1
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Attiach CM, Kumar A, Daniel J, Blanchard-Desce M, Maruani A, Dalko PI. Red-shifted two-photon-sensitive phenanthridine photocages: synthesis and characterisation. Chem Commun (Camb) 2024; 60:8260-8263. [PMID: 39011868 DOI: 10.1039/d4cc02852j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Herein we describe the rational design, synthesis and photophysical study of a novel class of phenanthridine-based, one- and two-photon sensitive, photoremovable protecting groups with absorption wavelengths extending beyond 400 nm. This design facilitated the development of scaffolds with enhanced uncaging quantum yield, paving the way for broader applications in controlled drug delivery and molecular manipulation.
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Affiliation(s)
- Célest M Attiach
- Université Paris Cité, CNRS, Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, 75006 Paris, France.
| | - Amit Kumar
- Université Paris Cité, CNRS, Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, 75006 Paris, France.
| | - Jonathan Daniel
- Univ. Bordeaux, CNRS, Bordeaux INP, ISM, UMR 5255, F-33400 Talence, France
| | | | - Antoine Maruani
- Université Paris Cité, CNRS, Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, 75006 Paris, France.
| | - Peter I Dalko
- Université Paris Cité, CNRS, Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, 75006 Paris, France.
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2
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Higashi SL, Isogami A, Takahashi J, Shibata A, Hirosawa KM, Suzuki KGN, Sawada S, Tsukiji S, Matsuura K, Ikeda M. Construction of a Reduction-responsive DNA Microsphere using a Reduction-cleavable Spacer based on a Nitrobenzene Scaffold. Chem Asian J 2022; 17:e202200142. [PMID: 35338588 DOI: 10.1002/asia.202200142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/24/2022] [Indexed: 11/07/2022]
Abstract
Here, we describe the design and synthesis of a new reduction-cleavable spacer (RCS) based on a nitrobenzene scaffold for constructing reduction-responsive oligonucleotides according to standard phosphoramidite chemistry. In addition, we demonstrate that the introduction of the RCS in the middle of an oligonucleotide (30 nt) enables the construction of a self-assembled microsphere capable of exhibiting a reduction-responsive disassembly.
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Affiliation(s)
- Sayuri L Higashi
- Gifu University: Gifu Daigaku, United Graduate School of Drug Discovery and Medical Information Sciences, 1-1 Yanagido, Gifu, 501-1193, Gifu, JAPAN
| | - Ayaka Isogami
- Gifu University: Gifu Daigaku, Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, JAPAN
| | - Junko Takahashi
- Gifu University: Gifu Daigaku, Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, JAPAN
| | - Aya Shibata
- Gifu University: Gifu Daigaku, Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, JAPAN
| | - Koichiro M Hirosawa
- Gifu University: Gifu Daigaku, Institute for Glyco-core Research (iGCORE), JAPAN
| | - Kenichi G N Suzuki
- Gifu University: Gifu Daigaku, Institute for Glyco-core Research (iGCORE), JAPAN
| | - Shunsuke Sawada
- Nagoya Institute of Technology: Nagoya Kogyo Daigaku, Department of Nanopharmaceutical Sciences, JAPAN
| | - Shinya Tsukiji
- Nagoya Institute of Technology: Nagoya Kogyo Daigaku, Department of Nanopharmaceutical Sciences, JAPAN
| | - Kazunori Matsuura
- Tottori University: Tottori Daigaku, Department of Chemistry and Biotechnology, JAPAN
| | - Masato Ikeda
- GIFU University, Chemistry and Biomolecular Science, 1-1, Yanagido, 501-1193, Gifu, JAPAN
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3
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Shirakami N, Kawaki Y, Higashi SL, Shibata A, Kitamura Y, Abu Hanifah S, Wah LL, Ikeda M. Introduction of an Oxidation-responsive 4-Boronobenzyl Group into an Oligonucleotide through a Postmodification Approach. CHEM LETT 2021. [DOI: 10.1246/cl.210204] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Nanami Shirakami
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Yugo Kawaki
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Sayuri L. Higashi
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Aya Shibata
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Yoshiaki Kitamura
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Sharina Abu Hanifah
- Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Selangor, Malaysia
| | - Lim Lee Wah
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Masato Ikeda
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- Center for Highly Advanced Integration of Nano and Life Sciences, Gifu University (G-CHAIN), 1-1 Yanagido, Gifu 501-1193, Japan
- Institute for Glyco-core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
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4
