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Flemmich L, Bereiter R, Micura R. Chemical Synthesis of Modified RNA. Angew Chem Int Ed Engl 2024; 63:e202403063. [PMID: 38529723 DOI: 10.1002/anie.202403063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/16/2024] [Accepted: 03/26/2024] [Indexed: 03/27/2024]
Abstract
Ribonucleic acids (RNAs) play a vital role in living organisms. Many of their cellular functions depend critically on chemical modification. Methods to modify RNA in a controlled manner-both in vitro and in vivo-are thus essential to evaluate and understand RNA biology at the molecular and mechanistic levels. The diversity of modifications, combined with the size and uniformity of RNA (made up of only 4 nucleotides) makes its site-specific modification a challenging task that needs to be addressed by complementary approaches. One such approach is solid-phase RNA synthesis. We discuss recent developments in this field, starting with new protection concepts in the ongoing effort to overcome current size limitations. We continue with selected modifications that have posed significant challenges for their incorporation into RNA. These include deazapurine bases required for atomic mutagenesis to elucidate mechanistic aspects of catalytic RNAs, and RNA containing xanthosine, N4-acetylcytidine, 5-hydroxymethylcytidine, 3-methylcytidine, 2'-OCF3, and 2'-N3 ribose modifications. We also discuss the all-chemical synthesis of 5'-capped mRNAs and the enzymatic ligation of chemically synthesized oligoribonucleotides to obtain long RNA with multiple distinct modifications, such as those needed for single-molecule FRET studies. Finally, we highlight promising developments in RNA-catalyzed RNA modification using cofactors that transfer bioorthogonal functionalities.
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Affiliation(s)
- Laurin Flemmich
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Raphael Bereiter
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
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2
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Sato K, Nukaga Y, Wada T. Solid-phase synthesis and properties of stereocontrolled boranophosphate/phosphate and phosphorothioate/phosphate chimeric oligouridylates. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230095. [PMID: 37063986 PMCID: PMC10090885 DOI: 10.1098/rsos.230095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
This study describes the stereoselective synthesis of boranophosphate/phosphate (PB/PO) and phosphorothioate/phosphate (PS/PO) chimeric oligouridylates using the solid-phase method. Oxazaphospholidine monomer was used to construct the stereodefined PB and PS linkages. The study introduces modifications to oligouridylate derivatives in the intended positions with the intended stereochemistry of phosphorous atoms. Additionally, biophysical and biochemical properties of the synthesized oligomers were evaluated. Notably, it was found that a (Sp)-PB/PO chimeric oligouridylate had higher hybridization ability than the unmodified counterpart to an unmodified oligoadenylate. This is the first report that elucidates the effect of both stereochemistry and type of P-modification (PB and PS) on properties of oligoribonucleotides.
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Affiliation(s)
- Kazuki Sato
- Department of Medicinal and Life Sciences, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Yohei Nukaga
- Department of Medicinal and Life Sciences, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Takeshi Wada
- Department of Medicinal and Life Sciences, Tokyo University of Science, Noda, Chiba 278-8510, Japan
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3
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Olenginski LT, Becette OB, Beaucage SL, Dayie TK. Synthesis of an Atom-Specifically 2 H/ 13 C-Labeled Uridine Ribonucleoside Phosphoramidite. Curr Protoc 2022; 2:e481. [PMID: 35862131 DOI: 10.1002/cpz1.481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A combined enzymatic and chemical synthesis of a 2'-O-cyanoethoxymethyl (CEM) protected [1',6-13 C2 , 5-2 H]-uridine phosphoramidite is described herein. This is the first report of an atom-specific nucleobase and ribose labeled 2'-O-CEM protected ribonucleoside phosphoramidite. Importantly, the CEM 2'-OH protecting group permits the efficient solid-phase synthesis of large (>60 nucleotides) RNAs with good yield and purity. The new isotope-labeled phosphoramidite can therefore be applied to nuclear magnetic resonance (NMR) spectroscopy studies. Specifically, the [1',6-13 C2 , 5-2 H]-uridine phosphoramidite can be used to make position-specifically labeled RNAs for NMR analysis without complications from resonance overlap and scalar and dipolar couplings. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of the ribonucleoside 6 Basic Protocol 2: Synthesis of the ribonucleoside phosphoramidite 11.
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Affiliation(s)
- Lukasz T Olenginski
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland
| | - Owen B Becette
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland
- Current Address: Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, Maryland
| | - Serge L Beaucage
- Laboratory of Biological Chemistry, Division of Biotechnology Review and Research IV, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
| | - Theodore K Dayie
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland
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Takahashi M, Cawrse BM, Grajkowski A, Beaucage SL. Use of Arabinonucleosides for Development and Implementation of a Novel 2'-O-Protecting Group for Efficient Solid-Phase Synthesis and 2'-O-Deprotection of RNA Sequences. Curr Protoc 2022; 2:e346. [PMID: 35030289 DOI: 10.1002/cpz1.346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The implementation of protecting groups for 2'-hydroxyl function of ribonucleosides is very demanding in that synthetic RNA sequences must be highly pure to ensure the safety and efficacy of nucleic acid-based drugs for treatment of human diseases. A synthetic approach consisting of a condensation reaction between 2'-O-aminoribonucleosides with ethyl pyruvate has been employed to provide stable 2'-O-imino-2-methyl propanoic acid ethyl esters. Conversion of these esters to fully protected ribonucleoside phosphoramidite monomers has allowed rapid and efficient incorporation of 2'-O-protected ribonucleosides into RNA sequences while minimizing the formation of process-related impurities during solid-phase synthesis. Two chimeric 20-mer RNA sequences have been synthesized and then exposed to a solution of sodium hydroxide to saponify the 2'-O-imino-2-methyl propanoic acid ethyl ester protecting groups to their sodium salts. When subjected to ion-exchange conditions at 65°C and near neutral pH, fully deprotected RNA sequences are isolated without production of alkylating side-products and/or formation of mutagenic nucleobase adducts. © 2022 Wiley Periodicals LLC. This article has been contributed to by US Government employees and their work is in the public domain in the USA. Basic Protocol 1: Synthesis of uridine 2'-O-imino-2-propanoic acid ethyl ester and its fully protected 3'-O-phosphoramidite Basic Protocol 2: Synthesis of N6 -protected adenosine 2'-O-imino-2-propanoic acid ethyl ester and its fully protected 3'-O-phosphoramidite Basic Protocol 3: Synthesis of N4 -protected cytidine 2'-O-imino-2-propanoic acid ethyl ester and its fully protected 3'-O-phosphoramidite Basic Protocol 4: Synthesis of N2 -protected guanosine 2'-O-imino-2-propanoic acid ethyl ester and its fully protected 3'-O-phosphoramidite Basic Protocol 5: Automated solid-phase RNA synthesis and deprotection using 2'-O-imino-2-proponate-protected phosphoramidites.
