1
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Nakao J, Mikame Y, Eshima H, Yamamoto T, Dohno C, Wada T, Yamayoshi A. Unique Crosslinking Properties of Psoralen-Conjugated Oligonucleotides Developed by Novel Psoralen N-Hydroxysuccinimide Esters. Chembiochem 2023; 24:e202200789. [PMID: 36896628 DOI: 10.1002/cbic.202200789] [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] [Received: 12/29/2022] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/11/2023]
Abstract
Psoralens and their derivatives, such as trioxsalen, have unique crosslinking features to DNA. However, psoralen monomers do not have sequence-specific crosslinking ability with the target DNA. With the development of psoralen-conjugated oligonucleotides (Ps-Oligos), sequence-specific crosslinking with target DNA has become achievable, thereby expanding the application of psoralen-conjugated molecules in gene transcription inhibition, gene knockout, and targeted recombination by genome editing. In this study, we developed two novel psoralen N-hydroxysuccinimide (NHS) esters that allow the introduction of psoralens into any amino-modified oligonucleotides. Quantitative evaluation of the photo-crosslinking efficiencies of the Ps-Oligos to target single-stranded DNAs revealed that the crosslinking selectivity to 5-mC is the unique feature of trioxsalen. We found that the introduction of an oligonucleotide via a linker at the C-5 position of psoralen can promote favorable crosslinking to target double-stranded DNA. We believe our findings are essential information for the development of Ps-Oligos as novel gene regulation tools.
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Affiliation(s)
- Juki Nakao
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki, Nagasaki, 852-8521, Japan
| | - Yu Mikame
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki, Nagasaki, 852-8521, Japan
| | - Honoka Eshima
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki, Nagasaki, 852-8521, Japan
| | - Tsuyoshi Yamamoto
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki, Nagasaki, 852-8521, Japan
| | - Chikara Dohno
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Takehiko Wada
- IMRAM (Institute of Multidisciplinary Research for Advanced Materials), Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Asako Yamayoshi
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki, Nagasaki, 852-8521, Japan
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2
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Kojima A, Nakao J, Shimada N, Yoshida N, Abe Y, Mikame Y, Yamamoto T, Wada T, Maruyama A, Yamayoshi A. Selective Photo-Crosslinking Detection of Methylated Cytosine in DNA Duplex Aided by a Cationic Comb-Type Copolymer. ACS Biomater Sci Eng 2022; 8:1799-1805. [PMID: 35263539 DOI: 10.1021/acsbiomaterials.2c00048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the process of cell development and differentiation, C-5-methylation of cytosine (5-methylcytosine: 5-mC) in genome DNA is an important transcriptional regulator that switches between differentiated and undifferentiated states. Further, abnormal DNA methylations are often present in tumor suppressor genes and are associated with many diseases. Therefore, 5-mC detection technology is an important tool in the most exciting fields of molecular biology and diagnosing diseases such as cancers. In this study, we found a novel photo-crosslinking property of psoralen-conjugated oligonucleotide (Ps-Oligo) to the double-stranded DNA (ds-DNA) containing 5-mC in the presence of a cationic comb-type copolymer, poly(allylamine)-graft-dextran (PAA-g-Dex). Photo-crosslinking efficiency of Ps-Oligo to 5-mC in ds-DNA was markedly enhanced in the presence of PAA-g-Dex, permitting 5-mC-targeted crosslinking. We believe that the combination of PAA-g-Dex and Ps-Oligo will be an effective tool for detecting 5-mC in genomic DNA.