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Photolytical reactions for light induced biological effectors release: on the road to the phototherapeutic window. J INCL PHENOM MACRO 2021. [DOI: 10.1007/s10847-021-01071-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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5
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Mattay J, Dittmar M, Rentmeister A. Chemoenzymatic strategies for RNA modification and labeling. Curr Opin Chem Biol 2021; 63:46-56. [PMID: 33690011 DOI: 10.1016/j.cbpa.2021.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 01/20/2021] [Accepted: 01/31/2021] [Indexed: 12/17/2022]
Abstract
RNA is a central molecule in numerous cellular processes, including transcription, translation, and regulation of gene expression. To reveal the numerous facets of RNA function and metabolism in cells, labeling has become indispensable and enables the visualization, isolation, characterization, and even quantification of certain RNA species. In this review, we will cover chemoenzymatic approaches for covalent RNA labeling. These approaches rely on an enzymatic step to introduce an RNA modification before conjugation with a label for detection or isolation. We start with in vitro manipulation of RNA, sorted according to the enzymatic reaction exploited. Then, metabolic approaches for co- and post-transcriptional RNA labeling will be treated. We focus on recent advances in the field and highlight the most relevant applications for cellular imaging, RNA isolation and sequencing.
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Affiliation(s)
- Johanna Mattay
- Department of Chemistry, Institute of Biochemistry, University of Münster, Correnstr. 36, 48149, Münster, Germany
| | - Maria Dittmar
- Department of Chemistry, Institute of Biochemistry, University of Münster, Correnstr. 36, 48149, Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, University of Münster, Correnstr. 36, 48149, Münster, Germany; Cells in Motion Interfaculty Center, University of Münster, 48149, Münster, Germany.
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6
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Construction of a reduction-responsive oligonucleotide via a post-modification approach utilizing 4-nitrophenyl diazomethane. Polym J 2021. [DOI: 10.1038/s41428-021-00464-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
AbstractHerein, we describe the construction of a reduction-responsive oligonucleotide by post-modification of an oligonucleotide with a diazo compound bearing a 4-nitrobenzyl group as a reduction-responsive cleavable moiety. High-performance liquid chromatography and mass spectrometry were used to reveal the introduction of a 4-nitrobenzyl group to the 5′-phosphate group of an oligonucleotide, and the subsequent reduction-triggered recovery of the original oligonucleotide. The protocol used for the preparation of this reduction-responsive oligonucleotide is simple and it will have various applications in the fields of chemical and synthetic biology.
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7
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Bollu A, Sharma NK. Biased photo cleavage of N-/N-nitrobenzyl from 2’-hydroxyethyl-adenosine and their DNA/RNA Caged-analogues. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2020.112864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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8
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Takezawa Y, Suzuki A, Nakaya M, Nishiyama K, Shionoya M. Metal-Dependent DNA Base Pairing of 5-Carboxyuracil with Itself and All Four Canonical Nucleobases. J Am Chem Soc 2020; 142:21640-21644. [DOI: 10.1021/jacs.0c11437] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Akira Suzuki
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Manabu Nakaya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kotaro Nishiyama
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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9
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Chakrapani A, Vaňková Hausnerová V, Ruiz-Larrabeiti O, Pohl R, Krásný L, Hocek M. Photocaged 5-(Hydroxymethyl)pyrimidine Nucleoside Phosphoramidites for Specific Photoactivatable Epigenetic Labeling of DNA. Org Lett 2020; 22:9081-9085. [PMID: 33156631 DOI: 10.1021/acs.orglett.0c03462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
5-Hydroxymethylcytosine and uracil are epigenetic nucleobases, but their biological roles are still unclear. We present the synthesis of 2-nitrobenzyl photocaged 5-hydroxymethyl-2'-deoxycytidine and uridine 3'-O-phosphoramidites and their use in automated solid-phase synthesis of oligonucleotides (ONs) modified at specific positions. The ONs were used as primers for PCR to construct DNA templates modified in the promoter region that allowed switching of transcription through photochemical uncaging.
