1
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Chen X, Xie L, Zhang C, Tian S, Tang Z, Tian W, Lu P, Yang X. A Convenient Method for the Synthesis of 2'-O-Cyanoethylated Nucleotides and Their Application in the Solid-Phase Synthesis of Related RNA Analogs. Curr Protoc 2023; 3:e923. [PMID: 37962485 DOI: 10.1002/cpz1.923] [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: 11/15/2023]
Abstract
Although small interfering RNA (siRNA) is a key player among gene inhibition therapeutics, there are many obstacles to the development of siRNA drugs due to inherent properties of oligonucleotides, including the unsatisfactory stability of unmodified siRNA, poor pharmacokinetic distribution, and the toxicity induced by off-target effects. To maximize treatment potency, chemical modification of siRNA has undoubtedly been the most successful strategy by far. Widely applied modifications include phosphorothioate linkages, 2'-O-methyl modifications, and 2'-fluoro modifications, among others. To extend the family of chemical modifications for oligonucleotides, 2'-O-cyanoethylated RNA analogs were developed through the replacement of the 2'-hydroxyl group with a 2'-O-cyanoethyl group (-OCH2 CH2 CN). This modification can provide several advantages over unmodified RNA, such as increased stability, improved binding affinity to complementary DNA or RNA strands, and resistance to degradation by cellular nucleases. The 2'-O-cyanoethyl-modified RNAs not only are applied in RNA silencing machinery but also act as research tools for studying RNA structure and function or for developing RNA-based diagnostics. Therefore, the efficient synthesis, deprotection, purification, and characterization of 2'-O-cyanoethylated RNAs deserves more attention. This protocol describes the chemical synthesis of 2'-O-cyanoethylated nucleotides and the solid-phase synthesis, deprotection, and purification of 2'-O-cyanoethylated RNAs. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Preparation of 6-N-dimethylformamidyl-5'-O-dimethoxytrityl-2'-O-cyanoethyl adenosine 3'-(2-cyanoethyl N,N-diisopropyl)phosphoramidite Basic Protocol 2: Preparation of 4-N-acetyl-5'-O-dimethoxytrityl-2'-O-cyanoethyl cytidine 3'-(2-cyanoethyl N,N-diisopropyl)phosphoramidite Basic Protocol 3: Preparation of 2-N-dimethylformamidyl-5'-O-dimethoxytrityl-2'-O-cyanoethyl guanine 3'-(2-cyanoethyl N,N-diisopropyl)phosphoramidite Basic Protocol 4: Preparation of 5'-O-dimethoxytrityl-2'-O-2-cyanoethyl uridine 3'-(2-cyanoethyl N,N-diisopropyl)phosphoramidite Basic Protocol 5: Solid-phase synthesis of 2'-O-cyanoethylated RNA analogs Basic Protocol 6: Deprotection and purification of synthesized 2'-O-cyanoethyl-RNAs.
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Affiliation(s)
- Xuan Chen
- Sirnaomics Ltd. Suzhou, Suzhou, China
| | - Long Xie
- Sirnaomics Ltd. Suzhou, Suzhou, China
| | | | - Shen Tian
- Sirnaomics Ltd. Suzhou, Suzhou, China
| | - Zeyu Tang
- Sirnaomics Ltd. Suzhou, Suzhou, China
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2
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Das G, Harikrishna S, Gore KR. Influence of Sugar Modifications on the Nucleoside Conformation and Oligonucleotide Stability: A Critical Review. CHEM REC 2022; 22:e202200174. [PMID: 36048010 DOI: 10.1002/tcr.202200174] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/16/2022] [Indexed: 12/15/2022]
Abstract
Ribofuranose sugar conformation plays an important role in the structure and dynamics of functional nucleic acids such as siRNAs, AONs, aptamers, miRNAs, etc. To improve their therapeutic potential, several chemical modifications have been introduced into the sugar moiety over the years. The stability of the oligonucleotide duplexes as well as the formation of stable and functional protein-oligonucleotide complexes are dictated by the conformation and dynamics of the sugar moiety. In this review, we systematically categorise various ribofuranose sugar modifications employed in DNAs and RNAs so far. We discuss different stereoelectronic effects imparted by different substituents on the sugar ring and how these effects control sugar puckering. Using this data, it would be possible to predict the precise use of chemical modifications and design novel sugar-modified nucleosides for therapeutic oligonucleotides that can improve their physicochemical properties.
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Affiliation(s)
- Gourav Das
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal-721302, India
| | - S Harikrishna
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Kiran R Gore
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal-721302, India
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3
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Synthesis of 2'-O-[3-(N-methylsulfamoyl)propan-1-yl]ribothymidine as a potentially applicable 2'-modified nucleoside for antisense oligonucleotides. Bioorg Med Chem 2022; 73:117002. [PMID: 36170759 DOI: 10.1016/j.bmc.2022.117002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/30/2022] [Accepted: 09/04/2022] [Indexed: 11/02/2022]
Abstract
A synthetic scheme was developed to derive a modified ribothymidine bearing a 3-(N-methylsulfamoyl)propyl group on 2'-oxygen (TMSP). For synthesis initiation, a nucleophilic attack of 1,2-ethanediol on 5'-protected 2,2'-anhydro-ribothymidine was performed to selectively modify the 2'-position. After protection of the 3'-hydroxy group, the hydroxyethyl group was oxidized to the aldehyde, which was coupled with isobutyl (diethoxyphosphinyl)methanesulfonate through the Horner-Wadsworth-Emmons reaction to yield the sulfonate intermediate. The intermediate was further converted to the desired TMSP. Using the phosphoramidite units derived from nucleosides, we synthesized oligonucleotides incorporating TMSP. Oligonucleotides modified with TMSP were found to have duplex stability, resistance toward 3'-exonuclease digestion, and antisense activity comparable to that of the oligonucleotide modified with a previously reported 2'-O-methylcarbamoylethyl group. Based on these results and the generality of the synthetic scheme, 2'-O-sulfamoylalkyl modification is expected to be used for the modulation of the properties of oligonucleotides by changing the substituents on the nitrogen, enabling the oligonucleotides to possess suitable properties for antisense oligonucleotides.