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Affiliation(s)
- Mayumi Takahashi
- Laboratory of Biological Chemistry, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
| | - Brian M Cawrse
- Laboratory of Biological Chemistry, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
| | - Andrzej Grajkowski
- Laboratory of Biological Chemistry, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
| | - Serge L Beaucage
- Laboratory of Biological Chemistry, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
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Matsuda H, Ito H, Nukaga Y, Uehara S, Sato K, Hara RI, Wada T. Solid-phase synthesis of oligouridine boranophosphates using the H-boranophosphonate method with 2′-O-(2-cyanoethoxymethyl) protection. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2021.153526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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6
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Synthesis of atom-specific nucleobase and ribose labeled uridine phosphoramidite for NMR analysis of large RNAs. MONATSHEFTE FUR CHEMIE 2021. [DOI: 10.1007/s00706-021-02851-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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7
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Moorthy R, Kennelly SA, Rodriguez DJ, Harki DA. An efficient synthesis of RNA containing GS-441524: the nucleoside precursor of remdesivir. RSC Adv 2021; 11:31373-31376. [PMID: 35496844 PMCID: PMC9041347 DOI: 10.1039/d1ra06589k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 09/14/2021] [Indexed: 01/18/2023] Open
Abstract
Remdesivir is an antiviral nucleoside phosphoramidate with activity against multiple viruses, including SARS-CoV-2. To enable studies of viral polymerases with RNA containing remdesivir, we report an efficient synthesis of a phosphoramidite of GS-441524, the nucleoside precursor of remdesivir, and its incorporation into RNA using automated solid-phase RNA synthesis.
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Affiliation(s)
- Ramkumar Moorthy
- Department of Medicinal Chemistry, University of Minnesota 2231 6th Street S.E. Minneapolis MN 55455 USA
| | - Samantha A Kennelly
- Department of Medicinal Chemistry, University of Minnesota 2231 6th Street S.E. Minneapolis MN 55455 USA
| | - Deborah J Rodriguez
- Department of Medicinal Chemistry, University of Minnesota 2231 6th Street S.E. Minneapolis MN 55455 USA
| | - Daniel A Harki
- Department of Medicinal Chemistry, University of Minnesota 2231 6th Street S.E. Minneapolis MN 55455 USA
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8
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Takahashi M, Grajkowski A, Cawrse BM, Beaucage SL. Innovative 2'- O-Imino-2-propanoate-Protecting Group for Effective Solid-Phase Synthesis and 2'- O-Deprotection of RNA Sequences. J Org Chem 2021; 86:4944-4956. [PMID: 33706514 DOI: 10.1021/acs.joc.0c02773] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The implementation of protecting groups for the 2'-hydroxyl function of ribonucleosides is still challenging, particularly when RNA sequences must be of the highest purity for therapeutic applications as nucleic acid-based drugs. A 2'-hydroxyl-protecting group should optimally (i) be easy to install; (ii) allow rapid and efficient incorporation of the 2'-O-protected ribonucleosides into RNA sequences to minimize, to the greatest extent possible, the formation of process-related impurities (e.g., shorter than full-length sequences) during solid-phase synthesis; and (iii) be completely cleaved from RNA sequences without the production of alkylating side products and/or formation of mutagenic nucleobase adducts. The reaction of 2'-O-aminoribonucleosides with ethyl pyruvate results in the formation of stable 2'-O-imino-2-methyl propanoic acid ethyl esters and, subsequently, of the fully protected ribonucleoside phosphoramidite monomers, which are required for the solid-phase synthesis of two chimeric RNA sequences (20-mers) containing the four canonical ribonucleosides. Upon treatment of the RNA sequences with a solution of sodium hydroxide, the 2'-O-imino-2-methyl propanoic acid ethyl ester-protecting groups are saponified to their sodium salts, which after ion exchange underwent quantitative intramolecular decarboxylation under neutral conditions at 65 °C to provide fully deprotected RNA sequences in marginally better yields than those obtained from commercial 2'-O-tert-butyldimethylsilyl ribonucleoside phosphoramidites under highly similar conditions.
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Affiliation(s)
- Mayumi Takahashi
- Laboratory of Biological Chemistry, Division of Biotechnology Review and Research IV, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, United States
| | - Andrzej Grajkowski
- Laboratory of Biological Chemistry, Division of Biotechnology Review and Research IV, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, United States
| | - Brian M Cawrse
- Laboratory of Biological Chemistry, Division of Biotechnology Review and Research IV, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, United States
| | - Serge L Beaucage
- Laboratory of Biological Chemistry, Division of Biotechnology Review and Research IV, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, United States
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9
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Advanced approaches for elucidating structures of large RNAs using NMR spectroscopy and complementary methods. Methods 2020; 183:93-107. [DOI: 10.1016/j.ymeth.2020.01.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/11/2019] [Accepted: 01/16/2020] [Indexed: 11/23/2022] Open
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Krasheninina OA, Fishman VS, Lomzov AA, Ustinov AV, Venyaminova AG. Postsynthetic On-Column 2' Functionalization of RNA by Convenient Versatile Method. Int J Mol Sci 2020; 21:E5127. [PMID: 32698484 PMCID: PMC7404181 DOI: 10.3390/ijms21145127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/08/2020] [Accepted: 07/14/2020] [Indexed: 12/26/2022] Open
Abstract
We report a universal straightforward strategy for the chemical synthesis of modified oligoribonucleotides containing functional groups of different structures at the 2' position of ribose. The on-column synthetic concept is based on the incorporation of two types of commercial nucleotide phosphoramidites containing orthogonal 2'-O-protecting groups, namely 2'-O-thiomorpholine-carbothioate (TC, as "permanent") and 2'-O-tert-butyl(dimethyl)silyl (tBDMS, as "temporary"), to RNA during solid-phase synthesis. Subsequently, the support-bound RNA undergoes selective deprotection and follows postsynthetic 2' functionalization of the naked hydroxyl group. This convenient method to tailor RNA, utilizing the advantages of solid phase approaches, gives an opportunity to introduce site-specifically a wide range of linkers and functional groups. By this strategy, a series of RNAs containing diverse 2' functionalities were synthesized and studied with respect to their physicochemical properties.
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Affiliation(s)
- Olga A. Krasheninina
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, Innsbruck 6020, Austria
| | - Veniamin S. Fishman
- Institute of Cytology and Genetics SB RAS Lavrentiev Ave. 10, 630090 Novosibirsk, Russia;
| | - Alexander A. Lomzov
- Institute of Chemical Biology and Fundamental Medicine SB RAS Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (A.A.L.); (A.G.V.)
| | - Alexey V. Ustinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia;
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (A.A.L.); (A.G.V.)