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Affiliation(s)
- Aswathi Chakrapani
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Viola Vaňková Hausnerová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic
| | - Olatz Ruiz-Larrabeiti
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic
| | - Libor Krásný
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
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10
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Vaníková Z, Janoušková M, Kambová M, Krásný L, Hocek M. Switching transcription with bacterial RNA polymerase through photocaging, photorelease and phosphorylation reactions in the major groove of DNA. Chem Sci 2019; 10:3937-3942. [PMID: 31015933 PMCID: PMC6457204 DOI: 10.1039/c9sc00205g] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/01/2019] [Indexed: 12/14/2022] Open
Abstract
We report proof of principle biomimetic switching of transcription in vitro through non-natural chemical reactions in the major groove of DNA templates. Photocaged DNA templates containing nitrobenzyl-protected 5-hydroxymethyluracil or - cytosine permitted no transcription with E. coli RNA polymerase (OFF state). Their irradiation with 400 nm light resulted in DNA templates containing hydroxymethylpyrimidines, which switched transcription ON with a higher yield (250-350%) compared to non-modified DNA. Phosphorylation of templates containing 5-hydroxymethyluracil (but not 5-hydroxymethylcytosine) then turned transcription OFF again. It is the first step towards artificial bioorthogonal chemical epigenetics.
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Affiliation(s)
- Zuzana Vaníková
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nam. 2 , 16610 Prague 6 , Czech Republic . .,Department of Organic Chemistry , Faculty of Science , Charles University in Prague , Hlavova 8 , CZ-12843 Prague 2 , Czech Republic
| | - Martina Janoušková
- Dept. of Molecular Genetics of Bacteria , Institute of Microbiology , Czech Academy of Sciences , CZ-14220 Prague 4 , Czech Republic .
| | - Milada Kambová
- Dept. of Molecular Genetics of Bacteria , Institute of Microbiology , Czech Academy of Sciences , CZ-14220 Prague 4 , Czech Republic .
| | - Libor Krásný
- Dept. of Molecular Genetics of Bacteria , Institute of Microbiology , Czech Academy of Sciences , CZ-14220 Prague 4 , Czech Republic .
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nam. 2 , 16610 Prague 6 , Czech Republic . .,Department of Organic Chemistry , Faculty of Science , Charles University in Prague , Hlavova 8 , CZ-12843 Prague 2 , Czech Republic
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11
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Boháčová S, Ludvíková L, Poštová Slavětínská L, Vaníková Z, Klán P, Hocek M. Protected 5-(hydroxymethyl)uracil nucleotides bearing visible-light photocleavable groups as building blocks for polymerase synthesis of photocaged DNA. Org Biomol Chem 2019; 16:1527-1535. [PMID: 29431832 DOI: 10.1039/c8ob00160j] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nucleosides, nucleotides and 2'-deoxyribonucleoside triphosphates (dNTPs) containing 5-(hydroxymethyl)uracil protected with photocleavable groups (2-nitrobenzyl-, 6-nitropiperonyl or 9-anthrylmethyl) were prepared and tested as building blocks for the polymerase synthesis of photocaged oligonucleotides and DNA. Photodeprotection (photorelease) reactions were studied in detail on model nucleoside monophosphates and their photoreaction quantum yields were determined. Photocaged dNTPs were then tested and used as substrates for DNA polymerases in primer extension or PCR. DNA probes containing photocaged or free 5-hydroxymethylU in the recognition sequence of restriction endonucleases were prepared and used for the study of photorelease of caged DNA by UV or visible light at different wavelengths. The nitropiperonyl-protected nucleotide was found to be a superior building block because the corresponding dNTP is a good substrate for DNA polymerases, and the protecting group is efficiently cleavable by irradiation by UV or visible light (up to 425 nm).
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Affiliation(s)
- Soňa Boháčová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic.
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12
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Banno A, Higashi S, Shibata A, Ikeda M. A stimuli-responsive DNAzyme displaying Boolean logic-gate responses. Chem Commun (Camb) 2019; 55:1959-1962. [PMID: 30681683 DOI: 10.1039/c8cc09345h] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Introducing a desired stimuli-responsive function into catalytically active biomacromolecules is potentially useful in developing molecular tools for various bio-applications. In this paper, we discuss the development of a stimuli-responsive DNAzyme (catalytic deoxyribozyme) capable of displaying Boolean logic-gate responses.