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Affiliation(s)
- Atsuhiro Kojima
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki-shi, Nagasaki 852-8521, Japan
| | - Juki Nakao
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki-shi, Nagasaki 852-8521, Japan
| | - Naohiko Shimada
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Naoki Yoshida
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Yota Abe
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Yu Mikame
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki-shi, Nagasaki 852-8521, Japan
| | - Tsuyoshi Yamamoto
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki-shi, Nagasaki 852-8521, Japan
| | - Takehiko Wada
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Atsushi Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.,The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International (ATR), Hikaridai, Seika-cho, Soraku-gun, Kyoto 619-0288, Japan
| | - Asako Yamayoshi
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki-shi, Nagasaki 852-8521, Japan.,PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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3
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Hornung JE, Weinrich T, Göbel MW. Directed Crosslinking of RNA by Glutathione‐Triggered PNA‐Quinone‐Methide‐Conjugates. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jan-Erik Hornung
- Goethe-Universitat Frankfurt am Main Institut für Organische Chemie und Chemische Biologie GERMANY
| | - Timo Weinrich
- Goethe-Universitat Frankfurt am Main Institut für Organische Chemie und Chemische Biologie GERMANY
| | - Michael W. Göbel
- Goethe-Universität Frankfurt Institut für Organische Chemie und Chemi Max-von-Laue-Str. 7 60438 Frankfurt am Main GERMANY
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4
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Abdelhady AM, Onizuka K, Ishida K, Yajima S, Mano E, Nagatsugi F. Rapid Alkene-Alkene Photo-Cross-Linking on the Base-Flipping-Out Field in Duplex DNA. J Org Chem 2022; 87:2267-2276. [PMID: 34978198 DOI: 10.1021/acs.joc.1c01498] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Specific chemical reactions by enzymes acting on a nucleobase are realized by flipping the target base out of the helix. Similarly, artificial oligodeoxynucleotides (ODNs) can also induce the base flipping and a specific chemical reaction. We now report an easily prepared and unique structure-providing photo-cross-linking reaction by taking advantage of the base-flipping-out field formed by alkene-type base-flipping-inducing artificial bases. Two 3-arylethenyl-5-methyl-2-pyridone nucleosides with the Ph or An group were synthesized and incorporated into the ODNs. We found that the two Ph derivatives provided the cross-linked product in a high yield only by a 10 s photoirradiation when their alkenes overlap each other in the duplex DNA. The highly efficient reaction enabled forming a cross-linked product even when using the duplex with a low Tm value.
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Affiliation(s)
- Ahmed Mostafa Abdelhady
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan.,Department of Chemistry, Faculty of Science, Al-Azhar University, Nasr City, Cairo 11884, Egypt
| | - Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan.,Division for the Establishment of Frontier Sciences of Organization for Advanced Studies, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Kei Ishida
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Sayaka Yajima
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Eriko Mano
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
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5
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Abdelhady AM, Hirano Y, Onizuka K, Okamura H, Komatsu Y, Nagatsugi F. Synthesis of Crosslinked 2'-OMe RNA Duplexes Using 2-Amino-6-Vinylpurine and Their Application for Effective Inhibition of miRNA Function. Curr Protoc 2022; 2:e386. [PMID: 35316581 DOI: 10.1002/cpz1.386] [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: 06/14/2023]
Abstract
Crosslinking reactions to nucleic acids are an effective way to prepare stable complexes formed by covalent bonding. We demonstrated that fully 2'-O-methylated (2'-OMe) RNAs having a 2-amino-6-vinylpurine (AVP) exhibited an efficient crosslinking to uracil in the target RNA. Recently, we reported the preparation of crosslinked 2'-OMe RNA duplexes using AVP and the anti-miRNA oligonucleotides (AMOs) containing crosslinked duplexes at the terminal positions. These AMOs exhibited efficient microRNA (miRNA) inhibition at very low concentrations. In this article, we describe the chemical synthesis of 2'-OMe oligonucleotides containing AVP and preparation of the AMOs bearing crosslinked 2'-OMe RNA duplexes using AVP. In addition, we describe in detail the miRNA inhibition assay using these AMOs. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of phosphoramidite of 2-amino-6-vinylguanosine derivative Basic Protocol 2: Synthesis of AVP-2'-OMe RNA Basic Protocol 3: Evaluation of the crosslink reactivity of CFO containing AVP to the 2'-OMe RNA and preparation of AMOs containing crosslinked duplex Basic Protocol 4: miRNA inhibition assays.