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11
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Solid-Phase Chemical Synthesis of Stable Isotope-Labeled RNA to Aid Structure and Dynamics Studies by NMR Spectroscopy. Molecules 2019; 24:molecules24193476. [PMID: 31557861 PMCID: PMC6804060 DOI: 10.3390/molecules24193476] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 09/22/2019] [Accepted: 09/23/2019] [Indexed: 02/05/2023] Open
Abstract
RNA structure and dynamic studies by NMR spectroscopy suffer from chemical shift overlap and line broadening, both of which become worse as RNA size increases. Incorporation of stable isotope labels into RNA has provided several solutions to these limitations. Nevertheless, the only method to circumvent the problem of spectral overlap completely is the solid-phase chemical synthesis of RNA with labeled RNA phosphoramidites. In this review, we summarize the practical aspects of this methodology for NMR spectroscopy studies of RNA. These types of investigations lie at the intersection of chemistry and biophysics and highlight the need for collaborative efforts to tackle the integrative structural biology problems that exist in the RNA world. Finally, examples of RNA structure and dynamic studies using labeled phosphoramidites are highlighted.
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12
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Simulescu V, Ilia G. Solid-phase Synthesis of Phosphorus Derivatives. CURR ORG CHEM 2019. [DOI: 10.2174/1385272823666190213112019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The solid-phase synthesis (SPS) of phosphorus-containing compounds is based mainly on the fact that the chemical process is conducted in a two-phase system. One of the components is connected via covalent bonds to a solid support, which is in general an insoluble polymer, representing the solid phase of the process. The other components involved into the process are solubilized in a solution. The method is suitable to be applied to almost any organic compounds. A common example of using solid-phase synthesis is for obtaining products nucleotide containing, similar to nucleic acids. During the whole process, the nucleotide is always on the solid phase, after the condensation reaction, except for the last step, when the synthesis is already finished. Then, the product is released and separated very easily by filtration. The obtained polymer-oligonucleotide product can participate further in condensation reactions as well. Other important biomolecules synthesized by solid-phase approach during the last decades are nucleoside di- and triphosphates, nucleoside diphosphate sugars and dinucleoside polyphosphates. Those products are precursors of deoxysugars, aminodeoxysugars, uronic acids or glycoconjugates, and are also necessary for DNA and RNA synthesis. The use of the solid-phase method in the context of immobilized oligomers is of great interest nowadays. The solid-phase synthesis offers many advantages in comparison with the conventional solution-phase method, because it takes much less time, it is highly stereoselective, the products are separated and purified usually by a simple filtration or decantation, solvents with high boiling points could be used, the whole process is based on solid polymer support and the obtained compounds should not be isolated.
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Affiliation(s)
- Vasile Simulescu
- Institute of Chemistry Timisoara of Romanian Academy, 24 Mihai Viteazul Bvd., 300223 Timisoara, Romania
| | - Gheorghe Ilia
- Institute of Chemistry Timisoara of Romanian Academy, 24 Mihai Viteazul Bvd., 300223 Timisoara, Romania
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13
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Flamme M, McKenzie LK, Sarac I, Hollenstein M. Chemical methods for the modification of RNA. Methods 2019; 161:64-82. [PMID: 30905751 DOI: 10.1016/j.ymeth.2019.03.018] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/18/2019] [Accepted: 03/19/2019] [Indexed: 02/06/2023] Open
Abstract
RNA is often considered as being the vector for the transmission of genetic information from DNA to the protein synthesis machinery. However, besides translation RNA participates in a broad variety of fundamental biological roles such as gene expression and regulation, protein synthesis, and even catalysis of chemical reactions. This variety of function combined with intricate three-dimensional structures and the discovery of over 100 chemical modifications in natural RNAs require chemical methods for the modification of RNAs in order to investigate their mechanism, location, and exact biological roles. In addition, numerous RNA-based tools such as ribozymes, aptamers, or therapeutic oligonucleotides require the presence of additional chemical functionalities to strengthen the nucleosidic backbone against degradation or enhance the desired catalytic or binding properties. Herein, the two main methods for the chemical modification of RNA are presented: solid-phase synthesis using phosphoramidite precursors and the enzymatic polymerization of nucleoside triphosphates. The different synthetic and biochemical steps required for each method are carefully described and recent examples of practical applications based on these two methods are discussed.
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Affiliation(s)
- Marie Flamme
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France; Sorbonne Université, Collège doctoral, F-75005 Paris, France
| | - Luke K McKenzie
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Ivo Sarac
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France.
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Sarac I, Hollenstein M. Terminal Deoxynucleotidyl Transferase in the Synthesis and Modification of Nucleic Acids. Chembiochem 2019; 20:860-871. [PMID: 30451377 DOI: 10.1002/cbic.201800658] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Indexed: 12/26/2022]
Abstract
The terminal deoxynucleotidyl transferase (TdT) belongs to the X family of DNA polymerases. This unusual polymerase catalyzes the template-independent addition of random nucleotides on 3'-overhangs during V(D)J recombination. The biological function and intrinsic biochemical properties of the TdT have spurred the development of numerous oligonucleotide-based tools and methods, especially if combined with modified nucleoside triphosphates. Herein, we summarize the different applications stemming from the incorporation of modified nucleotides by the TdT. The structural, mechanistic, and biochemical properties of this polymerase are also discussed.
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Affiliation(s)
- Ivo Sarac
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Marcel Hollenstein
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
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15
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A theoretical study on the elimination reaction of acrylonitrile from 2′-O-cyanoethylated nucleosides by Bu4NF. Tetrahedron 2019. [DOI: 10.1016/j.tet.2018.11.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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16
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Marchanka A, Kreutz C, Carlomagno T. Isotope labeling for studying RNA by solid-state NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2018; 71:151-164. [PMID: 29651587 DOI: 10.1007/s10858-018-0180-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 04/07/2018] [Indexed: 06/08/2023]
Abstract
Nucleic acids play key roles in most biological processes, either in isolation or in complex with proteins. Often they are difficult targets for structural studies, due to their dynamic behavior and high molecular weight. Solid-state nuclear magnetic resonance spectroscopy (ssNMR) provides a unique opportunity to study large biomolecules in a non-crystalline state at atomic resolution. Application of ssNMR to RNA, however, is still at an early stage of development and presents considerable challenges due to broad resonances and poor dispersion. Isotope labeling, either as nucleotide-specific, atom-specific or segmental labeling, can resolve resonance overlaps and reduce the line width, thus allowing ssNMR studies of RNA domains as part of large biomolecules or complexes. In this review we discuss the methods for RNA production and purification as well as numerous approaches for isotope labeling of RNA. Furthermore, we give a few examples that emphasize the instrumental role of isotope labeling and ssNMR for studying RNA as part of large ribonucleoprotein complexes.
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Affiliation(s)
- Alexander Marchanka
- Centre for Biomolecular Drug Research (BMWZ) and Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167, Hanover, Germany
| | - Christoph Kreutz
- Organic Chemistry, University of Innsbruck (CCB), Innrain 80/82, 6020, Innsbruck, Austria
| | - Teresa Carlomagno
- Centre for Biomolecular Drug Research (BMWZ) and Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167, Hanover, Germany.