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4
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Liczner C, Hanna CC, Payne RJ, Wilds CJ. Generation of oligonucleotide conjugates via one-pot diselenide-selenoester ligation-deselenization/alkylation. Chem Sci 2022; 13:410-420. [PMID: 35126973 PMCID: PMC8729807 DOI: 10.1039/d1sc04937b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/17/2021] [Indexed: 12/23/2022] Open
Abstract
A breadth of strategies are needed to efficiently modify oligonucleotides with peptides or lipids to capitalize on their therapeutic and diagnostic potential, including the modulation of in vivo chemical stability and for applications in cell-targeting and cell-permeability. The chemical linkages typically used in peptide oligonucleotide conjugates (POCs) have limitations in terms of stability and/or ease of synthesis. Herein, we report an efficient method for POC synthesis using a diselenide-selenoester ligation (DSL)-deselenization strategy that rapidly generates a stable amide linkage between the two biomolecules. This conjugation strategy is underpinned by a novel selenide phosphoramidite building block that can be incorporated into an oligonucleotide by solid-phase synthesis to generate diselenide dimer molecules. These can be rapidly ligated with peptide selenoesters and, following in situ deselenization, lead to the efficient generation of POCs. The diselenide within the oligonucleotide also serves as a flexible functionalisation handle that can be leveraged for fluorescent labelling, as well as for alkylation to generate micelles.
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Affiliation(s)
- Christopher Liczner
- Department of Chemistry and Biochemistry, Concordia University 7141 Rue Sherbrooke Ouest Montréal Québec H4B 1R6 Canada
| | - Cameron C Hanna
- School of Chemistry, The University of Sydney Sydney NSW 2006 Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney Sydney NSW 2006 Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney Sydney NSW 2006 Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney Sydney NSW 2006 Australia
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University 7141 Rue Sherbrooke Ouest Montréal Québec H4B 1R6 Canada
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5
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Kishimura T, Tomori T, Masaki Y, Seio K. Synthesis of 2'-O-alkylcarbamoylethyl-modified oligonucleotides with enhanced nuclease resistance that form isostable duplexes with complementary RNA. Bioorg Med Chem Lett 2021; 35:127779. [PMID: 33434643 DOI: 10.1016/j.bmcl.2021.127779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/14/2020] [Accepted: 01/03/2021] [Indexed: 10/22/2022]
Abstract
To expand the variety of 2'-O-modified oligonucleotides, we synthesized 2'-O-carbamoylethyl-modified oligonucleotides bearing ethyl, n-propyl, n-butyl, n-pentyl, and n-octyl groups on their nitrogen atoms. The corresponding nucleosides were synthesized using 2'-O-benzyloxycarbonylethylthymidine, which was easily converted into the carboxylic acid through hydrogeneration; subsequent condensation with the appropriate amine gave the desired nucleoside. We evaluated the effect of the 2'-O-alkylcarbamoylethyl modifications on duplex stability by analyzing melting temperature, which revealed the formation of isostable duplexes. In addition, we also revealed that these modifications, especially octylcarbamoylethyl, endowed these oligonucleotides with resistance toward a 3'-exonuclease. These results highlight the usefulness of the 2'-O-alkylcarbamoylethyl modification for various biological applications.
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Affiliation(s)
- Tomohiro Kishimura
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Takahito Tomori
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Yoshiaki Masaki
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan; JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
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6
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Oka N, Mori A, Suzuki K, Ando K. Stereoselective Synthesis of Ribofuranoid exo-Glycals by One-Pot Julia Olefination Using Ribofuranosyl Sulfones. J Org Chem 2021; 86:657-673. [PMID: 33225690 DOI: 10.1021/acs.joc.0c02297] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
One-pot Julia olefination using ribofuranosyl sulfones is described. The α-anomers of the ribofuranosyl sulfones were synthesized with complete α-selectivity via the glycosylation of heteroarylthiols using ribofuranosyl iodides as glycosyl donors and the subsequent oxidation of the resulting heteroaryl 1-thioribofuranosides with magnesium monoperphthalate (MMPP). The Julia olefination of the α-ribofuranosyl sulfones with aldehydes proceeded smoothly in one pot to afford the thermodynamically less stable (E)-exo-glycals with modest-to-excellent stereoselectivity (up to E/Z = 94:6) under the optimized conditions. The E selectivity was especially high for aromatic aldehydes. In contrast, the (Z)-exo-glycal was obtained as the main product with low stereoselectivity when the corresponding β-ribofuranosyl sulfone was used (E/Z = 41:59). The remarkable impact of the anomeric configuration of the ribofuranosyl sulfones on the stereoselectivity of the Julia olefination has been rationalized using density functional theory (DFT) calculations. The protected ribose moiety of the resulting exo-glycals induced completely α-selective cyclopropanation on the exocyclic carbon-carbon double bond via the Simmons-Smith-Furukawa reaction. The 2-cyanoethyl group was found to be useful for the protection of the exo-glycals, as it could be removed without affecting the exocyclic C═C bond.