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Affiliation(s)
- Ahmed Mostafa Abdelhady
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan
- Department of Chemistry, Faculty of Science, Al-Azhar University, Nasr City, Cairo, Egypt
| | - Yu Hirano
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Toyohira-ku, Sapporo, Hokkaido, Japan
| | - Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan
- Division for the Establishment of Frontier Sciences of Organization for Advanced Studies, Tohoku University, Sendai, Miyagi, Japan
| | - Hidenori Okamura
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan
| | - Yasuo Komatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Toyohira-ku, Sapporo, Hokkaido, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan
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6
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Nakao J, Yamamoto T, Yamayoshi A. Therapeutic application of sequence-specific binding molecules for novel genome editing tools. Drug Metab Pharmacokinet 2021; 42:100427. [PMID: 34974332 DOI: 10.1016/j.dmpk.2021.100427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 12/18/2022]
Abstract
Genome editing has been expected to widely increase the available treatment options for various diseases and permit pharmaceutical interventions in previously untreatable conditions. The availability of genome editing tools was dramatically increased by the development of the CRISPR-Cas9 system. However, a number of issues limit the use of the CRISPR-Cas9 system and other gene-editing tools in the clinical treatment of diseases. This review summarized the history and types of genome editing tools and limitations of their use. In addition, the study addressed several next-generation technologies aiming to overcome the limitations of current gene therapy protocols in an effort to accelerate the clinical development of potential treatment options. This review has provided an extensive foundation of the current state of genome editing technology and its clinical development. This review also indicate that the study additionally highlighted the need for multidisciplinary approaches to overcome current bottlenecks in the development of genome editing.
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Affiliation(s)
- Juki Nakao
- Chemist. of Funct. Mol., Grad. Sch. Biomed. Sci., Nagasaki Univ, Japan
| | - Tsuyoshi Yamamoto
- Chemist. of Funct. Mol., Grad. Sch. Biomed. Sci., Nagasaki Univ, Japan
| | - Asako Yamayoshi
- Chemist. of Funct. Mol., Grad. Sch. Biomed. Sci., Nagasaki Univ, Japan; PRESTO, JST, Japan.
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7
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Malinowska AL, Laski A, Hall J. Design and Application of Mini-libraries of miRNA Probes for an Efficient and Versatile miRNA-mRNA Cross-linking. Chemistry 2021; 27:10193-10200. [PMID: 34000095 PMCID: PMC8362200 DOI: 10.1002/chem.202101171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Indexed: 01/02/2023]
Abstract
MicroRNAs constitute a class of endogenous, non-coding RNAs that influence various processes within the cell. By base-pairing to partially-complementary sites located in the 3' untranslated region of target messenger RNAs, microRNAs participate in post-transcriptional regulation of the majority of human protein-coding genes. Their dysregulation has been related to many pathological processes and diseases. Thus, an in-depth understanding of the microRNA mechanisms of action is crucial. Here, we present a new concept of probe design to achieve an efficient and sequence-independent miRNA-mRNA cross-linking. The new strategy is based on the utilization of a controlled mixture of probes for a chosen miRNA, in which a trioxsalen moiety is introduced at the N4 -position of a selected cytidine through short oligoethylene glycol-based linkers. In vitro photo-cross-linking experiments with mini-libraries of probes for microRNAs of interest showed variable cross-linking efficiencies, demonstrating a general applicability of the presented approach.
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Affiliation(s)
- Anna L. Malinowska
- Institute of Pharmaceutical SciencesDepartment of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 48093Zurich
| | - Artur Laski
- Institute of Pharmaceutical SciencesDepartment of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 48093Zurich
| | - Jonathan Hall
- Institute of Pharmaceutical SciencesDepartment of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 48093Zurich
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8
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Hornung JE, Hellwig N, Göbel MW. Peptide Nucleic Acid Conjugates of Quinone Methide Precursors Alkylate Ribonucleic Acid after Activation with Light. Bioconjug Chem 2020; 31:639-645. [PMID: 31904221 DOI: 10.1021/acs.bioconjchem.9b00796] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Quinone methide precursors 2 and 3 were protected with a photoreactive 2-nitrobenzyl group and conjugated to peptide nucleic acids (PNA) using a Huisgen click reaction. After brief irradiation at 365 nm, cross-linking with complementary RNA strands started and was analyzed with an ALFexpress sequencer. When this method was used, the gel temperature had a major influence on apparent rates. Quinone methides are known to form transient as well as stable bonds with nucleotides. Although both were detected at 25 °C, analysis at 57 °C only recorded the stable types of cross-links, suggesting much slower alkylation kinetics. Linker 11 allowed us to attach quinone methides to internal positions of the PNA/RNA duplex and to capture a model of miR-20a with good efficiency.
