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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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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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Lietard J, Somoza MM. Spotting, Transcription and In Situ Synthesis: Three Routes for the Fabrication of RNA Microarrays. Comput Struct Biotechnol J 2019; 17:862-868. [PMID: 31321002 PMCID: PMC6612525 DOI: 10.1016/j.csbj.2019.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/04/2019] [Accepted: 06/08/2019] [Indexed: 12/11/2022] Open
Abstract
DNA microarrays have become commonplace in the last two decades, but the synthesis of other nucleic acids biochips, most importantly RNA, has only recently been developed to a similar extent. RNA microarrays can be seen as organized surfaces displaying a potentially very large number of unique sequences and are of invaluable help in understanding the complexity of RNA structure and function as they allow the probing and treatment of each of the many different sequences simultaneously. Three approaches have emerged for the fabrication of RNA microarrays. The earliest examples used a direct, manual or mechanical, deposition of pre-synthesized, purified RNA oligonucleotides onto the surface in a process called spotting. In a second approach, pre-spotted or in situ-synthesized DNA microarrays are employed as templates for the transcription of RNA, subsequently or immediately captured on the surface. Finally, a third approach attempts to mirror the phosphoramidite-based protocols for in situ synthesis of high-density DNA arrays in order to produce in situ synthesized RNA microarrays. In this mini-review, we describe the chemistry and the engineering behind the fabrications methods, underlining the advantages and shortcomings of each, and illustrate how versatile these platforms can be by presenting some of their applications.
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Lietard J, Ameur D, Damha MJ, Somoza MM. High-Density RNA Microarrays Synthesized In Situ by Photolithography. Angew Chem Int Ed Engl 2018; 57:15257-15261. [PMID: 30187993 PMCID: PMC6237118 DOI: 10.1002/anie.201806895] [Citation(s) in RCA: 24] [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: 06/14/2018] [Indexed: 02/03/2023]
Abstract
While high-density DNA microarrays have been available for over three decades, the synthesis of equivalent RNA microarrays has proven intractable until now. Herein we describe the first in situ synthesis of mixed-based, high-density RNA microarrays using photolithography and light-sensitive RNA phosphoramidites. With coupling efficiencies comparable to those of DNA monomers, RNA oligonucleotides at least 30 nucleotides long can now efficiently be prepared using modified phosphoramidite chemistry. A two-step deprotection route unmasks the phosphodiester, the exocyclic amines and the 2' hydroxyl. Hybridization and enzymatic assays validate the quality and the identity of the surface-bound RNA. We show that high-density is feasible by synthesizing a complex RNA permutation library with 262144 unique sequences. We also introduce DNA/RNA chimeric microarrays and explore their applications by mapping the sequence specificity of RNase HII.
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Affiliation(s)
- Jory Lietard
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaAlthanstraße 14, UZA II1090ViennaAustria
| | - Dominik Ameur
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaAlthanstraße 14, UZA II1090ViennaAustria
| | - Masad J. Damha
- Department of ChemistryMcGill University801 Rue Sherbrooke OMontréalQC H3A 0B8Canada
| | - Mark M. Somoza
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaAlthanstraße 14, UZA II1090ViennaAustria
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5
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Lietard J, Ameur D, Damha MJ, Somoza MM. In‐situ‐Synthese von hochdichten RNA‐Mikroarrays mittels Photolithographie. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jory Lietard
- Institute für Anorganische ChemieFakultät für ChemieUniversität Wien Althanstraße 14, UZA II 1090 Wien Österreich
| | - Dominik Ameur
- Institute für Anorganische ChemieFakultät für ChemieUniversität Wien Althanstraße 14, UZA II 1090 Wien Österreich
| | - Masad J. Damha
- Department of ChemistryMcGill University 801 Rue Sherbrooke O Montréal QC H3A 0B8 Kanada
| | - Mark M. Somoza
- Institute für Anorganische ChemieFakultät für ChemieUniversität Wien Althanstraße 14, UZA II 1090 Wien Österreich
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Lietard J, Hassler MR, Fakhoury J, Damha MJ. An orthogonal photolabile linker for the complete "on-support" synthesis/fast deprotection/hybridization of RNA. Chem Commun (Camb) 2015; 50:15063-6. [PMID: 25329642 DOI: 10.1039/c4cc07153k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The preparation of a polystyrene solid support decorated with a photolabile linker is described. The entire post-synthetic processing of RNA can be carried out in the solid phase in a minimum amount of time. The deprotected RNA is available for "on-support" hybridization and photolysis releases siRNA duplexes under mild, neutral conditions.