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Affiliation(s)
- Natsuhisa Oka
- Institute for Glyco-core Research (iGCORE), Tokai National Higher Education and Research System Furo-cho, Gifu University, Chikusa-ku, Nagoya 464-8601, Japan
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7
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Masaki Y, Yamamoto K, Yoshida K, Maruyama A, Tomori T, Iriyama Y, Nakajima H, Kanaki T, Seio K. Modification of oligonucleotides with weak basic residues via the 2'-O-carbamoylethyl linker for improving nuclease resistance without loss of duplex stability and antisense activity. Org Biomol Chem 2020; 17:4835-4842. [PMID: 31033986 DOI: 10.1039/c9ob00668k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
For the improvement of nuclease resistance, four kinds of new modifications through a carbamoylethyl linker were designed. Among them, the 2'-O-[2-N-{2-(benzimidazol-1-yl)ethyl}carbamoylethyl] modification showed 20-fold longer half-life when treated with a 3' to 5' exonuclease compared to the 2'-O-methoxyethyl (MOE) modification, which is used in approved drugs. In addition, this large modification did not disturb the binding affinity or RNase H-dependent antisense activity. From these findings, it could be concluded that an adequate linker, such as carbamoylethyl in this study, could extend the utility of 2'-O-modification without loss of the properties of nucleic acids. This strategy would be useful for the development of nucleic acid therapeutics.
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Affiliation(s)
- Yoshiaki Masaki
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 J2-16, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.
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8
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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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9
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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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10
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Masaki Y, Yamamoto K, Inde T, Yoshida K, Maruyama A, Nagata T, Tanihata J, Takeda S, Sekine M, Seio K. Synthesis of 2'-O-(N-methylcarbamoylethyl) 5-methyl-2-thiouridine and its application to splice-switching oligonucleotides. Bioorg Med Chem Lett 2018; 29:160-163. [PMID: 30551900 DOI: 10.1016/j.bmcl.2018.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 11/27/2018] [Accepted: 12/04/2018] [Indexed: 01/16/2023]
Abstract
The effect of 2'-O-(N-methylcarbamoyl)ethyl (MCE) modification on splice-switching oligonucleotides (SSO) was systematically evaluated. The incorporation of five MCE nucleotides at the 5'-termini of SSOs effectively improved the splice switching effect. In addition, the incorporation of 2'-O-(N-methylcarbamoylethyl)-5-methyl-2-thiouridine (s2TMCE), a duplex-stabilizing nucleotide with an MCE modification, into SSOs further improved splice switching. These SSOs may be useful for the treatment of genetic diseases associated with splicing errors.
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Affiliation(s)
- Yoshiaki Masaki
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 J2-16, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Keishi Yamamoto
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 J2-16, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Takeshi Inde
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 J2-16, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Keita Yoshida
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 J2-16, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Atsuya Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 J2-16, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Tetsuya Nagata
- Department of Neurology and Neurological Science, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Jun Tanihata
- Department of Molecular Therapy, Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo 187-8502, Japan
| | - Shin'ichi Takeda
- Department of Molecular Therapy, Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo 187-8502, Japan
| | - Mitsuo Sekine
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 J2-16, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 J2-16, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.
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11
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Meng M, Schmidtgall B, Ducho C. Enhanced Stability of DNA Oligonucleotides with Partially Zwitterionic Backbone Structures in Biological Media. Molecules 2018; 23:molecules23112941. [PMID: 30423832 PMCID: PMC6278555 DOI: 10.3390/molecules23112941] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/06/2018] [Accepted: 11/08/2018] [Indexed: 11/16/2022] Open
Abstract
Deficient stability towards nuclease-mediated degradation is one of the most relevant tasks in the development of oligonucleotide-derived biomedical agents. This hurdle can be overcome through modifications to the native oligonucleotide backbone structure, with the goal of simultaneously retaining the unique hybridization properties of nucleic acids. The nucleosyl amino acid (NAA)-modification is a recently introduced artificial cationic backbone linkage. Partially zwitterionic NAA-modified oligonucleotides had previously shown hybridization with DNA strands with retained base-pairing fidelity. In this study, we report the significantly enhanced stability of NAA-modified oligonucleotides towards 3′- and 5′-exonuclease-mediated degradation as well as in complex biological media such as human plasma and whole cell lysate. This demonstrates the potential versatility of the NAA-motif as a backbone modification for the development of biomedically active oligonucleotide analogues.
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Affiliation(s)
- Melissa Meng
- Saarland University, Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Campus C2 3, 66123 Saarbrücken, Germany.
| | - Boris Schmidtgall
- Saarland University, Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Campus C2 3, 66123 Saarbrücken, Germany.
- University of Paderborn, Department of Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Christian Ducho
- Saarland University, Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Campus C2 3, 66123 Saarbrücken, Germany.