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9
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Yamayoshi A, Higuchi M, Sakai Y, Kobori A, Yamamoto T, Shibata T, Murakami A. Selective cross-linking behavior of oligodeoxyribonucleotides containing 2'- O-[ N-(4,5',8-trimethylpsoralen-4'-ylmethylcarbamoyl)]adenosine to mutant H-ras DNA. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 39:119-130. [PMID: 31645189 DOI: 10.1080/15257770.2019.1677912] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Point mutations are well characterized activators of oncogenes but are often indistinguishable using common gene technologies. In general, the precise sites of point-mutated oncogenes are difficult to distinguish under physiological conditions primarily because single nucleotide mismatch do not affect the annealing temperatures of DNA probes sufficiently. To address this limitation, we developed photo-responsive oligodeoxyribonucleotides containing 2'-O-[N-(4,5',8-trimethylpsoralen-4'-ylmethylcarbamoyl)]adenosine (Ps-amd-Oligo), which can be used to selectively manipulate and identify genes with point mutations. Here we present time course analyses of the photo-cross-linking efficiency of Ps-amd-Oligo with DNA and RNA and show promising selectivity for the oncogene H-ras.
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Affiliation(s)
- Asako Yamayoshi
- Chemistry of Functional Molecules, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.,PRSTO, JST, Kawaguchi, Saitama, Japan
| | - Maiko Higuchi
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Kyoto, Japan
| | - Yui Sakai
- Chemistry of Functional Molecules, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Akio Kobori
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Kyoto, Japan
| | - Tsuyoshi Yamamoto
- Chemistry of Functional Molecules, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Takayuki Shibata
- Graduate School of Health Sciences, Gunma University, Gunma, Japan
| | - Akira Murakami
- Chemistry of Functional Molecules, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
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10
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Salem ESB, Vonberg AD, Borra VJ, Gill RK, Nakamura T. RNAs and RNA-Binding Proteins in Immuno-Metabolic Homeostasis and Diseases. Front Cardiovasc Med 2019; 6:106. [PMID: 31482095 PMCID: PMC6710452 DOI: 10.3389/fcvm.2019.00106] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 07/17/2019] [Indexed: 12/16/2022] Open
Abstract
The increasing prevalence of worldwide obesity has emerged as a major risk factor for type 2 diabetes (T2D), hepatosteatosis, and cardiovascular disease. Accumulating evidence indicates that obesity has strong inflammatory underpinnings tightly linked to the development of metabolic diseases. However, the molecular mechanisms by which obesity induces aberrant inflammation associated with metabolic diseases are not yet clearly defined. Recently, RNAs have emerged as important regulators of stress responses and metabolism. RNAs are subject to changes in modification status, higher-order structure, and cellular localization; all of which could affect the affinity for RNA-binding proteins (RBPs) and thereby modify the RNA-RBP networks. Proper regulation and management of RNA characteristics are fundamental to cellular and organismal homeostasis, as well as paramount to health. Identification of multiple single nucleotide polymorphisms (SNPs) within loci of fat mass- and obesity-associated protein (FTO) gene, an RNA demethylase, through genome-wide association studies (GWAS) of T2D, and functional assessments of FTO in mice, support the concept that disruption in RNA modifications leads to the development of human diseases including obesity and metabolic disorder. In obesity, dynamic alterations in modification and localization of RNAs appear to modulate the RNA-RBP networks and activate proinflammatory RBPs, such as double-stranded RNA (dsRNA)-dependent protein kinase (PKR), Toll-like receptor (TLR) 3 and TLR7, and RNA silencing machinery. These changes induce aberrant inflammation and the development of metabolic diseases. This review will describe the current understanding of the underlying causes of these common and altered characteristics of RNA-RBP networks which will pave the way for developing novel approaches to tackle the pandemic issue of obesity.