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Affiliation(s)
- Ayaka Banno
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
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13
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14
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Hayakawa Y, Banno A, Kitagawa H, Higashi S, Kitade Y, Shibata A, Ikeda M. Reduction-Responsive DNA Duplex Containing O 6-Nitrobenzyl-Guanine. ACS OMEGA 2018; 3:9267-9275. [PMID: 31459058 PMCID: PMC6645092 DOI: 10.1021/acsomega.8b01177] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/01/2018] [Indexed: 05/27/2023]
Abstract
Stimuli-controlled structural transitions of nucleic acids have received growing attentions owing to their potential applications in the fields of chemical and synthetic biology. Here, we describe the development of reduction-responsive deoxyribonucleic acid (DNA) duplexes, in which guanine rings bearing a reduction-responsive cleavable nitrobenzyl (NB) group at the O 6 position (GNB) are introduced at defined positions. We demonstrate that the artificial NB group can be removed in response to reduction stimulus without the dissociation of the intermolecular duplex structure, which comprises a G-quadruplex forming nucleic acid strand with one GNB and its complementary sequence with one mismatch pair. Meanwhile, another duplex that comprised a G-quadruplex forming nucleic acid strand with two GNB and its complementary sequence with three mismatch pairs exhibited reduction-responsive structural transitions from intermolecular duplex to intramolecular quadruplex. These findings might be useful for the development of DNA architectures endowed with reduction-responsive functions.
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Affiliation(s)
- Yukiko Hayakawa
- Department
of Life Science and Chemistry, Graduate School of Natural
Science and Technology and United Graduate School of Drug Discovery and Medical
Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Ayaka Banno
- Department
of Life Science and Chemistry, Graduate School of Natural
Science and Technology and United Graduate School of Drug Discovery and Medical
Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Hiroaki Kitagawa
- Department
of Life Science and Chemistry, Graduate School of Natural
Science and Technology and United Graduate School of Drug Discovery and Medical
Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Sayuri Higashi
- Department
of Life Science and Chemistry, Graduate School of Natural
Science and Technology and United Graduate School of Drug Discovery and Medical
Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Yukio Kitade
- Department
of Life Science and Chemistry, Graduate School of Natural
Science and Technology and United Graduate School of Drug Discovery and Medical
Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Aya Shibata
- Department
of Life Science and Chemistry, Graduate School of Natural
Science and Technology and United Graduate School of Drug Discovery and Medical
Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Masato Ikeda
- Department
of Life Science and Chemistry, Graduate School of Natural
Science and Technology and United Graduate School of Drug Discovery and Medical
Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- Center
for Highly Advanced Integration of Nano and Life Sciences, Gifu University (G-CHAIN), Gifu 501-1193, Japan
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15
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Debart F, Dupouy C, Vasseur JJ. Stimuli-responsive oligonucleotides in prodrug-based approaches for gene silencing. Beilstein J Org Chem 2018; 14:436-469. [PMID: 29520308 PMCID: PMC5827813 DOI: 10.3762/bjoc.14.32] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 01/26/2018] [Indexed: 12/14/2022] Open
Abstract
Oligonucleotides (ONs) have been envisaged for therapeutic applications for more than thirty years. However, their broad use requires overcoming several hurdles such as instability in biological fluids, low cell penetration, limited tissue distribution, and off-target effects. With this aim, many chemical modifications have been introduced into ONs definitively as a means of modifying and better improving their properties as gene silencing agents and some of them have been successful. Moreover, in the search for an alternative way to make efficient ON-based drugs, the general concept of prodrugs was applied to the oligonucleotide field. A prodrug is defined as a compound that undergoes transformations in vivo to yield the parent active drug under different stimuli. The interest in stimuli-responsive ONs for gene silencing functions has been notable in recent years. The ON prodrug strategies usually help to overcome limitations of natural ONs due to their low metabolic stability and poor delivery. Nevertheless, compared to permanent ON modifications, transient modifications in prodrugs offer the opportunity to regulate ON activity as a function of stimuli acting as switches. Generally, the ON prodrug is not active until it is triggered to release an unmodified ON. However, as it will be described in some examples, the opposite effect can be sought. This review examines ON modifications in response to various stimuli. These stimuli may be internal or external to the cell, chemical (glutathione), biochemical (enzymes), or physical (heat, light). For each stimulus, the discussion has been separated into sections corresponding to the site of the modification in the nucleotide: the internucleosidic phosphate, the nucleobase, the sugar or the extremities of ONs. Moreover, the review provides a current and detailed account of stimuli-responsive ONs with the main goal of gene silencing. However, for some stimuli-responsive ONs reported in this review, no application for controlling gene expression has been shown, but a certain potential in this field could be demonstrated. Additionally, other applications in different domains have been mentioned to extend the interest in such molecules.