- Helmholtz Centre for Infection Research, Group of NMR-based Structural Chemistry, Inhoffenstraße 7, 38124, Brunswick, Germany.
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Kremser J, Strebitzer E, Plangger R, Juen MA, Nußbaumer F, Glasner H, Breuker K, Kreutz C. Chemical synthesis and NMR spectroscopy of long stable isotope labelled RNA. Chem Commun (Camb) 2018; 53:12938-12941. [PMID: 29155431 DOI: 10.1039/c7cc06747j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We showcase the high potential of the 2'-cyanoethoxymethyl (CEM) methodology to synthesize RNAs with naturally occurring modified residues carrying stable isotope (SI) labels for NMR spectroscopic applications. The method was applied to synthesize RNAs with sizes ranging between 60 to 80 nucleotides. The presented approach gives the possibility to selectively modify larger RNAs (>60 nucleotides) with atom-specifically 13C/15N-labelled building blocks. The method harbors the unique potential to address structural as well as dynamic features of these RNAs with NMR spectroscopy but also using other biophysical methods, such as mass spectrometry (MS), or small angle neutron/X-ray scattering (SANS, SAXS).
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Affiliation(s)
- J Kremser
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria.
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18
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Chemical Modifications of Nucleic Acid Aptamers for Therapeutic Purposes. Int J Mol Sci 2017; 18:ijms18081683. [PMID: 28767098 PMCID: PMC5578073 DOI: 10.3390/ijms18081683] [Citation(s) in RCA: 187] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 07/27/2017] [Accepted: 08/01/2017] [Indexed: 01/16/2023] Open
Abstract
Nucleic acid aptamers have minimal immunogenicity, high chemical synthesis production, low cost and high chemical stability when compared with antibodies. However, the susceptibility to nuclease degradation, rapid excretion through renal filtration and insufficient binding affinity hindered their development as drug candidates for therapeutic applications. In this review, we will discuss methods to conquer these challenges and highlight recent developments of chemical modifications and technological advances that may enable early aptamers to be translated into clinical therapeutics.
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19
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Hara RI, Kageyama M, Arai K, Uchiyama N, Wada T. Synthesis of 2′-O-monohaloethoxymethyl-modified RNAs and their duplex formation ability. RSC Adv 2017. [DOI: 10.1039/c7ra07767j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
We synthesized 2′-O-monohaloethoxymethyl-modified RNAs and evaluated their duplex formation ability.
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Affiliation(s)
| | - Masayuki Kageyama
- Graduate School of Frontier Sciences
- The University of Tokyo
- Kashiwa
- Japan
| | - Koichiro Arai
- Graduate School of Frontier Sciences
- The University of Tokyo
- Kashiwa
- Japan
| | - Naoki Uchiyama
- Graduate School of Frontier Sciences
- The University of Tokyo
- Kashiwa
- Japan
| | - Takeshi Wada
- Faculty of Pharmaceutical Sciences
- Tokyo University of Science
- Noda
- Japan
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Cieślak J, Grajkowski A, Ausín C, Beaucage SL. Protection of the 2′-Hydroxy Function of Ribonucleosides as an Iminooxymethyl Propanoate and Its 2′-O-Deprotection through an Intramolecular Decarboxylative Elimination Process. European J Org Chem 2016. [DOI: 10.1002/ejoc.201601308] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Jacek Cieślak
- Division of Biotechnology Review and Research IV; Center for Drug Evaluation and Research; Food and Drug Administration; 10903 New Hampshire Avenue 20933 Silver Spring MD USA
| | - Andrzej Grajkowski
- Division of Biotechnology Review and Research IV; Center for Drug Evaluation and Research; Food and Drug Administration; 10903 New Hampshire Avenue 20933 Silver Spring MD USA
| | - Cristina Ausín
- Division of Biotechnology Review and Research IV; Center for Drug Evaluation and Research; Food and Drug Administration; 10903 New Hampshire Avenue 20933 Silver Spring MD USA
| | - Serge L. Beaucage
- Division of Biotechnology Review and Research IV; Center for Drug Evaluation and Research; Food and Drug Administration; 10903 New Hampshire Avenue 20933 Silver Spring MD USA
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21
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On the Reactivity of Gulose and Guluronic Acid Building Blocks in the Context of Alginate Assembly. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600336] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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22
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Affiliation(s)
- Natsuhisa Oka
- Department of Biomolecular Science, Faculty of Engineering, Gifu University
| | - Takeshi Wada
- Department of Medicinal and Life Science, Faculty of Pharmaceutical Sciences, Tokyo University of Science
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23
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Ochi Y, Nakagawa O, Hayashi J, Wada SI, Urata H. A New Nucleic Acid Prodrug Responsive to High Thiol Concentration: Synthesis of 2'-O-Methyldithiomethyl-Modified Oligonucleotides by Post-Synthetic Modification. ACTA ACUST UNITED AC 2015; 62:4.63.1-4.63.20. [PMID: 26380903 DOI: 10.1002/0471142700.nc0463s62] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
This unit describes the synthesis of 2'-O-methyldithiomethyluridine-containing oligonucleotides, which can be deprotected to yield the parental oligoribonucleotides under high concentrations of glutathione similar in cytoplasm. The 2'-O-methyldithiomethyl group is sensitive to reductive conditions, so that it is incompatible to 3'-O-phosphoramidite modification in nucleosides. Thus, a novel post-synthetic approach to obtain 2'-O-methyldithiomethyluridine-containing oligonucleotides was developed, in which 2'-O-(2,4,6-trimethoxybenzylthiomethyl)uridine-modified oligonucleotides are readily converted by treatment with dimethyl(methylthio)sulfonium tetrafluoroborate to the 2'-O-methyldithiomethyluridine-modified oligonucleotides. The 2'-O-methyldithiomethyluridine-modified oligonucleotides are readily and cleanly converted to the parental oligonucleotides under high thiol conditions, such as 10 mM glutathione and dithiothreitol.
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Affiliation(s)
- Yosuke Ochi
- Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan
| | - Osamu Nakagawa
- Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan.,Present address: Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Junsuke Hayashi
- Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan
| | - Shun-Ichi Wada
- Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan
| | - Hidehito Urata
- Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan
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24
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Sarac I, Meier C. Efficient Automated Solid-Phase Synthesis of DNA and RNA 5'-Triphosphates. Chemistry 2015; 21:16421-6. [PMID: 26517040 DOI: 10.1002/chem.201502844] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Indexed: 12/13/2022]
Abstract
A fast, high-yielding and reliable method for the synthesis of DNA- and RNA 5'-triphosphates is reported. After synthesizing DNA or RNA oligonucleotides by automated oligonucleotide synthesis, 5-chloro-saligenyl-N,N-diisopropylphosphoramidite was coupled to the 5'-end. Oxidation of the formed 5'-phosphite using the same oxidizing reagent used in standard oligonucleotide synthesis led to 5'-cycloSal-oligonucleotides. Reaction of the support-bonded 5'-cycloSal-oligonucleotide with pyrophosphate yielded the corresponding 5'-triphosphates. The 5'-triphosphorylated DNA and RNA oligonucleotides were obtained after cleavage from the support in high purity and excellent yields. The whole reaction sequence was adapted to be used on a standard oligonucleotide synthesizer.