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Affiliation(s)
- Esam S B Salem
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Andrew D Vonberg
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Vishnupriya J Borra
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Rupinder K Gill
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Takahisa Nakamura
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Department of Metabolic Bioregulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
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11
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Fujimoto K, Sasago S, Mihara J, Nakamura S. DNA Photo-cross-linking Using Pyranocarbazole and Visible Light. Org Lett 2018; 20:2802-2805. [DOI: 10.1021/acs.orglett.8b00593] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Kenzo Fujimoto
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, Asahidai 1-1, Nomi, Ishikawa, 923-1292, Japan
| | - Shinobu Sasago
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, Asahidai 1-1, Nomi, Ishikawa, 923-1292, Japan
| | - Junichi Mihara
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, Asahidai 1-1, Nomi, Ishikawa, 923-1292, Japan
| | - Shigetaka Nakamura
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, Asahidai 1-1, Nomi, Ishikawa, 923-1292, Japan
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12
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De Laet N, Llamas EM, Madder A. Templated DNA Cross-Linking: Towards a Non-Invasive Singlet-Oxygen-Based Triggering Method. CHEMPHOTOCHEM 2018. [DOI: 10.1002/cptc.201700175] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Nathalie De Laet
- Organic and Biomimetic Chemistry Research Group Krijgslaan 281, S4; B-9000 Ghent Belgium
| | - Eva M. Llamas
- Organic and Biomimetic Chemistry Research Group Krijgslaan 281, S4; B-9000 Ghent Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group Krijgslaan 281, S4; B-9000 Ghent Belgium
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13
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Abstract
Only 20 years after the discovery of small non-coding, single-stranded ribonucleic acids, so-called microRNAs (miRNAs), as post-transcriptional gene regulators, the first miRNA-targeting drug Miravirsen for the treatment of hepatitis C has been successfully tested in clinical Phase II trials. Addressing miRNAs as drug targets may enable the cure, or at least the treatment of diseases, which presently seems impossible. However, due to miRNAs' chemical structure, generation of potential drug molecules with necessary pharmacokinetic properties is still challenging and requires a re-thinking of the drug discovery process. Therefore, this chapter highlights the potential of miRNAs as drug targets, discusses the challenges, and tries to give a complete overview of recent strategies in miRNA drug discovery.
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Affiliation(s)
- Marco F Schmidt
- BEROCEUTICA GmbH, c/o Universität Potsdam, August-Bebel-Strasse 89, 14482, Potsdam, Germany.
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14
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Sugihara Y, Nakata Y, Yamayoshi A, Murakami A, Kobori A. Inhibition Effect of Photoresponsive α-Haloaldehyde-conjugated Oligonucleotides on the Gene Expression in HeLa Cells Stably Expressing GFP. CHEM LETT 2017. [DOI: 10.1246/cl.170298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Yuta Sugihara
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585
| | - Yuki Nakata
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585
| | - Asako Yamayoshi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502
- The Hakubi Center for Advanced Research, Kyoto University, Yoshida-Ushinomiyacho, Sakyo-ku, Kyoto 606-8501
| | - Akira Murakami
- Kyoto Pharmaceutical University, 1 Misasagi-Shichonocho, Yamashina-ku, Kyoto 607-8412
| | - Akio Kobori
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585
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15
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Ariyoshi J, Eimori N, Kobori A, Murakami A, Sugiyama H, Yamayoshi A. Characterization of the Releasing Profile of MicroRNA from RISC Using Anti-miRNA Oligonucleotides. CHEM LETT 2017. [DOI: 10.1246/cl.160895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jumpei Ariyoshi
- Department of Biomolecular Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502
| | - Nao Eimori
- Department of Biomolecular Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502
| | - Akio Kobori
- Department of Biomolecular Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585
| | - Akira Murakami
- Kyoto Pharmaceutical University, 1 Misasagi-Shichonocho, Yamashina-ku, Kyoto 607-8412
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502
- Institute for Integrated Cell-Materials Sciences (iCeMS), Kyoto University, Yoshida-Ushinomiyacho, Sakyo-ku, Kyoto 606-8501
| | - Asako Yamayoshi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502
- The Hakubi Center for Advanced Research, Kyoto University, Yoshida-Ushinomiyacho, Sakyo-ku, Kyoto 606-8501
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16
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Kamiya Y, Iishiba K, Doi T, Tsuda K, Kashida H, Asanuma H. Terminus-free siRNA prepared by photo-crosslinking activated via slicing by Ago2. Biomater Sci 2015; 3:1534-8. [PMID: 26526389 DOI: 10.1039/c5bm00231a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report the development of photo-crosslinked siRNA strands modified at each terminus with p-cyanostilbene. The siRNA was nuclease resistant and retained RNAi activity. We further studied the activation mechanism of the covalently-crosslinked siRNA. Interestingly Dicer, which is known to generate siRNA with overhanging 3' ends from the precursor siRNA, did not cleave the crosslinked siRNA at all. Our results suggest that the activation of the crosslinked siRNAs required cleavage by Argonaute2.
