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Kim BS, Naito M, Kamegawa R, Kim HJ, Iizuka R, Funatsu T, Ueno S, Ichiki T, Kishimura A, Miyata K. Photo-reactive oligodeoxynucleotide-embedded nanovesicles (PROsomes) with switchable stability for efficient cellular uptake and gene knockdown. Chem Commun (Camb) 2021; 56:9477-9480. [PMID: 32677638 DOI: 10.1039/d0cc01750g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A photo-responsive nanovesicle is fabricated by polyion complex (PIC) formation between poly(ethylene glycol) (PEG)-block-polypeptides and photo-reactive oligodeoxynucleotides (PROs)/anti-sense oligonucleotides (ASOs). The ultraviolet (UV) light triggers reversible crosslinking between PROs and ASOs in the vesicular membrane, providing the nanovesicle with switchable stability under physiological conditions. The resulting nanovesicle allows efficient cellular internalization, leading to significant UV-triggered gene knockdown in cultured cells.
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Affiliation(s)
- Beob Soo Kim
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Mitsuru Naito
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Rimpei Kamegawa
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Hyun Jin Kim
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ryo Iizuka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takashi Funatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shingo Ueno
- Innovation Center of NanoMedicine, Kawasaki Institute of Inductrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Takanori Ichiki
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan. and Innovation Center of NanoMedicine, Kawasaki Institute of Inductrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Akihiro Kishimura
- Center for Molecular Systems, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kanjiro Miyata
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
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Vu LT, Tsukahara T. C-to-U editing and site-directed RNA editing for the correction of genetic mutations. Biosci Trends 2017; 11:243-253. [DOI: 10.5582/bst.2017.01049] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Luyen Thi Vu
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST)
| | - Toshifumi Tsukahara
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST)
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Vu LT, Nguyen TTK, Md Thoufic AA, Suzuki H, Tsukahara T. Chemical RNA Editing for Genetic Restoration: The Relationship between the Structure and Deamination Efficiency of Carboxyvinyldeoxyuridine Oligodeoxynucleotides. Chem Biol Drug Des 2015; 87:583-93. [DOI: 10.1111/cbdd.12693] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 10/08/2015] [Accepted: 11/09/2015] [Indexed: 01/31/2023]
Affiliation(s)
- Luyen Thi Vu
- School of Materials Science; Japan Advanced Institute of Science and Technology (JAIST); 1-1 Asahidai Nomi City Ishikawa 923-1292 Japan
| | - Thanh Thi Kim Nguyen
- School of Materials Science; Japan Advanced Institute of Science and Technology (JAIST); 1-1 Asahidai Nomi City Ishikawa 923-1292 Japan
| | - Azad Anam Md Thoufic
- School of Materials Science; Japan Advanced Institute of Science and Technology (JAIST); 1-1 Asahidai Nomi City Ishikawa 923-1292 Japan
| | - Hitoshi Suzuki
- School of Materials Science; Japan Advanced Institute of Science and Technology (JAIST); 1-1 Asahidai Nomi City Ishikawa 923-1292 Japan
| | - Toshifumi Tsukahara
- School of Materials Science; Japan Advanced Institute of Science and Technology (JAIST); 1-1 Asahidai Nomi City Ishikawa 923-1292 Japan
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Vu LT, Nguyen TTK, Alam S, Sakamoto T, Fujimoto K, Suzuki H, Tsukahara T. Changing blue fluorescent protein to green fluorescent protein using chemical RNA editing as a novel strategy in genetic restoration. Chem Biol Drug Des 2015; 86:1242-52. [PMID: 26031895 DOI: 10.1111/cbdd.12592] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 04/15/2015] [Accepted: 05/14/2015] [Indexed: 11/29/2022]
Abstract
Using the transition from cytosine of BFP (blue fluorescent protein) gene to uridine of GFP (green fluorescent protein) gene at position 199 as a model, we successfully controlled photochemical RNA editing to effect site-directed deamination of cytidine (C) to uridine (U). Oligodeoxynucleotides (ODNs) containing 5'-carboxyvinyl-2'-deoxyuridine ((CV) U) were used for reversible photoligation, and single-stranded 100-nt BFP DNA and in vitro-transcribed full-length BFP mRNA were the targets. Photo-cross-linking with the responsive ODNs was performed using UV (366 nm) irradiation, which was followed by heat treatment, and the cross-linked nucleotide was cleaved through photosplitting (UV, 312 nm). The products were analyzed using restriction fragment length polymorphism (RFLP) and fluorescence measurements. Western blotting and fluorescence-analysis results revealed that in vitro-translated proteins were synthesized from mRNAs after site-directed RNA editing. We detected substantial amounts of the target-base-substituted fragment using RFLP and observed highly reproducible spectra of the transition-GFP signal using fluorescence spectroscopy, which indicated protein stability. ODNc restored approximately 10% of the C-to-U transition. Thus, we successfully used non-enzymatic site-directed deamination for genetic restoration in vitro. In the near future, in vivo studies that include cultured cells and model animals will be conducted to treat genetic disorders.
