elucidate the roles of RNA and the regulation of underlying processes. In addition to existing synthetic routes to 5'-cap RNA based on enzymatic, chemical or chemo-enzymatic methods, we present here an all-chemical method for synthetic RNA capping. The novelty of this study lies in the fact that the capping reaction is performed on solid-support after automated RNA assembly using commercial 2'-O-propionyloxymethyl ribonucleoside phosphoramidites, which enable final RNA deprotection under mild conditions while preserving both 7m G-cap and RNA integrity. The capping reaction is efficiently carried out between a 5'-phosphoroimidazolide RNA anchored on the support and 7m GDP in DMF in the presence of zinc chloride. Substantial amounts of 7m G-cap RNA (from 1 to 28 nucleotides in length and of any sequence with or without internal methylations) containing various cap structures (7m GpppA, 7m GpppAm , 7m Gpppm6 A, 7m Gpppm6 Am , 7m GpppG, 7m GpppGm ) were obtained with high purity after IEX-HPLC purification. This capping method using solid-phase chemistry is convenient to perform and provides access to valuable RNA substrates as useful research tools to unravel specific issues regarding cap-related processes.
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Affiliation(s)
- Mathieu Noël
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS-University of Montpellier-ENSCM, Equipe ChemBioNAC, Pôle Chimie Balard Recherche, 1919 Route de Mende, 34293, Montpellier Cedex 5, France
| | - Theo Guez
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS-University of Montpellier-ENSCM, Equipe ChemBioNAC, Pôle Chimie Balard Recherche, 1919 Route de Mende, 34293, Montpellier Cedex 5, France
| | - Yann Thillier
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS-University of Montpellier-ENSCM, Equipe ChemBioNAC, Pôle Chimie Balard Recherche, 1919 Route de Mende, 34293, Montpellier Cedex 5, France
- Present address: Chemgenes, 900 Middlesex Turnpike, Billerica, MA 01821, USA
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS-University of Montpellier-ENSCM, Equipe ChemBioNAC, Pôle Chimie Balard Recherche, 1919 Route de Mende, 34293, Montpellier Cedex 5, France
| | - Françoise Debart
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS-University of Montpellier-ENSCM, Equipe ChemBioNAC, Pôle Chimie Balard Recherche, 1919 Route de Mende, 34293, Montpellier Cedex 5, France
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2
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Inagaki M, Abe N, Li Z, Nakashima Y, Acharyya S, Ogawa K, Kawaguchi D, Hiraoka H, Banno A, Meng Z, Tada M, Ishida T, Lyu P, Kokubo K, Murase H, Hashiya F, Kimura Y, Uchida S, Abe H. Cap analogs with a hydrophobic photocleavable tag enable facile purification of fully capped mRNA with various cap structures. Nat Commun 2023; 14:2657. [PMID: 37169757 PMCID: PMC10175277 DOI: 10.1038/s41467-023-38244-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 04/21/2023] [Indexed: 05/13/2023] Open
Abstract
Starting with the clinical application of two vaccines in 2020, mRNA therapeutics are currently being investigated for a variety of applications. Removing immunogenic uncapped mRNA from transcribed mRNA is critical in mRNA research and clinical applications. Commonly used capping methods provide maximum capping efficiency of around 80-90% for widely used Cap-0- and Cap-1-type mRNAs. However, uncapped and capped mRNA possesses almost identical physicochemical properties, posing challenges to their physical separation. In this work, we develop hydrophobic photocaged tag-modified cap analogs, which separate capped mRNA from uncapped mRNA by reversed-phase high-performance liquid chromatography. Subsequent photo-irradiation recovers footprint-free native capped mRNA. This approach provides 100% capping efficiency even in Cap-2-type mRNA with versatility applicable to 650 nt and 4,247 nt mRNA. We find that the Cap-2-type mRNA shows up to 3- to 4-fold higher translation activity in cultured cells and animals than the Cap-1-type mRNA prepared by the standard capping method.
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Affiliation(s)
- Masahito Inagaki
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Naoko Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Zhenmin Li
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Yuko Nakashima
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Susit Acharyya
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Kazuya Ogawa
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Daisuke Kawaguchi
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Haruka Hiraoka
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Ayaka Banno
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Zheyu Meng
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Mizuki Tada
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Tatsuma Ishida
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Pingxue Lyu
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Kengo Kokubo
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Hirotaka Murase
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Fumitaka Hashiya
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Yasuaki Kimura
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Satoshi Uchida
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
- Innovation Center of NanoMedicine (iCONM), Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan
- Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Hiroshi Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.