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Affiliation(s)
- Yukiko Kamiya
- Department of Molecular Design and Engineering, Graduate school of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
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17
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Kusano S, Ishiyama S, Lam SL, Mashima T, Katahira M, Miyamoto K, Aida M, Nagatsugi F. Crosslinking reactions of 4-amino-6-oxo-2-vinylpyrimidine with guanine derivatives and structural analysis of the adducts. Nucleic Acids Res 2015; 43:7717-30. [PMID: 26245348 PMCID: PMC4652779 DOI: 10.1093/nar/gkv797] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/28/2015] [Indexed: 12/28/2022] Open
Abstract
DNA interstrand crosslinks (ICLs) are the primary mechanism for the cytotoxic activity of many clinical anticancer drugs, and numerous strategies for forming ICLs have been developed. One such method is using crosslink-forming oligonucleotides (CFOs). In this study, we designed a 4-amino-6-oxo-2-vinylpyrimidine (AOVP) derivative with an acyclic spacer to react selectively with guanine. The AOVP CFO exhibited selective crosslinking reactivity with guanine and thymine in DNA, and with guanine in RNA. These crosslinking reactions with guanine were accelerated in the presence of CoCl2, NiCl2, ZnCl2 and MnCl2. In addition, we demonstrated that the AOVP CFO was reactive toward 8-oxoguanine opposite AOVP in the duplex DNA. The structural analysis of each guanine and 8-oxoguanine adduct in the duplex DNA was investigated by high-resolution NMR. The results suggested that AOVP reacts at the N2 amine in guanine and at the N1 or N2 amines in 8-oxoguanine in the duplex DNA. This study demonstrated the first direct determination of the adduct structure in duplex DNA without enzyme digestion.
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Affiliation(s)
- Shuhei Kusano
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi, Miyagi 980-8577, Japan
| | - Shogo Ishiyama
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi, Miyagi 980-8577, Japan
| | - Sik Lok Lam
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Tsukasa Mashima
- Institute of Advanced Energy, Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Masato Katahira
- Institute of Advanced Energy, Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Kengo Miyamoto
- Department of Chemistry, Graduate School of Science, Hiroshima University,1-3-1, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Misako Aida
- Department of Chemistry, Graduate School of Science, Hiroshima University,1-3-1, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi, Miyagi 980-8577, Japan
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18
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Sakamoto T, Ooe M, Fujimoto K. Critical Effect of Base Pairing of Target Pyrimidine on the Interstrand Photo-Cross-Linking of DNA via 3-Cyanovinylcarbazole Nucleoside. Bioconjug Chem 2015; 26:1475-8. [PMID: 26190032 DOI: 10.1021/acs.bioconjchem.5b00352] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To evaluate the effect of base pairing of the target pyrimidine on the interstrand photo-cross-linking reaction of DNA via 3-cyanovinylcarbazole nucleoside ((CNV)K), a complementary base of target pyrimidine was substituted with noncanonical purine bases or 1,3-propandiol (S). As the decrease of the hydrogen bonds in the base pairing of target C accelerated the photo-cross-linking reaction markedly (3.6- to 7.7-fold), it can be concluded that the number of hydrogen bonds in the base pairing, i.e., the stability of base pairing, of the target pyrimidine plays a critical role in the interstrand photo-cross-linking reaction. In the case of G to S substitution, the highest photoreactivity toward C was observed, whose photoreaction rate constant (k = 2.0 s(-1)) is comparable to that of (CNV)K toward T paired with A (k = 3.5 s(-1)). This is the most reactive photo-cross-linking reaction toward C in the sequence specific interstrand photo-cross-linking. This might facilitate the design of the photo-cross-linkable oligodeoxyribonucleotides for various target sequences.