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Affiliation(s)
- Ivo Sarac
- Organic Chemistry, Department of Chemistry, Faculty of Sciences, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg (Germany)
| | - Chris Meier
- Organic Chemistry, Department of Chemistry, Faculty of Sciences, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg (Germany).
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25
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Catalytic isomerization of allyl functionalities in water by hexaaquaruthenium(II) tosylate. Inorganica Chim Acta 2015. [DOI: 10.1016/j.ica.2015.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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26
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Aralov AV, Chakhmakhchieva OG. [Protection of 2'-hydroxyls in the chemical synthesis of oligoribonucleotides]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2013; 39:3-25. [PMID: 23844504 DOI: 10.1134/s1068162013010020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The review is devoted to the chemical synthesis of oligoribonucleotides and the protecting groups used. In particular the existent methods of blocking 2'-OH function in nucleotide monomers for the RNA synthesis are discussed in detail.
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Cieślak J, Ausín C, Grajkowski A, Beaucage SL. The 2-Cyano-2,2-dimethylethanimine-N-oxymethyl Group for the 2′-Hydroxyl Protection of Ribonucleosides in the Solid-Phase Synthesis of RNA Sequences. Chemistry 2013; 19:4623-32. [DOI: 10.1002/chem.201204235] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Indexed: 11/11/2022]
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29
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Nukaga Y, Yamada K, Ogata T, Oka N, Wada T. Stereocontrolled solid-phase synthesis of phosphorothioate oligoribonucleotides using 2'-O-(2-cyanoethoxymethyl)-nucleoside 3'-O-oxazaphospholidine monomers. J Org Chem 2012; 77:7913-22. [PMID: 22931131 DOI: 10.1021/jo301052v] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A method for the synthesis of P-stereodefined phosphorothioate oligoribonucleotides (PS-ORNs) was developed. PS-ORNs of mixed sequence (up to 12mers) were successfully synthesized by this method with sufficient coupling efficiency (94-99%) and diastereoselectivity (≥98:2). The coupling efficiency was greatly improved by the use of 2-cyanoethoxymethyl (CEM) groups in place of the conventional TBS groups for the 2'-O-protection of nucleoside 3'-O-oxazaphospholidine monomers. The resultant diastereopure PS-ORNs allowed us to clearly demonstrate that an ORN containing an all-(Rp)-PS-backbone stabilizes its duplex with the complementary ORN, whereas its all-(Sp)-counterpart has a destabilizing effect.
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Affiliation(s)
- Yohei Nukaga
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bioscience Building 702, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
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30
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Huang J, Xi Z. Chemical synthesis of bioactive siRNA in solution phase by using 2-(azidomethyl)benzoyl as 3′-hydroxyl group protecting group. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.05.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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31
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Synthesis and properties of novel 2′-O-alkoxymethyl-modified nucleic acids. Bioorg Med Chem Lett 2011; 21:6285-7. [DOI: 10.1016/j.bmcl.2011.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 08/30/2011] [Accepted: 09/01/2011] [Indexed: 11/18/2022]
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32
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Páv O, Košiová I, Barvík I, Pohl R, Buděšínský M, Rosenberg I. Synthesis of oligoribonucleotides with phosphonate-modified linkages. Org Biomol Chem 2011; 9:6120-6. [PMID: 21769370 DOI: 10.1039/c1ob05488k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Solid phase synthesis of phosphonate-modified oligoribonucleotides using 2'-O-benzoyloxymethoxymethyl protected monomers is presented in both 3'→5' and 5'→3' directions. Hybridisation properties and enzymatic stability of oligoribonucleotides modified by regioisomeric 3'- and 5'-phosphonate linkages are evaluated. The introduction of the 5'-phosphonate units resulted in moderate destabilisation of the RNA/RNA duplexes (ΔT(m)-1.8 °C/mod.), whereas the introduction of the 3'-phosphonate units resulted in considerable destabilisation of the duplexes (ΔT(m)-5.7 °C/mod.). Molecular dynamics simulations have been used to explain this behaviour. Both types of phosphonate linkages exhibited remarkable resistance in the presence of ribonuclease A, phosphodiesterase I and phosphodiesterase II.
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Affiliation(s)
- Ondřej Páv
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nam. 2, 16610, Prague, Czech Republic
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33
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Terasawa K, Shimizu K, Tsujimoto G. Synthetic Pre-miRNA-Based shRNA as Potent RNAi Triggers. J Nucleic Acids 2011; 2011:131579. [PMID: 21776374 PMCID: PMC3139136 DOI: 10.4061/2011/131579] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 04/14/2011] [Accepted: 05/17/2011] [Indexed: 12/11/2022] Open
Abstract
RNA interference (RNAi) is a powerful tool for studying gene function owing to the ease with which it can selectively silence genes of interest, and it has also attracted attention because of its potential for therapeutic applications. Chemically synthesized small interfering RNAs (siRNAs) and DNA vector-based short hairpin RNAs (shRNAs) are now widely used as RNAi triggers. In contrast to expressed shRNAs, the use of synthetic shRNAs is limited. Here we designed shRNAs modeled on a precursor microRNA (pre-miRNA) and evaluated their biological activity. We demonstrated that chemically synthetic pre-miRNA-based shRNAs have more potent RNAi activity than their corresponding siRNAs and found that their antisense strands are more efficiently incorporated into the RNA-induced silencing complex. Although greater off-target effects and interferon responses were induced by shRNAs than by their corresponding siRNAs, these effects could be overcome by simply using a lower concentration or by optimizing and chemically modifying shRNAs similar to synthetic siRNAs. These are challenges for the future.