- CREST, Japan Science and Technology Agency, 7, Gobancho, Chiyoda-ku, Tokyo, 102-0076, Japan.
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan.
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3
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Abe N, Imaeda A, Inagaki M, Li Z, Kawaguchi D, Onda K, Nakashima Y, Uchida S, Hashiya F, Kimura Y, Abe H. Complete Chemical Synthesis of Minimal Messenger RNA by Efficient Chemical Capping Reaction. ACS Chem Biol 2022; 17:1308-1314. [PMID: 35608277 DOI: 10.1021/acschembio.1c00996] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Site-specific chemical modification of mRNA can improve its translational efficiency and stability. For this purpose, it is desirable to develop a complete chemical synthesis method for chemically modified mRNA. The key is a chemical reaction that introduces a cap structure into the chemically synthesized RNA. In this study, we developed a fast and quantitative chemical capping reaction between 5'-phosphorylated RNA and N7-methylated GDP imidazolide in the presence of 1-methylimidazole in the organic solvent dimethyl sulfoxide. It enabled quantitative preparation of capping RNA within 3 h. We prepared chemically modified 107-nucleotide mRNAs, including N6-methyladenosine, insertion of non-nucleotide linkers, and 2'-O-methylated nucleotides at the 5' end and evaluated their effects on translational activity in cultured HeLa cells. The results showed that mRNAs with non-nucleotide linkers in the untranslated regions were sufficiently tolerant to translation and that mRNAs with the Cap_2 structure had higher translational activity than those with the Cap_0 structure.
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Affiliation(s)
- Naoko Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Akihiro Imaeda
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Masahito Inagaki
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Zhenmin Li
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Daisuke Kawaguchi
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Kaoru Onda
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Yuko Nakashima
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Satoshi Uchida
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Fumitaka Hashiya
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Yasuaki Kimura
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Hiroshi Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
- CREST, Japan Science and Technology Agency, 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
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4
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Donegà S, Rogalska ME, Pianigiani G, Igreja S, Amaral MD, Pagani F. Rescue of common exon-skipping mutations in cystic fibrosis with modified U1 snRNAs. Hum Mutat 2020; 41:2143-2154. [PMID: 32935393 DOI: 10.1002/humu.24116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/31/2020] [Accepted: 09/07/2020] [Indexed: 01/22/2023]
Abstract
In cystic fibrosis (CF), the correction of splicing defects represents an interesting therapeutic approach to restore normal CFTR function. In this study, we focused on 10 common mutations/variants 711+3A>G/C, 711+5G>A, TG13T3, TG13T5, TG12T5, 1863C>T, 1898+3A>G, 2789+5G>A, and 3120G>A that induce skipping of the corresponding CFTR exons 5, 10, 13, 16, and 18. To rescue the splicing defects we tested, in a minigene assay, a panel of modified U1 small nuclear RNAs (snRNAs), named Exon Specific U1s (ExSpeU1s), that was engineered to bind to intronic sequences downstream of each defective exon. Using this approach, we show that all 10 splicing mutations analyzed are efficiently corrected by specific ExSpeU1s. Using complementary DNA-splicing competent minigenes, we also show that the ExspeU1-mediated splicing correction at the RNA level recovered the full-length CFTR protein for 1863C>T, 1898+3A>G, 2789+5G>A variants. In addition, detailed mutagenesis experiments performed on exon 13 led us to identify a novel intronic regulatory element involved in the ExSpeU1-mediated splicing rescue. These results provide a common strategy based on modified U1 snRNAs to correct exon skipping in a group of disease-causing CFTR mutations.
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Affiliation(s)
- Stefano Donegà
- Human Molecular Genetics, ICGEB - International Center for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Malgorzata Ewa Rogalska
- Human Molecular Genetics, ICGEB - International Center for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Giulia Pianigiani
- Human Molecular Genetics, ICGEB - International Center for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Susana Igreja
- BioISI - Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Margarida Duarte Amaral
- BioISI - Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Franco Pagani
- Human Molecular Genetics, ICGEB - International Center for Genetic Engineering and Biotechnology, Trieste, Italy
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5
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Inde T, Nishizawa S, Hattori Y, Kanamori T, Yuasa H, Seio K, Sekine M, Ohkubo A. Synthesis of and triplex formation in oligonucleotides containing 2'-deoxy-6-thioxanthosine. Bioorg Med Chem 2018; 26:3785-3790. [PMID: 29914771 DOI: 10.1016/j.bmc.2018.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 05/30/2018] [Accepted: 06/04/2018] [Indexed: 12/18/2022]
Abstract
This study aimed to synthesize triplex-forming oligonucleotides (TFOs) containing 2'-deoxy-6-thioxanthosine (s6X) and 2'-deoxy-6-thioguanosine (s6Gs) residues and examined their triplex-forming ability. Consecutive arrangement of s6X and s6Gs residues increased the triplex-forming ability of the oligonucleotides more than 50 times, compared with the unmodified TFOs. Moreover, the stability of triplex containing a mismatched pair was much lower than that of the full-matched triplex, though s6X could form a s6X-GC mismatched pair via tautomerization of s6X. The present results reveal excellent properties of modified TFOs containing s6Xs and s6Gs residues, which may be harnessed in gene therapy and DNA nanotechnology.