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Affiliation(s)
- Takashi Sakamoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan
| | - Minako Ooe
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan
| | - 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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19
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Yang C, Huang W, Yan L, Wang Y, Wang W, Liu D, Zuo X. Downregulation of the expression of B‑cell lymphoma-extra large by RNA interference induces apoptosis and enhances the radiosensitivity of non‑small cell lung cancer cells. Mol Med Rep 2015; 12:449-55. [PMID: 25683634 DOI: 10.3892/mmr.2015.3346] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 01/27/2015] [Indexed: 11/05/2022] Open
Abstract
B-cell lymphoma-extra large (Bcl-xL), an important member of anti-apoptotic Bcl-2 family, is involved in tumor progression and development. The overexpression of Bcl-xL is associated with radioresistance of human malignancies. The present study aimed to investigate the inhibitory effect of small interfering RNA (siRNA) on the expression of Bcl-xL in the A549 non-small lung cancer (NSCLC) cell line, and its role in inducing the apoptosis and increasing the radiosensitivity of A549 cells. An siRNA expression vector, pSilencer4-CMVneo-short hairpin (sh)RNA, was constructed and stably transfected into A549 cells. The effects of Bcl-xL-shRNA on cell proliferation, apoptosis and the protein expression levels of associated proteins were assessed in vitro in the A549 cells. The radiosensitivity of the A549 cells was evaluated using a clonogenic cell survival assay. The results demonstrated that the sequence-specific siRNA targeting Bcl-xL efficiently and specifically downregulated the mRNA and protein expression levels of Bcl-xL. The RNA interference-mediated downregulation in the expression of Bcl-xL inhibited cell proliferation, induced apoptosis and reduced the radioresistance of the NSCLC cells. These findings suggested that Bcl-xL may be a promising therapeutic approach for the treatment of NSCLC.
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Affiliation(s)
- Changbin Yang
- Department of Radiation Oncology, The Tumor Hospital of Jilin Province, Changchun, Jilin 130012, P.R. China
| | - Wei Huang
- Department of Radiation Oncology, The Tumor Hospital of Jilin Province, Changchun, Jilin 130012, P.R. China
| | - Ling Yan
- Department of Radiation Oncology, The Tumor Hospital of Jilin Province, Changchun, Jilin 130012, P.R. China
| | - Yu Wang
- Department of Radiation Oncology, The Tumor Hospital of Jilin Province, Changchun, Jilin 130012, P.R. China
| | - Weili Wang
- Department of Radiation Oncology, The Tumor Hospital of Jilin Province, Changchun, Jilin 130012, P.R. China
| | - Dezhi Liu
- Department of Radiation Oncology, The Tumor Hospital of Jilin Province, Changchun, Jilin 130012, P.R. China
| | - Xiaojun Zuo
- Department of Nuclear Medicine, The Tumor Hospital of Jilin Province, Changchun, Jilin 130012, P.R. China
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20
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Schmidt MF. Drug target miRNAs: chances and challenges. Trends Biotechnol 2014; 32:578-585. [PMID: 25304465 DOI: 10.1016/j.tibtech.2014.09.002] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/09/2014] [Accepted: 09/09/2014] [Indexed: 11/28/2022]
Abstract
miRNAs, short ribonucleic acid gene regulators, are increasingly popular drug targets. Traditionally 'undruggable' proteins can be targeted via their miRNA gene regulators, enabling the treatment of diseases that, at present, seem impossible to cure. However, addressing miRNAs requires innovation at the level of drug discovery. This review article outlines the potential of miRNAs as drug targets, focuses on the challenges of developing miRNA-targeting drugs, and surveys new advances. The aim is to provide an orientation guide for scientists, as well business analysts, to help them navigate the jungle of different approaches in miRNA drug discovery.
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Affiliation(s)
- Marco F Schmidt
- University Chemical Laboratory, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK.
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21
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Kobori A, Yamayoshi A, Murakami A. Synthesis of Oligonucleotides Containing 4,5',8-Trimethylpsoralen at the 2'-O Position and Their Cross-Linking Properties with RNAs. ACTA ACUST UNITED AC 2014; 58:5.15.1-15. [PMID: 25199638 DOI: 10.1002/0471142700.nc0515s58] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
4,5',8-Trimethylpsoralen-conjugated oligonucleotides have been used in the study of photo-cross-linking with target oligonucleotides and in the field of the photodynamic therapy. This unit describes synthetic procedures for oligonucleotides using 2'-O-methylphosphoramidite units and an adenosine phosphoramidite unit containing a 4,5',8-trimethylpsoralen derivative attached at the 2' position of an adenosine sugar moiety via an ethoxymethylene linkage. Procedures for obtaining the photo-cross-linking efficiency of 2'-O-methyloligonucleotides containing a 4,5',8-trimethylpsoralen derivative with a target oligonucleotide under UV irradiation conditions are also described, together with the procedure for preparation of (32)P-radiolabeled RNA.
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Affiliation(s)
- Akio Kobori
- Kyoto Institute of Technology, Graduate School of Science and Technology, Department of Biomolecular Engineering, Matsugasaki, Sakyo-ku, Kyoto, Japan
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