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Affiliation(s)
- Kazuya Terasawa
- Department of Pharmacogenomics, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
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34
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Dellinger DJ, Timár Z, Myerson J, Sierzchala AB, Turner J, Ferreira F, Kupihár Z, Dellinger G, Hill KW, Powell JA, Sampson JR, Caruthers MH. Streamlined Process for the Chemical Synthesis of RNA Using 2′-O-Thionocarbamate-Protected Nucleoside Phosphoramidites in the Solid Phase. J Am Chem Soc 2011; 133:11540-56. [DOI: 10.1021/ja201561z] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Douglas J. Dellinger
- Agilent Laboratories, Agilent Technologies, Inc., 5301 Stevens Creek Boulevard, Santa Clara, California 95051, United States
| | - Zoltán Timár
- Agilent Laboratories, Agilent Technologies, Inc., 5301 Stevens Creek Boulevard, Santa Clara, California 95051, United States
| | - Joel Myerson
- Agilent Laboratories, Agilent Technologies, Inc., 5301 Stevens Creek Boulevard, Santa Clara, California 95051, United States
| | - Agnieszka B. Sierzchala
- Agilent Nucleic Acids Solutions Division, 5555 Airport Boulevard, Suite 100, Boulder, Colorado 80301, United States
| | - John Turner
- Agilent Laboratories, Agilent Technologies, Inc., 5301 Stevens Creek Boulevard, Santa Clara, California 95051, United States
| | - Fernando Ferreira
- Agilent Laboratories, Agilent Technologies, Inc., 5301 Stevens Creek Boulevard, Santa Clara, California 95051, United States
| | - Zoltán Kupihár
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Geraldine Dellinger
- Agilent Laboratories, Agilent Technologies, Inc., 5301 Stevens Creek Boulevard, Santa Clara, California 95051, United States
| | - Kenneth W. Hill
- Agilent Nucleic Acids Solutions Division, 5555 Airport Boulevard, Suite 100, Boulder, Colorado 80301, United States
| | - James A. Powell
- Agilent Nucleic Acids Solutions Division, 5555 Airport Boulevard, Suite 100, Boulder, Colorado 80301, United States
| | - Jeffrey R. Sampson
- Agilent Laboratories, Agilent Technologies, Inc., 5301 Stevens Creek Boulevard, Santa Clara, California 95051, United States
| | - Marvin H. Caruthers
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United States
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35
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Terrazas M, Aviñó A, Siddiqui MA, Marquez VE, Eritja R. A Direct, Efficient Method for the Preparation of siRNAs Containing Ribo-like North Bicyclo[3.1.0]hexane Pseudosugars. Org Lett 2011; 13:2888-91. [DOI: 10.1021/ol200909j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Montserrat Terrazas
- Institute for Research in Biomedicine (IRB Barcelona), Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), and Institute for Advanced Chemistry of Catalonia (IQAC), Spanish Research Council (CSIC), Cluster Building, Baldiri i Reixac 10, E-08028 Barcelona, Spain, and Laboratory of Chemical Biology, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
| | - Anna Aviñó
- Institute for Research in Biomedicine (IRB Barcelona), Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), and Institute for Advanced Chemistry of Catalonia (IQAC), Spanish Research Council (CSIC), Cluster Building, Baldiri i Reixac 10, E-08028 Barcelona, Spain, and Laboratory of Chemical Biology, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
| | - Maqbool A. Siddiqui
- Institute for Research in Biomedicine (IRB Barcelona), Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), and Institute for Advanced Chemistry of Catalonia (IQAC), Spanish Research Council (CSIC), Cluster Building, Baldiri i Reixac 10, E-08028 Barcelona, Spain, and Laboratory of Chemical Biology, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
| | - Victor E. Marquez
- Institute for Research in Biomedicine (IRB Barcelona), Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), and Institute for Advanced Chemistry of Catalonia (IQAC), Spanish Research Council (CSIC), Cluster Building, Baldiri i Reixac 10, E-08028 Barcelona, Spain, and Laboratory of Chemical Biology, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
| | - Ramon Eritja
- Institute for Research in Biomedicine (IRB Barcelona), Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), and Institute for Advanced Chemistry of Catalonia (IQAC), Spanish Research Council (CSIC), Cluster Building, Baldiri i Reixac 10, E-08028 Barcelona, Spain, and Laboratory of Chemical Biology, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
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36
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Lavergne T, Janin M, Dupouy C, Vasseur JJ, Debart F. Chemical synthesis of RNA with base-labile 2'-o-(pivaloyloxymethyl)-protected ribonucleoside phosphoramidites. ACTA ACUST UNITED AC 2011; Chapter 3:Unit3.19. [PMID: 21154530 DOI: 10.1002/0471142700.nc0319s43] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The efficiency of chemical RNA synthesis has been radically improved by the use of pivaloyloxymethyl (PivOM) groups as 2'-protection, containing an acetal spacer that minimizes the steric effect of the ester group on the neighboring amidite during the coupling. However, the major benefit of the base-labile PivOM groups is their simple removal upon standard basic conditions applied to deprotect the RNA and release it from solid supports. Combined with standard acyl groups for nucleobases, cyanoethyl groups for phosphates, and base-cleavable linkers, PivOM groups make RNA deprotection as simple as DNA deprotection. Thus, no additional deprotection step with tedious desalting workup procedures is required, and RNA synthesis becomes as convenient and efficient as DNA synthesis.
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37
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Synthesis, gene-silencing activity and nuclease resistance of 3′–3′-linked double short hairpin RNA. Bioorg Med Chem 2010; 18:8277-83. [DOI: 10.1016/j.bmc.2010.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 09/30/2010] [Accepted: 10/01/2010] [Indexed: 02/04/2023]
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38
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Knapp DC, D'Onofrio J, Engels JW. Fluorescent labeling of (oligo)nucleotides by a new fluoride cleavable linker capable of versatile attachment modes. Bioconjug Chem 2010; 21:1043-55. [PMID: 20509599 DOI: 10.1021/bc900542f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The development of a fluoride cleavable linker 1 for reversibly labeling (oligo)nucleotides is described here. The linker allows different ways of chemical attachment of a reporter molecule, for example, click chemistry or amide formation. The versatile attachment modes of labels are demonstrated by derivatizations with pyrene and fluorescein. Besides the synthesis of the new linker, we also show the derivatization of iodobenzene as a model compound and a nucleoside to demonstrate the applicability. Further, cleavability studies in solution and on a solid-supported oligonucleotide are shown. The linker can be applied in the synthesis of reversible terminators, useful for new DNA sequencing technologies like cyclic reversibly terminating (CRT) sequencing.