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Affiliation(s)
- Jory Lietard
- Department of Chemistry, McGill University, Montréal, Québec H3A 0B8, Canada.
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Xu J, Duffy CD, Chan CKW, Sutherland JD. Solid-phase synthesis and hybrization behavior of partially 2'/3'-O-acetylated RNA oligonucleotides. J Org Chem 2014; 79:3311-26. [PMID: 24666354 PMCID: PMC4323357 DOI: 10.1021/jo5002824] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Indexed: 11/30/2022]
Abstract
Synthesis of partially 2'/3'-O-acetylated oligoribonucleotides has been accomplished by using a 2'/3'-O-acetyl orthogonal protecting group strategy in which non-nucleophilic strong-base (DBU) labile nucleobase protecting groups and a UV-light cleavable linker were used. Strong-base stability of the photolabile linker allowed on-column nucleobase and phosphate deprotection, followed by a mild cleavage of the acetylated oligonucleotides from the solid support with UV light. Two 17nt oligonucleotides, which were synthesized possessing one specific internal 2'- or 3'-acetyl group, were used as synthetic standards in a recent report from this laboratory detailing the prebiotically plausible ligation of RNA oligonucleotides. In order to further investigate the effect of 2'/3'-O-acetyl groups on the stability of RNA duplex structure, two complementary bis-acetylated RNA oligonucleotides were also expediently obtained with the newly developed protocols. UV melting curves of 2'-O-acetylated RNA duplexes showed a consistent ~3.1 °C decrease in Tm per 2'-O-acetyl group.
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Affiliation(s)
- Jianfeng Xu
- Medical Research Council
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K.
| | - Colm D. Duffy
- Medical Research Council
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K.
| | - Christopher K. W. Chan
- Medical Research Council
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K.
| | - John D. Sutherland
- Medical Research Council
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K.
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Maina A, Blackman BA, Parronchi CJ, Morozko E, Bender ME, Blake AD, Sabatino D. Solid-phase synthesis, characterization and RNAi activity of branch and hyperbranch siRNAs. Bioorg Med Chem Lett 2013; 23:5270-4. [DOI: 10.1016/j.bmcl.2013.08.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 07/26/2013] [Accepted: 08/05/2013] [Indexed: 12/20/2022]
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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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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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11
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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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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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13
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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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Abstract
The ability to manipulate the RNA interference (RNAi) machinery to specifically silence the expression of target genes could be a powerful therapeutic strategy. Since the discovery that RNAi can be triggered in mammalian cells by short double-stranded RNAs (small interfering RNA, siRNA), there has been a tremendous push by researchers, from academia to big pharma, to move siRNAs into clinical application. The challenges facing siRNA therapeutics are significant. The inherent properties of siRNAs (polyanionic, vulnerable to nuclease cleavage) make clinical application difficult due to poor cellular uptake and rapid clearance. Side effects of siRNAs have also proven to be a further complication. Fortunately, numerous chemical modification strategies have been identified that allow many of these obstacles to be overcome. This unit will present an overview of (1) the chemical modifications available to the nucleic acid chemist for modifying siRNAs, (2) the application of chemical modifications to address specific therapeutic obstacles, and (3) the factors that must be considered when assessing the activity of modified siRNAs.
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Chen CH, Chen WY, Chen YC, Lee MJ, Huang CD, Chanda K, Sun CM. Convergent Solution Phase Synthesis of Chimeric Oligonucleotides by a 2+2 and 3+3 Phosphoramidite Strategy. Aust J Chem 2010. [DOI: 10.1071/ch09298] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A chimeric oligonucleotide tetramer and hexamer were synthesized by the phosphoramidite approach using a 2+2 and 3+3 strategy, respectively. The concept of convergent synthesis provides an efficient route toward the synthesis of longer chimeric oligonucleotides, such as small interfering RNA oligonucleotides without the pollution of n – 1 or shorter failures. This methodology offers an efficient and economical way to scale-up the synthesis of high purity oligonucleotides for clinical trials and commercial uses.