- University of Paderborn, Department of Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
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12
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Heid C, Sowislok A, Schaller T, Niemeyer F, Klärner FG, Schrader T. Molecular Tweezers with Additional Recognition Sites. Chemistry 2018; 24:11332-11343. [DOI: 10.1002/chem.201801508] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Indexed: 01/13/2023]
Affiliation(s)
- Christian Heid
- Faculty of Chemistry; University of Duisburg-Essen; Universitätsstr. 7 45117 Essen Germany
| | - Andrea Sowislok
- Faculty of Chemistry; University of Duisburg-Essen; Universitätsstr. 7 45117 Essen Germany
| | - Torsten Schaller
- Faculty of Chemistry; University of Duisburg-Essen; Universitätsstr. 7 45117 Essen Germany
| | - Felix Niemeyer
- Faculty of Chemistry; University of Duisburg-Essen; Universitätsstr. 7 45117 Essen Germany
| | - Frank-Gerrit Klärner
- Faculty of Chemistry; University of Duisburg-Essen; Universitätsstr. 7 45117 Essen Germany
| | - Thomas Schrader
- Faculty of Chemistry; University of Duisburg-Essen; Universitätsstr. 7 45117 Essen Germany
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13
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Masaki Y, Sekine M, Seio K. Deformability Calculation for Estimation of the Relative Stability of Chemically Modified RNA Duplexes. ACTA ACUST UNITED AC 2017; 68:7.27.1-7.27.10. [PMID: 28252179 DOI: 10.1002/cpnc.25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Chemical modification of RNA duplexes alters their stability. We have attempted to develop a computational approach to estimate the thermal stability of chemically modified duplexes. These studies revealed that the deformability of chemically modified RNA duplexes, calculated from molecular dynamics simulations, could be used as a good indicator for estimating the effect of chemical modification on duplex thermal stability. This unit describes how deformability calculation can be applied to estimate the relative stability of chemically modified RNA duplexes. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Yoshiaki Masaki
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Mitsuo Sekine
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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14
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Murayama K, Asanuma H. Effect of Methyl Group on Acyclic Serinol Scaffold for Tethering Dyes on the DNA Duplex Stability. Chembiochem 2016; 18:142-149. [DOI: 10.1002/cbic.201600558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Keiji Murayama
- Graduate School of Engineering; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8603 Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8603 Japan
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15
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Synthesis of AB4-type carbohydrate scaffolds as branching units in the glycosciences. Carbohydr Res 2016; 425:1-9. [DOI: 10.1016/j.carres.2016.02.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 02/27/2016] [Indexed: 11/21/2022]
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16
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Abstract
Silencing gene expression by harnessing the RNA interference (RNAi) pathway with short interfering RNAs (siRNAs) has useful analytical and potentially therapeutic application. To augment silencing efficacy of siRNAs, chemical modification has been employed to improve stability, target specificity, and delivery to target tissues. siRNAs incorporating guanidinopropyl (GP) moieties have demonstrated enhanced target gene silencing in cell culture and in vivo models of hepatitis B virus replication. Here we describe the synthesis of GP-modified siRNAs and use of 5' rapid amplification of cDNA ends (5' RACE) to verify an RNAi-mediated mechanism of action of these novel chemically modified siRNAs.
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17
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Song Y, Yao Y, Jin S, Tang Y, Huang Y, Chen H, Wang Y, Mi H. Designed Synthesis of Natural DNA as a Main Chain-based Brush-shaped Copolymer. CHEM LETT 2015. [DOI: 10.1246/cl.150098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Yingying Song
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, Nankai University
| | - Yanhuan Yao
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, Nankai University
| | - Susu Jin
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, Nankai University
| | - Yating Tang
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, Nankai University
| | - Yapeng Huang
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, Nankai University
| | - Haiyang Chen
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, Nankai University
| | - Ying Wang
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, Nankai University
| | - Huaifeng Mi
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, Nankai University
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18
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Yamada T, Masaki Y, Okaniwa N, Kanamori T, Ohkubo A, Tsunoda H, Seio K, Sekine M. Synthesis and properties of oligonucleotides modified with 2'-O-(2-carboxyethyl)nucleotides and their carbamoyl derivatives. Org Biomol Chem 2015; 12:6457-64. [PMID: 25019462 DOI: 10.1039/c4ob01260g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
2'-O-Methyl oligoribonucleotides with four kinds of 2'-O-modified uridine derivatives were synthesised. Their duplex stability, hydration behavior and exonuclease resistance were studied by spectroscopic analyses and molecular dynamics simulations. Consequently, 2'-O-modification of the uridine residue with 2-carbamoylethyl or 2-(N-methylcarbamoyl)ethyl groups resulted in a significant improvement of the exonuclease resistance without the loss of duplex stability.
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Affiliation(s)
- Takeshi Yamada
- Department of Life Science, Tokyo Institute of Technology, J2-12, 4259 Nagatsuta-cho, Midoriku, Yokohama, Japan.
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Gimenez Molina A, Jabgunde AM, Virta P, Lönnberg H. Solution phase synthesis of short oligoribonucleotides on a precipitative tetrapodal support. Beilstein J Org Chem 2014; 10:2279-85. [PMID: 25298795 PMCID: PMC4187100 DOI: 10.3762/bjoc.10.237] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 09/18/2014] [Indexed: 12/19/2022] Open
Abstract
An effective method for the synthesis of short oligoribonucleotides in solution has been elaborated. Novel 2'-O-(2-cyanoethyl)-5'-O-(1-methoxy-1-methylethyl) protected ribonucleoside 3'-phosphoramidites have been prepared and their usefulness as building blocks in RNA synthesis on a soluble support has been demonstrated. As a proof of concept, a pentameric oligoribonucleotide, 3'-UUGCA-5', has been prepared on a precipitative tetrapodal tetrakis(4-azidomethylphenyl)pentaerythritol support. The 3'-terminal nucleoside was coupled to the support as a 3'-O-(4-pentynoyl) derivative by Cu(I) promoted 1,3-dipolar cycloaddition. Couplings were carried out with 1.5 equiv of the building block. In each coupling cycle, the small molecular reagents and byproducts were removed by two quantitative precipitations from MeOH, one after oxidation and the second after the 5'-deprotection. After completion of the chain assembly, treatment with triethylamine, ammonia and TBAF released the pentamer in high yields.