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Affiliation(s)
- Diana C Knapp
- Institut fur Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe Universitat, Frankfurt am Main, Germany
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Tomaya K, Takahashi M, Minakawa N, Matsuda A. Convenient RNA Synthesis Using a Phosphoramidite Possessing a Biotinylated Photocleavable Group. Org Lett 2010; 12:3836-9. [DOI: 10.1021/ol101489v] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kota Tomaya
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan, and Graduate School of Pharmaceutical Sciences, The University of Tokushima, Shomachi 1-78-1, Tokushima 770-8505, Japan
| | - Mayumi Takahashi
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan, and Graduate School of Pharmaceutical Sciences, The University of Tokushima, Shomachi 1-78-1, Tokushima 770-8505, Japan
| | - Noriaki Minakawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan, and Graduate School of Pharmaceutical Sciences, The University of Tokushima, Shomachi 1-78-1, Tokushima 770-8505, Japan
| | - Akira Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan, and Graduate School of Pharmaceutical Sciences, The University of Tokushima, Shomachi 1-78-1, Tokushima 770-8505, Japan
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Ali A, van den Berg RJ, Overkleeft HS, van der Marel GA, Codée JD. The methylsulfonylethoxymethyl (Msem) as a hydroxyl protecting group in oligosaccharide synthesis. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.06.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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41
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Nagata S, Hamasaki T, Uetake K, Masuda H, Takagaki K, Oka N, Wada T, Ohgi T, Yano J. Synthesis and biological activity of artificial mRNA prepared with novel phosphorylating reagents. Nucleic Acids Res 2010; 38:7845-57. [PMID: 20660478 PMCID: PMC2995060 DOI: 10.1093/nar/gkq638] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Though medicines that target mRNA are under active investigation, there has been little or no effort to develop mRNA itself as a medicine. Here, we report the synthesis of a 130-nt mRNA sequence encoding a 33-amino-acid peptide that includes the sequence of glucagon-like peptide-1, a peptide that stimulates glucose-dependent insulin secretion from the pancreas. The synthesis method used, which had previously been developed in our laboratory, was based on the use of 2-cyanoethoxymethyl as the 2′-hydroxy protecting group. We also developed novel, highly reactive phosphotriester pyrophosphorylating reagents to pyrophosphorylate the 5′-end of the 130-mer RNA in preparation for capping. We completed the synthesis of the artificial mRNA by the enzymatic addition of a 5′-cap and a 3′-poly(A) tail to the pyrophosphorylated 130-mer and showed that the resulting mRNA supported protein synthesis in a cell-free system and in whole cells. As far as we know, this is the first time that mRNA has been prepared from a chemically synthesized RNA sequence. As well as providing a research tool for the intracellular expression of peptides, the technology described here may be used for the production of mRNA for medical applications.
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Affiliation(s)
- Seigo Nagata
- Discovery Research Laboratories, Nippon Shinyaku Co, Ltd, 3-14-1 Sakura, Tsukuba, Ibaraki 305-0003, Japan.
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Beaucage SL, Reese CB. Recent advances in the chemical synthesis of RNA. ACTA ACUST UNITED AC 2009; Chapter 2:Unit 2.16 1-31. [PMID: 19746354 DOI: 10.1002/0471142700.nc0216s38] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
As a consequence largely of recent developments in RNA interference (RNAi) research, the availability of rapid and efficient methods for the chemical synthesis of RNA sequences has become a matter of considerable urgency. This unit is concerned mainly with work that has been carried out, especially in the past decade, on the design of new and improved methods of RNA synthesis. The main criteria for the choice of protecting groups for the 2'-hydroxy functions of the ribonucleoside building blocks, which is arguably the most crucial strategic decision to be made, are discussed. A number of new ether-, acetal-, orthoester-, and ester-based 2'-protecting groups are described and their application, mainly in phosphoramidite-based solid-phase synthesis, is discussed in some detail. Brief consideration is also given to solution-phase RNA synthesis, which may well prove to be of great importance if a systemic drug is developed and multikilogram quantities of synthetic RNA sequences are required.
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Lackey JG, Mitra D, Somoza MM, Cerrina F, Damha MJ. Acetal levulinyl ester (ALE) groups for 2'-hydroxyl protection of ribonucleosides in the synthesis of oligoribonucleotides on glass and microarrays. J Am Chem Soc 2009; 131:8496-502. [PMID: 19485360 DOI: 10.1021/ja9002074] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We describe a synthetic strategy that permits both the growth and deprotection of RNA chains that remain attached to a solid polymer support or chip surface. The key synthons for RNA synthesis are novel 5'-O-DMTr 2'-acetal levulinyl ester (2'-O-ALE) ribonucleoside 3'-phosphoramidite derivatives. In the presence of 4,5-dicyanoimidazole (DCI) as the activator, these monomers coupled to Q-CPG solid support with excellent coupling efficiency (approximately 98.7%). The method was extended to the light directed synthesis of poly rU and poly rA on a microarray through the use of a 5'-O-(2-(2-nitrophenyl)propoxycarbonyl)-2'-O-ALE-3'-phosphoramidite derivative. A two-stage deprotection strategy was employed to fully deblock the RNA directly on the Q-CPG or microarray support without releasing it from the support's surface: phosphate group deblocking with NEt(3) in acetonitrile (ACN) (2:3 v/v; 1 h, r.t.) followed by removal of the 2'-O-ALE groups under mild hydrazinolysis conditions (0.5-4 h, r.t.). This last treatment also removed the levulinyl (Lv) group on adenine (N(6)) and cytosine (N(4)) and the dimethylformamidine (dmf) group on guanine (N(2)). The chemistry and methods described here pave the way to the fabrication of microarrays of immobilized RNA probes for analyzing molecular interactions of biological interest.
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Affiliation(s)
- Jeremy G Lackey
- Department of Chemistry, McGill University, Montreal, Quebec, Canada H3A 2K6
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44
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Abe T, Goda K, Futami K, Furuichi Y. Detection of siRNA administered to cells and animals by using a fluorescence intensity distribution analysis polarization system. Nucleic Acids Res 2009; 37:e56. [PMID: 19282452 PMCID: PMC2673448 DOI: 10.1093/nar/gkp131] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Small interfering RNA (siRNA) has excellent pharmacological features and is expected to be used for therapeutic drug development. To this end, however, new RNA technology needs to be established so that extremely small amounts (less than 1 pmol) of siRNA can be detected in organs of experimental animals and in human blood to facilitate pharmacokinetics studies. An important feature is that this new technology is not dependent on radioisotopes and can detect siRNA molecules identical to those used for drug development in preclinical tests with experimental animals or in clinical tests with humans. We report a convenient method that can detect small amounts of siRNA. The method uses high-power confocal microscopic analysis of fluorescence polarization in DNA probes that are bound to one of the strands of siRNA and directly quantitates the copy number of siRNA molecule after extraction from specimens. A pharmacokinetic study to examine the blood retention time of siRNA/cationic liposomes in mice showed that this straightforward method is consistent with the other reverse transcriptase polymerase chain reaction amplification-based method. We believe that the entire process is simple and applicable for a high-throughput analysis, which provides excellent technical support for fundamental research on RNA interference and development of siRNA drugs.