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Affiliation(s)
- Luyen T Vu
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, Japan
| | - Thanh T K Nguyen
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, Japan
| | - Shafiul Alam
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, Japan
| | - Takashi Sakamoto
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, Japan
| | - Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, Japan
| | - Hitoshi Suzuki
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, Japan
| | - Toshifumi Tsukahara
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, Japan
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Fujimoto K, Futamura D, Sakamoto T. Diamine Derivatives Accelerate Photochemical C → U Transition in DNA Double Strand. CHEM LETT 2013. [DOI: 10.1246/cl.2013.289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology
- Research Center for Bio-Architecture, Japan Advanced Institute of Science and Technology
| | - Daiki Futamura
- School of Materials Science, Japan Advanced Institute of Science and Technology
| | - Takashi Sakamoto
- School of Materials Science, Japan Advanced Institute of Science and Technology
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Photochemically relevant DNA-based molecular systems enabling chemical and signal transductions and their analytical applications. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2012. [DOI: 10.1016/j.jphotochemrev.2012.03.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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7
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Oligonucleotide-templated reactions for sensing nucleic acids. Molecules 2012; 17:2446-63. [PMID: 22374329 PMCID: PMC6268776 DOI: 10.3390/molecules17032446] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 02/23/2012] [Accepted: 02/24/2012] [Indexed: 02/07/2023] Open
Abstract
Oligonucleotide-templated reactions are useful for applying nucleic acid sensing. Various chemistries for oligonucleotide-templated reaction have been reported so far. Major scientific interests are focused on the development of signal amplification systems and signal generation systems. We introduce the recent advances of oligonucleotide-templated reaction in consideration of the above two points.
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Fujimoto K, Konishi-Hiratsuka K, Sakamoto T, Yoshimura Y. Site-specific cytosine to uracil transition by using reversible DNA photo-crosslinking. Chembiochem 2010; 11:1661-4. [PMID: 20632434 DOI: 10.1002/cbic.201000274] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan.
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Fujimoto K, Konishi-Hiratsuka K, Sakamoto T, Yoshimura Y. Site-specific photochemical RNA editing. Chem Commun (Camb) 2010; 46:7545-7. [PMID: 20848024 DOI: 10.1039/c0cc03151h] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Photo-induced artificial RNA editing was demonstrated using photo-reactive oligonucleotides containing 3-cyanovinylcarbazole nucleoside. This non-enzymatic and sequence-specific methodology will make a major contribution to the elucidation of RNA functions including non-coding RNAs and to the development of drugs based on sequence-specific RNA editing.
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Affiliation(s)
- Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa, 923-1292, Japan.
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Ogino M, Taya Y, Fujimoto K. Highly selective detection of 5-methylcytosine using photochemical ligation. Chem Commun (Camb) 2008:5996-8. [PMID: 19030564 DOI: 10.1039/b813677g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We report the nonenzymatic detection of 5-methylcytosine by using template-directed photoligation through 5-cyanovinyl-2'-deoxyuridine ((C)U) with high selectivity and present a new methylation detection method using a photoligation-based DNA chip assay.
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Affiliation(s)
- Masayuki Ogino
- Japan Science and Technology Agency, Ishikawa, 923-1211, Japan
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Matsumura T, Ogino M, Nagayoshi K, Fujimoto K. Photochemical Site-specific Mutation of 5-Methylcytosine to Thymine. CHEM LETT 2008. [DOI: 10.1246/cl.2008.94] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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12
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Yoshimura Y, Okamura D, Ogino M, Fujimoto K. Highly selective and sensitive template-directed photoligation of DNA via 5-carbamoylvinyl-2'-deoxycytidine. Org Lett 2007; 8:5049-51. [PMID: 17048840 DOI: 10.1021/ol0619462] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe a highly efficient template-directed photoligation of oligodeoxynucleotides (ODNs) through 5-carbamoylvinyl-2'-deoxycytidine ((CV)C). When an ODN containing (CV)C at the 5' end was photoirradiated with an ODN containing a pyrimidine base at the 3' end in the presence of template DNA, efficient photoligation was observed without any byproduct formation. Single nucleotide differences can be successfully distinguished by using photoligation-based DNA chip assay. [structure: see text]
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Affiliation(s)
- Yoshinaga Yoshimura
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
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Yoshimura Y, Noguchi Y, Fujimoto K. Highly sequence specific RNA terminal labeling by DNA photoligation. Org Biomol Chem 2006; 5:139-42. [PMID: 17164918 DOI: 10.1039/b615715g] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We report the nonenzymatic terminal labeling of oligoribonucleotide (ORN) by using template-directed photoligation through 5-carboxyvinyl-2'-deoxyuridine ((CV)U) with high selectivity.
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Affiliation(s)
- Yoshinaga Yoshimura
- School of Materials Science, Japan Advanced Institute of Science and Technology, Ishikawa 923-1292, Japan
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