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Affiliation(s)
- Alejandro Gimenez Molina
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Turku, FI-20014, Turku, Finland
| | - Amit M Jabgunde
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Turku, FI-20014, Turku, Finland
| | - Pasi Virta
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Turku, FI-20014, Turku, Finland
| | - Harri Lönnberg
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Turku, FI-20014, Turku, Finland
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20
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Masaki Y, Miyasaka R, Hirai K, Kanamori T, Tsunoda H, Ohkubo A, Seio K, Sekine M. Properties of 5- and/or 2-modified 2′-O-cyanoethyl uridine residue: 2′-O-cyanoethyl-5-propynyl-2-thiouridine as an efficient duplex stabilizing component. Org Biomol Chem 2014; 12:1157-62. [DOI: 10.1039/c3ob41983e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Ohkubo A, Seio K, Sekine M. Development of New Methods for Synthesis of Artificial Nucleic Acids having Various Functional Groups. J SYN ORG CHEM JPN 2014. [DOI: 10.5059/yukigoseikyokaishi.72.899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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22
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Kotikam V, Kumar VA. Synthesis and properties of 2′-O-[R- and S-(2-amino-3-methoxy)propyl] (R-AMP and S-AMP) nucleic acids. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.05.104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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23
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Ikeda Y, Kawasaki H, Ichinohe S, Nagasaki Y. Facile solid-phase synthesis of a highly stable poly(ethylene glycol)-oligonucleotide conjugate. J Mater Chem B 2013; 1:529-535. [PMID: 32260824 DOI: 10.1039/c2tb00031h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel solid-phase synthesis method for poly(ethylene glycol) (PEG)-oligonucleotide conjugates was developed to increase the stability of therapeutic oligonucleotides such as antisense oligonucleotides and siRNA. A prepared solid phase was pre-installed with PEG to provide oligonucleotides modified with PEG at the 3' terminus. Compared with the conventional liquid-phase synthesis method, the developed solid-phase method is simple and reproducible. PEGylation at the 3' terminus was confirmed to stabilize not only DNA but also RNA more than PEGylation at the 5' terminus, which has been widely used so far.
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Affiliation(s)
- Yutaka Ikeda
- Graduate School of Pure and Applied Science, University of Tsukuba, Japan.
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24
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Baraguey C, Lescrinier E, Lavergne T, Debart F, Herdewijn P, Vasseur JJ. The biolabile 2′-O-pivaloyloxymethyl modification in an RNA helix: an NMR solution structure. Org Biomol Chem 2013; 11:2638-47. [DOI: 10.1039/c3ob27005j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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25
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Deleavey GF, Damha MJ. Designing chemically modified oligonucleotides for targeted gene silencing. ACTA ACUST UNITED AC 2012; 19:937-54. [PMID: 22921062 DOI: 10.1016/j.chembiol.2012.07.011] [Citation(s) in RCA: 423] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Revised: 06/28/2012] [Accepted: 07/02/2012] [Indexed: 02/07/2023]
Abstract
Oligonucleotides (ONs), and their chemically modified mimics, are now routinely used in the laboratory as a means to control the expression of fundamentally interesting or therapeutically relevant genes. ONs are also under active investigation in the clinic, with many expressing cautious optimism that at least some ON-based therapies will succeed in the coming years. In this review, we will discuss several classes of ONs used for controlling gene expression, with an emphasis on antisense ONs (AONs), small interfering RNAs (siRNAs), and microRNA-targeting ONs (anti-miRNAs). This review provides a current and detailed account of ON chemical modification strategies for the optimization of biological activity and therapeutic application, while clarifying the biological pathways, chemical properties, benefits, and limitations of oligonucleotide analogs used in nucleic acids research.
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Affiliation(s)
- Glen F Deleavey
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, QC H3A 0B8, Canada.
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26
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Synthesis of novel tetrazole C5-linked C0- and C2-ribonucleoside phosphoramidites using MePOM and POM groups for probing RNA catalysis. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.08.082] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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27
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Masaki Y, Miyasaka R, Hirai K, Tsunoda H, Ohkubo A, Seio K, Sekine M. Prediction of the stability of modified RNA duplexes based on deformability analysis: oligoribonucleotide derivatives modified with 2'-O-cyanoethyl-5-propynyl-2-thiouridine as a promising component. Chem Commun (Camb) 2012; 48:7313-5. [PMID: 22710854 DOI: 10.1039/c2cc33409g] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe a method to predict the stability of a modified RNA duplex. Ten unique modified RNA duplexes showed a linear relationship between the calculated and experimentally determined duplex stabilities.
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Affiliation(s)
- Yoshiaki Masaki
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, Japan
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28
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Seio K, Tokugawa M, Kanamori T, Tsunoda H, Ohkubo A, Sekine M. Synthesis and properties of cationic 2'-O-[N-(4-aminobutyl)carbamoyl] modified oligonucleotides. Bioorg Med Chem Lett 2012; 22:2470-3. [PMID: 22406150 DOI: 10.1016/j.bmcl.2012.02.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 01/21/2012] [Accepted: 02/03/2012] [Indexed: 01/11/2023]
Abstract
2'-O-[N-(4-Aminobutylcarbamoyl)]uridine (U(abcm)) was synthesized and incorporated into oligonucleotides. The oligonucleotides incorporating U(abcm) formed more stable duplexes with their complementary and mismatched RNAs than those containing 2'-O-carbamoyluridine (U(cm)). The stability of duplex with a U(abcm)-rG base pair showed higher thermostability than the duplex having unmodified U-rG base pair. The U(abcm) residue showed enhanced resistance to snake venome phosphodiesterase.
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Affiliation(s)
- Kohji Seio
- Department of Life Science, Tokyo Institute of Technology, J2-16, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan.