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Affiliation(s)
- Takashi Abe
- Micro-imaging Systems Division, Olympus Corporation, Tokyo, Japan
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45
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Lavergne T, Bertrand JR, Vasseur JJ, Debart F. A base-labile group for 2'-OH protection of ribonucleosides: a major challenge for RNA synthesis. Chemistry 2008; 14:9135-8. [PMID: 18767078 DOI: 10.1002/chem.200801392] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Thomas Lavergne
- Equipe Oligonucléotides Modifiés, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier 1-, Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
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46
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Ohgi T, Kitagawa H, Yano J. Chemical synthesis of oligoribonucleotides with 2'-O-(2-cyanoethoxymethyl)-protected phosphoramidites. ACTA ACUST UNITED AC 2008; Chapter 2:Unit 2.15. [PMID: 18819083 DOI: 10.1002/0471142700.nc0215s34] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
An RNA synthetic method with 2-cyanoethoxymethyl (CEM) as the 2'-hydroxyl protecting group allows the synthesis of long oligoribonucleotides from CEM-amidites with an efficiency and final purity comparable to that obtained in DNA synthesis. The CEM-amidites give a high coupling efficiency, because the CEM group minimizes steric hindrance in the coupling reaction. The CEM group shows satisfactory stability under solid-phase synthetic conditions, avoids the generation of asymmetric centers, and is easily cleaved to give the final product. This unit describes the synthesis of the four CEM-amidites, the preparation of reagents, the solid-phase synthesis of oligoribonucleotides on an automated DNA synthesizer, and their deprotection.
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Affiliation(s)
- Tadaaki Ohgi
- Discovery Research Laboratories, Nippon Shinyaku Co., Ltd., Ibaraki, Japan
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47
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Enya Y, Nagata S, Masutomi Y, Kitagawa H, Takagaki K, Oka N, Wada T, Ohgi T, Yano J. Chemical synthesis of diastereomeric diadenosine boranophosphates (ApbA) from 2'-O-(2-cyanoethoxymethyl)adenosine by the boranophosphotriester method. Bioorg Med Chem 2008; 16:9154-60. [PMID: 18824364 DOI: 10.1016/j.bmc.2008.09.040] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Revised: 09/08/2008] [Accepted: 09/09/2008] [Indexed: 11/28/2022]
Abstract
We have synthesized diastereomerically pure diadenosine 3',5'-boranophosphates (Ap(b)A) by using the boranophosphotriester method from ribonucleosides protected with the 2'-hydroxy protecting group 2-cyanoethoxymethyl (CEM). Melting curves of the triple-helical complex of the dimer Ap(b)A and 2poly(U) at high ionic strength revealed that presumptive (Sp)-Ap(b)A had a much higher affinity and presumptive (Rp)-Ap(b)A a much lower affinity for poly(U) than the natural dimer ApA did. In contrast, the affinities of these dimers for poly(dT) were similar. Both the (Rp)- and the (Sp)-boranophosphate diastereomers showed much higher resistance to digestion by snake venom phosphodiesterase and nuclease P1 than ApA did. They have potential for use as synthons to be incorporated into boranophosphate oligonucleotides. In particular, because oligonucleotides containing Sp boranophosphate nucleotides are expected to bind more strongly and specifically to RNA than natural oligoribonucleotides do, they may find application in the isolation and detection of functional RNA in basic research and diagnostics.
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Affiliation(s)
- Yukiko Enya
- Discovery Research Laboratories, Nippon Shinyaku Co., Ltd, 3-14-1 Sakura, Tsukuba City, Ibaraki 305-0003, Japan
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48
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Kwon T, Piton N, Grünewald C, Engels JW. Synthesis of pyrene labeled RNA for fluorescence measurements. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 26:1381-6. [PMID: 18066787 DOI: 10.1080/15257770701534048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The fluorophores 1-ethynylpyrene and 1-(p-ethynyl-phenylethynyl)-pyrene were attached to RNA through a Sonogashira cross-coupling with 5-iodocytidine either in solution through phosphoamidite synthesis or via on-column conjugation during solid-phase oligonucleotide synthesis. Six probes with the sequence 5'-CUU UUC UUU CUU-3' were derivatized with both fluorophores, whereby the position of the modified cytidine was varied. Fluorescence measurements showed sensitivity of the pyrene group to its environment in the single strands and corresponding duplexes.
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Affiliation(s)
- Taewoo Kwon
- Institut für Organische Chemie und Chemische Biologie (OCCB), Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, D-60438 Frankfurt am Main, Germany
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49
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Cieślak J, Grajkowski A, Kauffman JS, Duff RJ, Beaucage SL. The 4-(N-dichloroacetyl-N-methylamino)benzyloxymethyl group for 2'-hydroxyl protection of ribonucleosides in the solid-phase synthesis of oligoribonucleotides. J Org Chem 2008; 73:2774-83. [PMID: 18327953 DOI: 10.1021/jo702717g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Emerging RNA-based technologies for controlling gene expression have triggered a high demand for synthetic oligoribonucleotides and have motivated the development of ribonucleoside phosphoramidites that would exhibit coupling kinetics and coupling efficiencies comparable to those of deoxyribonucleoside phosphoramidites. To fulfill these needs, the novel 4-(N-dichloroacetyl-N-methylamino)benzyloxymethyl group for 2'-hydroxyl protection of ribonucleoside phosphoramidites 9a-d has been implemented (Schemes 1 and 2). The solid-phase synthesis of AUCCGUAGCUAACGUCAUGG was then carried out employing 9a-d as 0.2 M solutions in dry MeCN and 5-benzylthio-1H-tetrazole as an activator. The coupling efficiency of 9a-d averaged 99% within a coupling time of 180 s. Following removal of all base-sensitive protecting groups, cleavage of the remaining 2'-[4-(N-methylamino)benzyl] acetals from the RNA oligonucleotide was effected in buffered 0.1 M AcOH (pH 3.8) within 30 min at 90 degrees C. RP-HPLC and PAGE analyses of the fully deprotected AUCCGUAGCUAACGUCAUGG were comparable to those of a commercial RNA oligonucleotide sharing an identical sequence. Enzymatic digestion of the RNA oligomer catalyzed by bovine spleen phosphodiesterase and bacterial alkaline phosphatase revealed no significant amounts of RNA fragments containing (2'-->5')-internucleotidic phosphodiester linkages or noteworthy nucleobase modifications.
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Affiliation(s)
- Jacek Cieślak
- Division of Therapeutic Proteins, Center for Drug Evaluation and Research, Food and Drug Administration, 8800 Rockville Pike, Bethesda, MD 20892, USA
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50
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Chow CS, Mahto SK, Lamichhane TN. Combined Approaches to Site-Specific Modification of RNA. ACS Chem Biol 2008; 3:30-37. [PMID: 18177002 DOI: 10.1021/cb7002225] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Both natural and unnatural modifications in RNA are of interest to biologists and chemists. More than 100 different analogues of the four standard RNA nucleosides have been identified in nature. Unnatural modifications are useful for structure and mechanistic studies of RNA. This Review highlights chemical, enzymatic, and combined (semisynthesis) approaches to generate site specifically modified RNAs. The availability of these methods for site-specific modifications of RNAs of all sizes is important in order to study the relationships between RNA chemical composition, structure, and function.
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Affiliation(s)
- Christine S. Chow
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | - Santosh K. Mahto
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | - Tek N. Lamichhane
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202
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