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Affiliation(s)
- Takeshi Inde
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Shuhei Nishizawa
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Yuusaku Hattori
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Takashi Kanamori
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Hideya Yuasa
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Mitsuo Sekine
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Akihiro Ohkubo
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan.
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6
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Kaewsomboon T, Nishizawa S, Kanamori T, Yuasa H, Ohkubo A. pH-Dependent Switching of Base Pairs Using Artificial Nucleobases with Carboxyl Groups. J Org Chem 2018; 83:1320-1327. [PMID: 29322767 DOI: 10.1021/acs.joc.7b02828] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, we report the synthesis of modified oligonucleotides consisting of benzoic acid or isophthalic acid residues as new nucleobases. As evaluated by UV thermal denaturation analysis at different pH conditions (5.0, 6.0, 7.0, and 8.0), these modified oligonucleotides exhibited pH-dependent recognition of natural nucleobases and one is first found to be capable of base pair switching in response to a pH change. The isophthalic acid residue incorporated into the oligonucleotide on a d-threoninol backbone could preferentially bind with adenine but with guanine in response to a change in the pH conditions from pH 5 to pH 7 (or 8) without significant difference in duplex stability. These findings would be valuable for further developing pH-responsive DNA-based molecular devices.
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Affiliation(s)
- Tanasak Kaewsomboon
- Department of Life Science and Technology, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Shuhei Nishizawa
- Department of Life Science and Technology, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Takashi Kanamori
- Department of Life Science and Technology, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Hideya Yuasa
- Department of Life Science and Technology, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Akihiro Ohkubo
- Department of Life Science and Technology, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
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7
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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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8
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Warminski M, Kowalska J, Jemielity J. Synthesis of RNA 5'-Azides from 2'-O-Pivaloyloxymethyl-Protected RNAs and Their Reactivity in Azide-Alkyne Cycloaddition Reactions. Org Lett 2017. [PMID: 28636394 DOI: 10.1021/acs.orglett.7b01591] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Commercially available 2'-O-pivaloyloxymethyl (PivOM) phosphoramidites were employed in an SPS protocol for RNA 5' azides. The utility of the N3-RNAs in CuAAC and SPAAC was demonstrated by RNA 5' labeling, chemical ligation including fragment joining and cyclization, and bioconjugation. As a result, several new RNA conjugates that may be valuable tools for studies on biological events such as innate immune response (cyclic dinucleotides), post-transcriptional gene regulation (circular RNAs), or mRNA turnover (m7G capped RNAs) were obtained.
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Affiliation(s)
- Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw , Pasteura 5, 02-093 Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw , Pasteura 5, 02-093 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw , Banacha 2c, 02-097 Warsaw, Poland
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9
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Warminski M, Sikorski PJ, Kowalska J, Jemielity J. Applications of Phosphate Modification and Labeling to Study (m)RNA Caps. Top Curr Chem (Cham) 2017; 375:16. [PMID: 28116583 PMCID: PMC5396385 DOI: 10.1007/s41061-017-0106-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 01/10/2017] [Indexed: 02/07/2023]
Abstract
The cap is a natural modification present at the 5' ends of eukaryotic messenger RNA (mRNA), which because of its unique structural features, mediates essential biological functions during the process of gene expression. The core structural feature of the mRNA cap is an N7-methylguanosine moiety linked by a 5'-5' triphosphate chain to the first transcribed nucleotide. Interestingly, other RNA 5' end modifications structurally and functionally resembling the m7G cap have been discovered in different RNA types and in different organisms. All these structures contain the 'inverted' 5'-5' oligophosphate bridge, which is necessary for interaction with specific proteins and also serves as a cleavage site for phosphohydrolases regulating RNA turnover. Therefore, cap analogs containing oligophosphate chain modifications or carrying spectroscopic labels attached to phosphate moieties serve as attractive molecular tools for studies on RNA metabolism and modification of natural RNA properties. Here, we review chemical, enzymatic, and chemoenzymatic approaches that enable preparation of modified cap structures and RNAs carrying such structures, with emphasis on phosphate-modified mRNA cap analogs and their potential applications.