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29
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Baszczyňski O, Jansa P, Dračínský M, Kaiser MM, Špaček P, Janeba Z. An efficient oxa-Michael addition to diethyl vinylphosphonate under mild reaction conditions. RSC Adv 2012. [DOI: 10.1039/c2ra00938b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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30
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Efthymiou TC, Huynh V, Oentoro J, Peel B, Desaulniers JP. Efficient synthesis and cell-based silencing activity of siRNAS that contain triazole backbone linkages. Bioorg Med Chem Lett 2011; 22:1722-6. [PMID: 22260772 DOI: 10.1016/j.bmcl.2011.12.104] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 12/16/2011] [Accepted: 12/20/2011] [Indexed: 10/14/2022]
Abstract
An efficient synthesis of siRNAs modified at the backbone with a triazole functionality is reported. Through the use of 4,4'-dimethoxytrityl (DMT) phosphoramidite chemistry, triazole backbone dimers were site-specifically incorporated throughout various siRNAs targeting both firefly luciferase and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene transcripts as representatives of an exogenous and endogenous gene, respectively. Following the successful silencing of the firefly luciferase reporter gene, triazole-modified siRNAs were also found to be capable of silencing GAPDH in a dose-dependent manner. Backbone modifications approaching the 3'-end on the sense strand were tolerated without compromising siRNA potency. This study highlights the compatibility of triazole-modified siRNAs within the RNAi pathway, and the modification's potential to impart favorable properties to siRNAs designed to target other endogenous genes.
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Affiliation(s)
- Tim C Efthymiou
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario, Canada
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31
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Efimov VA, Aralov AV, Chakhmakhcheva OG. Synthesis of oligoribonucleotides containing 2'-O-methoxymethyl group by the phosphotriester method. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2011; 30:565-76. [PMID: 21888547 DOI: 10.1080/15257770.2011.586255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
An effective procedure for the synthesis of ribonucleotide monomers containing a 2 '-О-methoxymethyl-modifying group was developed. These monomers were used for the synthesis of RNA fragments by the solid-phase phosphotriester method under O-nucleophilic intramolecular catalysis. The properties of 2 '-О-methoxymethyl-containing oligoribonucleotides were examined.
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Affiliation(s)
- Vladimir A Efimov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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32
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Brzezinska J, D'Onofrio J, Buff MCR, Hean J, Ely A, Marimani M, Arbuthnot P, Engels JW. Synthesis of 2'-O-guanidinopropyl-modified nucleoside phosphoramidites and their incorporation into siRNAs targeting hepatitis B virus. Bioorg Med Chem 2011; 20:1594-606. [PMID: 22264759 DOI: 10.1016/j.bmc.2011.12.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 12/12/2011] [Accepted: 12/13/2011] [Indexed: 11/25/2022]
Abstract
Synthetic RNAi activators have shown considerable potential for therapeutic application to silencing of pathology-causing genes. Typically these exogenous RNAi activators comprise duplex RNA of approximately 21 bp with 2 nt overhangs at the 3' ends. To improve efficacy of siRNAs, chemical modification at the 2'-OH group of ribose has been employed. Enhanced stability, gene silencing and attenuated immunostimulation have been demonstrated using this approach. Although promising, efficient and controlled delivery of highly negatively charged nucleic acid gene silencers remains problematic. To assess the potential utility of introducing positively charged groups at the 2' position, our investigations aimed at assessing efficacy of novel siRNAs containing 2'-O-guanidinopropyl (GP) moieties. We describe the formation of all four GP-modified nucleosides using the synthesis sequence of Michael addition with acrylonitrile followed by Raney-Ni reduction and guanidinylation. These precursors were used successfully to generate antihepatitis B virus (HBV) siRNAs. Testing in a cell culture model of viral replication demonstrated that the GP modifications improved silencing. Moreover, thermodynamic stability was not affected by the GP moieties and their introduction into each position of the seed region of the siRNA guide strand did not alter the silencing efficacy of the intended HBV target. These results demonstrate that modification of siRNAs with GP groups confers properties that may be useful for advancing therapeutic application of synthetic RNAi activators.
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Affiliation(s)
- Jolanta Brzezinska
- Goethe-University, Institute of Organic Chemistry & Chemical Biology, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
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Uchiyama N, Ogata T, Oka N, Wada T. Trimethylsilyl trifluoromethanesulfonate-promoted reductive 2'-O-arylmethylation of ribonucleoside derivatives. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2011; 30:446-56. [PMID: 21780910 DOI: 10.1080/15257770.2011.592171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Arylmethyl groups such as benzyl, p-methoxybenzyl, and 1-pyrenylmethyl groups were introduced to the 2'-O-position of nucleosides by reductive etherification. Combining corresponding aromatic aldehydes with 2'-O-trimethylsilylnucleoside derivatives in the presence of trimethylsilyl trifluoromethanesulfonate (TMSOTf) resulted in moderate to good yields of the 2'-O-arylmethyluridine derivatives, whereas the corresponding cytidine and adenosine derivatives were obtained in low yields. The reaction of ribonucleosides with aliphatic aldehydes did not proceed smoothly. Anomerization of the uridine derivatives by TMSOTf was observed in CH(2)Cl(2), toluene, and CH(3)CN, but was completely suppressed when the reactions were conducted in 1,4-dioxane.
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Affiliation(s)
- Naoki Uchiyama
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
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34
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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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35
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Nyakas A, Stucki SR, Schürch S. Tandem mass spectrometry of modified and platinated oligoribonucleotides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:875-887. [PMID: 21472522 DOI: 10.1007/s13361-011-0106-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 02/04/2011] [Accepted: 02/09/2011] [Indexed: 05/30/2023]
Abstract
Therapeutic approaches for treatment of various diseases aim at the interruption of transcription or translation. Modified oligonucleotides, such as 2'-O-methyl- and methylphosphonate-derivatives, exhibit high resistance against cellular nucleases, thus rendering application for, e.g., antigene or antisense purposes possible. Other approaches are based on administration of cross-linking agents, such as cis-diamminedichloroplatinum(II) (cisplatin, DDP), which is still the most widely used anticancer drug worldwide. Due to the formation of 1,2-intrastrand cross links at adjacent guanines, replication of the double-strand is disturbed, thus resulting in significant cytotoxicity. Evidence for the gas-phase dissociation mechanism of platinated RNA is given, based on nano-electrospray ionization high-resolution multistage tandem mass spectrometry (MS(n)). Confirmation was found by investigating the fragmentation pattern of platinated and unplatinated 2'-methoxy oligoribonucleotide hexamers and their corresponding methylphosphonate derivatives. Platinated 2'-methoxy oligoribonucleotides exhibit a similar gas-phase dissociation behavior as the corresponding DNA and RNA sequences, with the 3'-C-O bond adjacent to the vicinal guanines being cleaved preferentially, leading to w(x)-ion formation. By examination of the corresponding platinated methylphosphonate derivatives of the 2'-methoxy oligoribonucleotides, the key role of the negatively charged phosphate oxygen atoms in direct proximity to the guanines was proven. The significant alteration of fragmentation due to platination is demonstrated by comparison of the fragment ion patterns of unplatinated and platinated 2'-O-methyl- and 2'-O-methyl methylphosphonate oligoribonucleotides, and the results obtained by H/D exchange experiments.