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Affiliation(s)
- Françoise Debart
- IBMM, Université de Montpellier, CNRS, ENSCM, Montpellier, France
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16
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Mori S, Morihiro K, Okuda T, Kasahara Y, Obika S. Hydrogen peroxide-triggered gene silencing in mammalian cells through boronated antisense oligonucleotides. Chem Sci 2018; 9:1112-1118. [PMID: 29629168 PMCID: PMC5875086 DOI: 10.1039/c7sc04318j] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/21/2017] [Indexed: 12/16/2022] Open
Abstract
Hydrogen peroxide (H2O2) is a reactive oxygen species (ROS) involved in various diseases, including neurodegeneration, diabetes, and cancer. Here, we introduce a new approach to use H2O2 to modulate specific gene expression in mammalian cells. H2O2-responsive nucleoside analogues, in which the Watson-Crick faces of the nucleobases are caged by arylboronate moieties, were synthesized. One of these analogues, boronated thymidine (dTB ), was incorporated into oligodeoxynucleotides (ODNs) using an automated DNA synthesizer. The hybridization ability of this boronated ODN to complementary RNA was clearly switched in the off-to-on direction upon H2O2 addition. Furthermore, we demonstrated H2O2-triggered gene silencing in mammalian cells using antisense oligonucleotides (ASOs) modified with dTB . Our approach can be used for the regulation of any gene of interest by the sequence design of boronated ASOs and will contribute to the development of targeted disease therapeutics.
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Affiliation(s)
- Shohei Mori
- Graduate School of Pharmaceutical Sciences , Osaka University , 1-6 Yamadaoka , Suita , Osaka 565-0871 , Japan . ;
| | - Kunihiko Morihiro
- Graduate School of Pharmaceutical Sciences , Osaka University , 1-6 Yamadaoka , Suita , Osaka 565-0871 , Japan . ;
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN) , 7-6-8 Saito-Asagi , Ibaraki , Osaka 567-0085 , Japan
| | - Takumi Okuda
- Graduate School of Pharmaceutical Sciences , Osaka University , 1-6 Yamadaoka , Suita , Osaka 565-0871 , Japan . ;
| | - Yuuya Kasahara
- Graduate School of Pharmaceutical Sciences , Osaka University , 1-6 Yamadaoka , Suita , Osaka 565-0871 , Japan . ;
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN) , 7-6-8 Saito-Asagi , Ibaraki , Osaka 567-0085 , Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences , Osaka University , 1-6 Yamadaoka , Suita , Osaka 565-0871 , Japan . ;
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN) , 7-6-8 Saito-Asagi , Ibaraki , Osaka 567-0085 , Japan
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17
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Boháčová S, Vaníková Z, Poštová Slavětínská L, Hocek M. Protected 2′-deoxyribonucleoside triphosphate building blocks for the photocaging of epigenetic 5-(hydroxymethyl)cytosine in DNA. Org Biomol Chem 2018; 16:5427-5432. [DOI: 10.1039/c8ob01106k] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
2′-Deoxyribonucleoside triphosphates containing 5-(hydroxymethyl)cytosine protected with photocleavable groups were prepared and studied as substrates for the enzymatic synthesis of DNA containing a photocaged epigenetic 5hmC base.
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Affiliation(s)
- Soňa Boháčová
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- CZ-16610 Prague 6
- Czech Republic
| | - Zuzana Vaníková
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- CZ-16610 Prague 6
- Czech Republic
- Department of Organic Chemistry
| | - Lenka Poštová Slavětínská
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- CZ-16610 Prague 6
- Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- CZ-16610 Prague 6
- Czech Republic
- Department of Organic Chemistry
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