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Affiliation(s)
- Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089, Warsaw, Poland
| | - Pawel J Sikorski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, 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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10
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Therapeutic activity of modified U1 core spliceosomal particles. Nat Commun 2016; 7:11168. [PMID: 27041075 PMCID: PMC4822034 DOI: 10.1038/ncomms11168] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 02/25/2016] [Indexed: 12/15/2022] Open
Abstract
Modified U1 snRNAs bound to intronic sequences downstream of the 5′ splice site correct exon skipping caused by different types of mutations. Here we evaluate the therapeutic activity and structural requirements of these exon-specific U1 snRNA (ExSpeU1) particles. In a severe spinal muscular atrophy, mouse model, ExSpeU1, introduced by germline transgenesis, increases SMN2 exon 7 inclusion, SMN protein production and extends life span. In vitro, RNA mutant analysis and silencing experiments show that while U1A protein is dispensable, the 70K and stem loop IV elements mediate most of the splicing rescue activity through improvement of exon and intron definition. Our findings indicate that precise engineering of the U1 core spliceosomal RNA particle has therapeutic potential in pathologies associated with exon-skipping mutations. Modification of the spliceosome is being tested as a potential therapy for exon-skipping diseases, such as spinal muscular atrophy (SMA). Here the authors show that 70K and stem loop IV structural elements of a modified U1 particle are essential for splicing enhancement and effective treatment of SMA mice.
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11
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Wojtczak BA, Warminski M, Kowalska J, Lukaszewicz M, Honcharenko M, Smith CIE, Strömberg R, Darzynkiewicz E, Jemielity J. Clickable trimethylguanosine cap analogs modified within the triphosphate bridge: synthesis, conjugation to RNA and susceptibility to degradation. RSC Adv 2016. [DOI: 10.1039/c5ra25684d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Phosphate-modified m3G cap analogs were synthesized, conjugated to RNA using “click chemistry”, and studied for susceptibility to hNUDT16 enzyme.
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Affiliation(s)
| | - Marcin Warminski
- Division of Biophysics
- Institute of Experimental Physics
- Faculty of Physics
- University of Warsaw
- Poland
| | - Joanna Kowalska
- Division of Biophysics
- Institute of Experimental Physics
- Faculty of Physics
- University of Warsaw
- Poland
| | - Maciej Lukaszewicz
- Division of Biophysics
- Institute of Experimental Physics
- Faculty of Physics
- University of Warsaw
- Poland
| | | | - C. I. Edvard Smith
- Department of Laboratory Medicine
- Karolinska Institutet
- Karolinska University Hospital
- Sweden
| | - Roger Strömberg
- Department of Biosciences and Nutrition
- Karolinska Institutet
- Sweden
| | | | - Jacek Jemielity
- Centre of New Technologies
- University of Warsaw
- 02-089 Warsaw
- Poland
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Zytek M, Kowalska J, Lukaszewicz M, Wojtczak BA, Zuberek J, Ferenc-Mrozek A, Darzynkiewicz E, Niedzwiecka A, Jemielity J. Towards novel efficient and stable nuclear import signals: synthesis and properties of trimethylguanosine cap analogs modified within the 5',5'-triphosphate bridge. Org Biomol Chem 2015; 12:9184-99. [PMID: 25296894 DOI: 10.1039/c4ob01579g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A trimethylguanosine (TMG) cap is present at the 5' end of several small nuclear and nucleolar RNAs. Recently, it has been reported that the TMG cap is a potential nuclear import signal for nucleus-targeting therapeutic nucleic acids and proteins. The import is mediated by recognition of the TMG cap by the snRNA transporting protein, snurportin1. This work describes the synthesis and properties of a series of dinucleotide TMG cap (m3(2,2,7)GpppG) analogs modified in the 5',5'-triphosphate bridge as tools to study TMG cap-dependent biological processes. The bridge was altered at different positions by introducing either bridging (imidodiphosphate, O to NH and methylenebisphosphonate, O to CH2) or non-bridging (phosphorothioate, O to S and boranophosphate, O to BH3) modifications, or by elongation to tetraphosphate. The stability of novel analogs in blood serum was studied to reveal that the α,β-bridging O to NH substitution (m3(2,2,7)GppNHpG) confers the highest resistance. Short RNAs capped with analogs containing α,β-bridging (m3(2,2,7)GppNHpG) or β-non-bridging (m3(2,2,7)GppSpG D2) modifications were resistant to decapping pyrophosphatase, hNudt16. Preliminary studies on binding by human snurportin1 revealed that both O to NH and O to S substitutions support this binding. Due to favorable properties in all three assays, m3(2,2,7)GppNHpG was selected as a promising candidate for further studies on the efficiency of the TMG cap as a nuclear import signal.