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Affiliation(s)
- Adrien Nyakas
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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36
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Yamada T, Okaniwa N, Saneyoshi H, Ohkubo A, Seio K, Nagata T, Aoki Y, Takeda S, Sekine M. Synthesis of 2'-O-[2-(N-methylcarbamoyl)ethyl]ribonucleosides using oxa-Michael reaction and chemical and biological properties of oligonucleotide derivatives incorporating these modified ribonucleosides. J Org Chem 2011; 76:3042-53. [PMID: 21425877 DOI: 10.1021/jo101963z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To develop oligonucleotides containing new 2'-O-modified ribonucleosides as nucleic acid drugs, we synthesized three types of ribonucleoside derivatives modified at the 2'-hydroxyl group with 2-(methoxycarbonyl)ethyl (MOCE), 2-(N-methylcarbamoyl)ethyl (MCE), and 2-(N,N-dimethylcarbamoyl)ethyl (DMCE) groups, as key intermediates, via the oxa-Michael reaction of the appropriately protected ribonucleoside (U, C, A, and G) derivatives. Among them, the 2'-O-MCE ribonucleosides were found to be the most stable under basic conditions. To study the effects of the 2'-O-modification on the nuclease resistance of oligonucleotides incorporating the 2'-O-modified ribonucleosides and their hybridization affinities for the complementary RNA and DNA strands, 2'-O-MCE-ribonucleoside phosphoramidite derivatives were successfully synthesized and subjected to the synthesis of 2'-O-MCE-oligonucleotides and 2'-O-methyl-oligonucleotides incorporating 2'-O-MCE-ribonucleosides. The 2'-O-MCE-oligonucleotides and chimeric oligomers with 2'-O-MCE and 2'-O-methyl groups thus obtained demonstrated complementary RNA strands and much higher nuclease resistances than the corresponding 2'-O-methylated species. Finally, we incorporated the 2'-O-MCE-ribonucleosides into antisense 2'-O-methyl-oligoribonucleotides to examine their exon-skipping activities in splicing reactions related to pre-mRNA of mouse dystrophin. The exon-skipping assay of these 2'-O-methyl-oligonucleotide incorporating 2'-O-MCE-uridines showed better efficacies than the corresponding 2'-O-methylated oligoribonucleotide phosphorothioate derivatives.
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Affiliation(s)
- Takeshi Yamada
- Department of Life Science, Tokyo Institute of Technology, J2-12, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
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Knapp DC, Serva S, D'Onofrio J, Keller A, Lubys A, Kurg A, Remm M, Engels JW. Fluoride-cleavable, fluorescently labelled reversible terminators: synthesis and use in primer extension. Chemistry 2011; 17:2903-15. [PMID: 21294195 PMCID: PMC3110862 DOI: 10.1002/chem.201001952] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 10/18/2010] [Indexed: 11/08/2022]
Abstract
Fluorescent 2′-deoxynucleotides containing a protecting group at the 3′-O-position are reversible terminators that enable array-based DNA sequencing-by-synthesis (SBS) approaches. Herein, we describe the synthesis and full characterisation of four reversible terminators bearing a 3′-blocking moiety and a linker-dye system that is removable under the same fluoride-based treatment. Each nucleotide analogue has a different fluorophore attached to the base through a fluoride-cleavable linker and a 2-cyanoethyl moiety as the 3′-blocking group, which can be removed by using a fluoride treatment as well. Furthermore, we identified a DNA polymerase, namely, RevertAid M-MuLV reverse transcriptase, which can incorporate the four modified reversible terminators. The synthesised nucleotides and the optimised DNA polymerase were used on CodeLink slides spotted with hairpin oligonucleotides to demonstrate their potential in a cyclic reversible terminating approach.
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Affiliation(s)
- Diana C Knapp
- Institut für Organische Chemie und Chemische Biologie, J.W. Goethe Universität Frankfurt am Main, Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
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38
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Harusawa S, Fujii K, Nishiura M, Araki L, Usami Y, Zhao ZY, M. J. Lilley D. Synthesis of Imidazole C1- and C3-Ribonucleoside Phosphoramidites for Probing Catalytic Mechanism in Ribozyme. HETEROCYCLES 2011. [DOI: 10.3987/com-11-12263] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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ARAKI L, HARUSAWA S. Synthetic Studies of Imidazole C-Nucleosides toward Biofunctional Molecules. YAKUGAKU ZASSHI 2010; 130:1707-24. [DOI: 10.1248/yakushi.130.1707] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Lisa ARAKI
- Osaka University of Pharmaceutical Sciences
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40
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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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41
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Yamada K, Taguchi H, Ohkubo A, Seio K, Sekine M. Synthesis and biochemical properties of oligodeoxynucleotides acylated by the chemically stable 2-(trimethylsilyl)benzoyl (TMSBz) group at the 5′ or 3′ terminus. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2010.07.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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42
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Ohkubo A, Kuwayama Y, Nishino Y, Tsunoda H, Seio K, Sekine M. Oligonucleotide synthesis involving deprotection of amidine-type protecting groups for nucleobases under acidic conditions. Org Lett 2010; 12:2496-9. [PMID: 20455549 DOI: 10.1021/ol100676j] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amidine-type protecting groups, i.e., N,N-dimethylformamidine (dmf) and N,N-dibutylformamidine (dbf) groups, introduced into nucleobases were rapidly removed under mild acidic conditions using imidazolium triflate (IMT) or 1-hydroxybenztriazole (HOBt). This new deprotection strategy allowed a 2'-O-methyl-RNA derivative bearing a base-labile group to be efficiently synthesized using a silyl-type linker. It was also found that our new method could be applied to the synthesis of an unmodified RNA oligomer.