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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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18
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Martin AR, Lavergne T, Vasseur JJ, Debart F. Assessment of new 2'-O-acetalester protecting groups for regular RNA synthesis and original 2'-modified proRNA. Bioorg Med Chem Lett 2009; 19:4046-9. [PMID: 19560920 DOI: 10.1016/j.bmcl.2009.06.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Revised: 06/03/2009] [Accepted: 06/05/2009] [Indexed: 11/29/2022]
Abstract
New base-labile acyloxymethyl groups were evaluated to protect 2'-OH functions of ribonucleotides for regular RNA synthesis in order to shorten the deprotection procedure upon ammonia. These same acetalester groups were assessed in 2'-modified proRNA as biolabile 2'-protections removable by cell enzymes to generate parent RNA. Demasking of 2'-modified pro-uridylates was studied in cell extracts.
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Affiliation(s)
- Anthony R Martin
- IBMM, UMR 5247 CNRS-UM1-UM2, cc1704, Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
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19
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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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Harding HP, Lackey JG, Hsu HC, Zhang Y, Deng J, Xu RM, Damha MJ, Ron D. An intact unfolded protein response in Trpt1 knockout mice reveals phylogenic divergence in pathways for RNA ligation. RNA (NEW YORK, N.Y.) 2008; 14:225-32. [PMID: 18094117 PMCID: PMC2212252 DOI: 10.1261/rna.859908] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2007] [Accepted: 11/08/2007] [Indexed: 05/23/2023]
Abstract
Unconventional mRNA splicing by an endoplasmic reticulum stress-inducible endoribonuclease, IRE1, is conserved in all known eukaryotes. It controls the expression of a transcription factor, Hac1p/XBP-1, that regulates gene expression in the unfolded protein response. In yeast, the RNA fragments generated by Ire1p are ligated by tRNA ligase (Trl1p) in a process that leaves a 2'-PO4(2-) at the splice junction, which is subsequently removed by an essential 2'-phosphotransferase, Tpt1p. However, animals, unlike yeast, have two RNA ligation/repair pathways that could potentially rejoin the cleaved Xbp-1 mRNA fragments. We report that inactivation of the Trpt1 gene, encoding the only known mammalian homolog of Tpt1p, eliminates all detectable 2'-phosphotransferase activity from cultured mouse cells but has no measurable effect on spliced Xbp-1 translation. Furthermore, the relative translation rates of tyrosine-rich proteins is unaffected by the Trpt1 genotype, suggesting that the pool of (normally spliced) tRNA(Tyr) is fully functional in the Trpt1-/- mouse cells. These observations argue against the presence of a 2'-PO4(2-) at the splice junction of ligated RNA molecules in Trpt1-/- cells, and suggest that Xbp-1 and tRNA ligation proceed by distinct pathways in yeast and mammals.
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Affiliation(s)
- Heather P Harding
- Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA.
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Abstract
Current studies of lariat RNA structure and function are hindered by the lack of access to synthetic lariats. A novel approach to the synthesis of both DNA and RNA lariats is presented here. Noteworthy features of the methodology are the regiospecific formation of the 2'-5'-phosphodiester linkage, the unusual parallel stranded DNA/RNA hybrid (or parallel RNA/RNA duplex) that forms between an RNA template and a folded 22-nt DNA (or RNA) substrate, and the efficiency of the chemical ligation step at an adenosine branchpoint (50-80%). The DNA and RNA lariats were purified by polyacrylamide gel electrophoresis, and their structure and nucleotide composition were confirmed by MALDI-TOF mass spectrometry. Thermal denaturation as well as enzymatic and chemical hydrolysis fully supported the proposed lariat structures. Characterization of control parallel duplexes was conducted by gel shift assays and enzymatic degradation with RNase H. The successful synthesis of the lariat molecules described here will allow structural and biochemical studies aimed at better understanding the splicing and debranching mechanisms in which these unusual nucleic acids are involved.
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Affiliation(s)
- Debbie Mitra
- Department of Chemistry, Otto Maass Chemistry Building, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada
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