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Affiliation(s)
- Malgorzata Zytek
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland.
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Kondo Y, Oubridge C, van Roon AMM, Nagai K. Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5' splice site recognition. eLife 2015; 4. [PMID: 25555158 PMCID: PMC4383343 DOI: 10.7554/elife.04986] [Citation(s) in RCA: 171] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 12/06/2014] [Indexed: 12/12/2022] Open
Abstract
U1 snRNP binds to the 5′ exon-intron junction of pre-mRNA and thus plays a
crucial role at an early stage of pre-mRNA splicing. We present two crystal
structures of engineered U1 sub-structures, which together reveal at atomic
resolution an almost complete network of protein–protein and RNA-protein
interactions within U1 snRNP, and show how the 5′ splice site of pre-mRNA is
recognised by U1 snRNP. The zinc-finger of U1-C interacts with the duplex between
pre-mRNA and the 5′-end of U1 snRNA. The binding of the RNA duplex is
stabilized by hydrogen bonds and electrostatic interactions between U1-C and the RNA
backbone around the splice junction but U1-C makes no base-specific contacts with
pre-mRNA. The structure, together with RNA binding assays, shows that the selection
of 5′-splice site nucleotides by U1 snRNP is achieved predominantly through
basepairing with U1 snRNA whilst U1-C fine-tunes relative affinities of mismatched
5′-splice sites. DOI:http://dx.doi.org/10.7554/eLife.04986.001 Genes are made up of long stretches of DNA. The regions of a gene that code for
proteins (known as exons) are interrupted by stretches of non-coding DNA called
introns. To produce proteins from a gene, the DNA is ‘transcribed’ to
form pre-mRNA molecules, from which the introns must be removed in a process called
splicing. The remaining exons are then joined together to form a mature mRNA molecule
that contains the instructions to build a protein. Errors in the splicing process can
lead to numerous diseases, such as cancer. A molecular machine known as a spliceosome is responsible for splicing the pre-mRNA
molecules. This consists of five different complexes called small nuclear
ribonucleoprotein particles (snRNPs), which are in turn made up from numerous
proteins and RNA molecules. The spliceosome assembles anew every time it splices, and
an early step in this assembly process involves the interaction of an snRNP called U1
with the start of an intron in the pre-mRNA. This interaction then stimulates the
assembly of the rest of the spliceosome. In 2009, researchers reported the structure
of the U1 snRNP, but the structure did not contain enough detail to reveal how the
snRNP recognizes the start of an intron. Kondo, Oubridge et al., including some of the researchers involved in the 2009 work,
now present the crystal structure of the human version of the U1 snRNP in more
detail. High-quality crystal structures of the complete U1 snRNP molecule could not
be obtained because the arrangement of the RNA molecules in the snRNP prevented a
regular crystal from forming. Kondo, Oubridge et al. instead engineered two
subcomponents of U1 snRNP that each crystallized well, and determined their
structures. This revealed that the interactions between the various parts of the U1
snRNP form a complex network. A protein present in the U1 snRNP, known as U1-C, had previously been reported to be
able to recognize introns on its own—without requiring the complete U1 snRNP.
Kondo, Oubridge et al. reveal that this is not the case and that U1-C does not read
the intron RNA sequence directly. Instead, U1 snRNP is able to find the start of the
intron because the U1 RNA can stably bind to this site. The U1-C protein can however
adjust the strength of this binding to ensure that the spliceosome can operate with a
variety of intron start sequences (or signals). DOI:http://dx.doi.org/10.7554/eLife.04986.002
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Affiliation(s)
- Yasushi Kondo
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Chris Oubridge
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Anne-Marie M van Roon
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Kiyoshi Nagai
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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Ohkubo A, Seio K, Sekine M. Development of New Methods for Synthesis of Artificial Nucleic Acids having Various Functional Groups. J SYN ORG CHEM JPN 2014. [DOI: 10.5059/yukigoseikyokaishi.72.899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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