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Affiliation(s)
- Akihiro Ohkubo
- Department of Life Science, Tokyo Institute of Technology, J2-12, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
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Masaki Y, Miyasaka R, Ohkubo A, Seio K, Sekine M. Linear relationship between deformability and thermal stability of 2'-O-modified RNA hetero duplexes. J Phys Chem B 2010; 114:2517-24. [PMID: 20108976 PMCID: PMC2825091 DOI: 10.1021/jp909851j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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We describe the relationship between the experimentally determined melting temperatures of 2′-O-modified-RNA/RNA duplexes and their deformability estimated from molecular dynamics simulations. To clarify this relationship, we synthesized several fully modified oligoribonucleotides such as 2′-O-cyanoethyl RNAs and 2′-O-methoxyethyl RNAs and compared the actual melting temperatures of the duplexes with their calculated deformabilities. An increase of the melting temperatures by 2′-O-modifications was found to correlate strongly with an increase of the helical elastic constants in U14/A14, (CU)7/(AG)7, and (GACU)3/(AGUC)3 sequences. Linear regression analyses could be used to estimate the melting temperature with an accuracy of ±2.0 °C in our model case. Although the strong correlation was observed in the same base sequence, the linear regression functions were different from each base sequence. Our results indicated the possibility of predicting the thermal stability of 2′-O-modified duplexes at the computer-aided molecular design stage.
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Affiliation(s)
- Yoshiaki Masaki
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 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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Kaczmarek O, Scheidt HA, Bunge A, Föse D, Karsten S, Arbuzova A, Huster D, Liebscher J. 2′-Linking of Lipids and Other Functions to Uridine through 1,2,3-Triazoles and Membrane Anchoring of the Amphiphilic Products. European J Org Chem 2010. [DOI: 10.1002/ejoc.200901073] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Harusawa S, Araki L, Zhao ZY, M. J. Lilley D. Efficient Synthesis of 2’-O-Cyanoethylated Imidazole C-Ribonucleoside Phosphoramidite: A Practical Building Block for Probing the Catalytic Mechanism of Ribozymes. HETEROCYCLES 2010. [DOI: 10.3987/com-10-11978] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Mukobata T, Ochi Y, Ito Y, Wada SI, Urata H. Facile and efficient approach for the synthesis of N2-dimethylaminomethylene-2′-O-methylguanosine. Bioorg Med Chem Lett 2010; 20:129-31. [DOI: 10.1016/j.bmcl.2009.11.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Revised: 11/02/2009] [Accepted: 11/06/2009] [Indexed: 11/29/2022]
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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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Oeda Y, Iijima Y, Taguchi H, Ohkubo A, Seio K, Sekine M. Microwave-Assisted Synthesis of 2′-O-Aryluridine Derivatives. Org Lett 2009; 11:5582-5. [DOI: 10.1021/ol902142w] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Yusuke Oeda
- Department of Life Science, Tokyo Institute of Technology, J2-12, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Yoshihiro Iijima
- Department of Life Science, Tokyo Institute of Technology, J2-12, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Haruhiko Taguchi
- Department of Life Science, Tokyo Institute of Technology, J2-12, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Akihiro Ohkubo
- Department of Life Science, Tokyo Institute of Technology, J2-12, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Khoji Seio
- Department of Life Science, Tokyo Institute of Technology, J2-12, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Mitsuo Sekine
- Department of Life Science, Tokyo Institute of Technology, J2-12, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
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Seio K, Tawarada R, Sasami T, Serizawa M, Ise M, Ohkubo A, Sekine M. Synthesis and hybridization of 2'-O-methyl-RNAs incorporating 2'-O-carbamoyluridine and unique participation of the carbamoyl group in U-G base pair. Bioorg Med Chem 2009; 17:7275-80. [PMID: 19783446 DOI: 10.1016/j.bmc.2009.08.053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 08/20/2009] [Accepted: 08/21/2009] [Indexed: 10/20/2022]
Abstract
2'-O-Carbamoyluridine (U(cm)) was synthesized and incorporated into DNAs and 2'-O-Me-RNAs. The oligonucleotides incorporating U(cm) formed less stable duplexes with their complementary and U(cm)-U, U(cm)-C single-base mismatched DNAs and RNAs in comparison with those without the carbamoyl group. On the contrary, the T(m) analyses revealed that the duplexes with a mismatched U(cm)-G base pair showed almost the same thermostability as the corresponding unmodified duplexes. Molecular dynamics (MD) simulations of the U(cm)-modified 2'-O-Me-RNA/RNA duplexes with U(cm)-G mismatched base pair suggested that the carbamoyl group could participate in the U(cm)-G base pair by an additional intermolecular hydrogen bond between the carbamoyl oxygen and the H2 of the guanine base.
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Affiliation(s)
- Kohji Seio
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan.
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