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Krasheninina OA, Fishman VS, Lomzov AA, Ustinov AV, Venyaminova AG. Postsynthetic On-Column 2' Functionalization of RNA by Convenient Versatile Method. Int J Mol Sci 2020; 21:E5127. [PMID: 32698484 PMCID: PMC7404181 DOI: 10.3390/ijms21145127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/08/2020] [Accepted: 07/14/2020] [Indexed: 12/26/2022] Open
Abstract
We report a universal straightforward strategy for the chemical synthesis of modified oligoribonucleotides containing functional groups of different structures at the 2' position of ribose. The on-column synthetic concept is based on the incorporation of two types of commercial nucleotide phosphoramidites containing orthogonal 2'-O-protecting groups, namely 2'-O-thiomorpholine-carbothioate (TC, as "permanent") and 2'-O-tert-butyl(dimethyl)silyl (tBDMS, as "temporary"), to RNA during solid-phase synthesis. Subsequently, the support-bound RNA undergoes selective deprotection and follows postsynthetic 2' functionalization of the naked hydroxyl group. This convenient method to tailor RNA, utilizing the advantages of solid phase approaches, gives an opportunity to introduce site-specifically a wide range of linkers and functional groups. By this strategy, a series of RNAs containing diverse 2' functionalities were synthesized and studied with respect to their physicochemical properties.
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Affiliation(s)
- Olga A. Krasheninina
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, Innsbruck 6020, Austria
| | - Veniamin S. Fishman
- Institute of Cytology and Genetics SB RAS Lavrentiev Ave. 10, 630090 Novosibirsk, Russia;
| | - Alexander A. Lomzov
- Institute of Chemical Biology and Fundamental Medicine SB RAS Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (A.A.L.); (A.G.V.)
| | - Alexey V. Ustinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia;
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (A.A.L.); (A.G.V.)
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Gauthier F, Malher A, Vasseur JJ, Dupouy C, Debart F. Conjugation of Small Molecules to RNA Using a Reducible Disulfide Linker Attached at the 2′-OH Position through a Carbamate Function. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900740] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Florian Gauthier
- Institut des Biomolécules Max Mousseron (IBMM); Université de Montpellier; CNRS, ENSCM; Montpellier France
| | - Astrid Malher
- Institut des Biomolécules Max Mousseron (IBMM); Université de Montpellier; CNRS, ENSCM; Montpellier France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron (IBMM); Université de Montpellier; CNRS, ENSCM; Montpellier France
| | - Christelle Dupouy
- Institut des Biomolécules Max Mousseron (IBMM); Université de Montpellier; CNRS, ENSCM; Montpellier France
| | - Françoise Debart
- Institut des Biomolécules Max Mousseron (IBMM); Université de Montpellier; CNRS, ENSCM; Montpellier France
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3
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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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Masaki Y, Ito H, Oda Y, Yamazaki K, Tago N, Ohno K, Ishii N, Tsunoda H, Kanamori T, Ohkubo A, Sekine M, Seio K. Enzymatic synthesis and reverse transcription of RNAs incorporating 2'-O-carbamoyl uridine triphosphate. Chem Commun (Camb) 2018; 52:12889-12892. [PMID: 27738673 DOI: 10.1039/c6cc05796a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Enzymatic synthesis and the reverse transcription of RNAs containing 2'-O-carbamoyl uridine were evaluated. A mild acidic deprotection procedure allowed the synthesis of 2'-O-carbamoyl uridine triphosphate (UcmTP). UcmTP was incorporated correctly into long RNAs, and its fidelity during reverse transcription using SuperScript III was sufficient for RNA aptamer selection.
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Affiliation(s)
- Yoshiaki Masaki
- Department of Life Science and Technology, Tokyo Institute of Technology, J2-16, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan.
| | - Hyugo Ito
- Department of Life Science and Technology, Tokyo Institute of Technology, J2-16, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan.
| | - Yuki Oda
- Department of Life Science and Technology, Tokyo Institute of Technology, J2-16, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan.
| | - Kazufumi Yamazaki
- Department of Life Science and Technology, Tokyo Institute of Technology, J2-16, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan.
| | - Nobuhiro Tago
- Department of Life Science and Technology, Tokyo Institute of Technology, J2-16, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan.
| | - Kentaro Ohno
- Department of Life Science and Technology, Tokyo Institute of Technology, J2-16, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan.
| | - Nozomi Ishii
- Department of Life Science and Technology, Tokyo Institute of Technology, J2-16, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan.
| | - Hirosuke Tsunoda
- Department of Life Science and Technology, Tokyo Institute of Technology, J2-16, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan.
| | - Takashi Kanamori
- Department of Life Science and Technology, Tokyo Institute of Technology, J2-16, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan.
| | - Akihiro Ohkubo
- Department of Life Science and Technology, Tokyo Institute of Technology, J2-16, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan.
| | - Mitsuo Sekine
- Department of Life Science and Technology, Tokyo Institute of Technology, J2-16, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan.
| | - Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology, J2-16, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan.
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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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Coppola C, Simeone L, Trotta R, De Napoli L, Randazzo A, Montesarchio D. Synthesis and NMR characterization of a novel crown-ether ring-fused uridine analogue. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.06.073] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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