1
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Kawamoto Y, Bando T, Sugiyama H. Sequence-specific DNA binding Pyrrole-imidazole polyamides and their applications. Bioorg Med Chem 2018; 26:1393-1411. [PMID: 29439914 DOI: 10.1016/j.bmc.2018.01.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/25/2018] [Accepted: 01/28/2018] [Indexed: 12/25/2022]
Abstract
Pyrrole-imidazole polyamides (Py-Im polyamides) are cell-permeable compounds that bind to the minor groove of double-stranded DNA in a sequence-specific manner without causing denaturation of the DNA. These compounds can be used to control gene expression and to stain specific sequences in cells. Here, we review the history, structural variations, and functional investigations of Py-Im polyamides.
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Affiliation(s)
- Yusuke Kawamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan.
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan; Institute for Integrated Cell-Material Science (iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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2
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Wei Y, Pandian GN, Zou T, Taniguchi J, Sato S, Kashiwazaki G, Vaijayanthi T, Hidaka T, Bando T, Sugiyama H. A Multi-target Small Molecule for Targeted Transcriptional Activation of Therapeutically Significant Nervous System Genes. ChemistryOpen 2016; 5:517-521. [PMID: 28032018 PMCID: PMC5167308 DOI: 10.1002/open.201600125] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Indexed: 12/17/2022] Open
Abstract
An integrated multi‐target small molecule capable of altering dynamic epigenetic and transcription programs associated with the brain and nervous system has versatile applications in the regulation of therapeutic and cell‐fate genes. Recently, we have been constructing targeted epigenetic ON switches by integrating sequence‐specific DNA binding pyrrole‐imidazole polyamides with a potent histone deacetylase inhibitor SAHA. Here, we identified a DNA‐based epigenetic ON switch termed SAHA‐L as the first‐ever multi‐target small molecule capable of inducing transcription programs associated with the human neural system and brain synapses networks in BJ human foreskin fibroblasts and 201B7‐iPS cells. Ingenuity pathway analysis showed that SAHA‐L activates the signaling of synaptic receptors like glutamate and γ‐aminobutyric acid, which are key components of autism spectrum disorders. The long‐term incubation of SAHA‐L in 201B7‐iPS cells induced morphology changes and promoted a neural progenitor state. Our finding suggests that the tunable SAHA‐L could be advanced as a cell‐type‐independent multi‐target small molecule for therapeutic and/or cell‐fate gene modulation.
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Affiliation(s)
- Yulei Wei
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Ganesh N Pandian
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS) Kyoto University Yoshida-ushinomiyacho, Sakyo-ku Kyoto 606-8501 Japan
| | - Tingting Zou
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Junichi Taniguchi
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Shinsuke Sato
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS) Kyoto University Yoshida-ushinomiyacho, Sakyo-ku Kyoto 606-8501 Japan
| | - Gengo Kashiwazaki
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Thangavel Vaijayanthi
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Takuya Hidaka
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Toshikazu Bando
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Hiroshi Sugiyama
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto606-8502 Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS) Kyoto University Yoshida-ushinomiyacho, Sakyo-ku Kyoto 606-8501 Japan
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3
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Kawamoto Y, Sasaki A, Chandran A, Hashiya K, Ide S, Bando T, Maeshima K, Sugiyama H. Targeting 24 bp within Telomere Repeat Sequences with Tandem Tetramer Pyrrole–Imidazole Polyamide Probes. J Am Chem Soc 2016; 138:14100-14107. [DOI: 10.1021/jacs.6b09023] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Yusuke Kawamoto
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Asuka Sasaki
- Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Anandhakumar Chandran
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kaori Hashiya
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Satoru Ide
- Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Toshikazu Bando
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kazuhiro Maeshima
- Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Hiroshi Sugiyama
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material
Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
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4
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Mandal PK, Baptiste B, Langlois d'Estaintot B, Kauffmann B, Huc I. Multivalent Interactions between an Aromatic Helical Foldamer and a DNA G-Quadruplex in the Solid State. Chembiochem 2016; 17:1911-1914. [DOI: 10.1002/cbic.201600281] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Indexed: 01/20/2023]
Affiliation(s)
- Pradeep K. Mandal
- University of Bordeaux; CBMN; UMR 5248); Institut Européen de Chimie et Biologie; 2 rue Escarpit 33600 Pessac France
- CNRS; CBMN; UMR 5248); 2 rue Escarpit 33600 Pessac France
- Bordeaux Institut National Polytechnique; CBMN; UMR 5248); 2 rue Escarpit 33600 Pessac France
| | - Benoît Baptiste
- University of Bordeaux; CBMN; UMR 5248); Institut Européen de Chimie et Biologie; 2 rue Escarpit 33600 Pessac France
- CNRS; CBMN; UMR 5248); 2 rue Escarpit 33600 Pessac France
- Bordeaux Institut National Polytechnique; CBMN; UMR 5248); 2 rue Escarpit 33600 Pessac France
| | - Béatrice Langlois d'Estaintot
- University of Bordeaux; CBMN; UMR 5248); Institut Européen de Chimie et Biologie; 2 rue Escarpit 33600 Pessac France
- CNRS; CBMN; UMR 5248); 2 rue Escarpit 33600 Pessac France
- Bordeaux Institut National Polytechnique; CBMN; UMR 5248); 2 rue Escarpit 33600 Pessac France
| | - Brice Kauffmann
- University of Bordeaux; IECB; UMS 3033); Institut Européen de Chimie et Biologie; 2 rue Escarpit 33600 Pessac France
- CNRS; IECB; UMS 3033); 2 rue Escarpit 33600 Pessac France
- INSERM; IECB; US001); 2 rue Escarpit 33600 Pessac France
| | - Ivan Huc
- University of Bordeaux; CBMN; UMR 5248); Institut Européen de Chimie et Biologie; 2 rue Escarpit 33600 Pessac France
- CNRS; CBMN; UMR 5248); 2 rue Escarpit 33600 Pessac France
- Bordeaux Institut National Polytechnique; CBMN; UMR 5248); 2 rue Escarpit 33600 Pessac France
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5
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Pandian GN, Sugiyama H. Nature-Inspired Design of Smart Biomaterials Using the Chemical Biology of Nucleic Acids. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2016. [DOI: 10.1246/bcsj.20160062] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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6
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Kashiwazaki G, Chandran A, Asamitsu S, Kawase T, Kawamoto Y, Sawatani Y, Hashiya K, Bando T, Sugiyama H. Comparative Analysis of DNA-Binding Selectivity of Hairpin and Cyclic Pyrrole-Imidazole Polyamides Based on Next-Generation Sequencing. Chembiochem 2016; 17:1752-8. [DOI: 10.1002/cbic.201600282] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Indexed: 12/23/2022]
Affiliation(s)
- Gengo Kashiwazaki
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawaoiwakecho Sakyo Kyoto 606-8502 Japan
| | - Anandhakumar Chandran
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawaoiwakecho Sakyo Kyoto 606-8502 Japan
| | - Sefan Asamitsu
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawaoiwakecho Sakyo Kyoto 606-8502 Japan
| | - Takashi Kawase
- Department of Systems Science; Graduate School of Informatics; Kyoto University; Yoshida-Honmachi 36-1 Sakyo Kyoto 606-8501 Japan
| | - Yusuke Kawamoto
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawaoiwakecho Sakyo Kyoto 606-8502 Japan
| | - Yoshito Sawatani
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawaoiwakecho Sakyo Kyoto 606-8502 Japan
| | - Kaori Hashiya
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawaoiwakecho Sakyo Kyoto 606-8502 Japan
| | - Toshikazu Bando
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawaoiwakecho Sakyo Kyoto 606-8502 Japan
| | - Hiroshi Sugiyama
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawaoiwakecho Sakyo Kyoto 606-8502 Japan
- Institute for Integrated Cell-Material Sciences (iCeMS); Kyoto University; Yoshida-Ushinomiyacho Sakyo Kyoto 606-8501 Japan
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7
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Zou T, Kizaki S, Pandian GN, Sugiyama H. Nucleosome Assembly Alters the Accessibility of the Antitumor Agent Duocarmycin B2
to Duplex DNA. Chemistry 2016; 22:8756-8. [DOI: 10.1002/chem.201600950] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Tingting Zou
- Department of Science; Graduate School of Science; Kyoto University; Sakyo Kyoto 606-8501 Japan
| | - Seiichiro Kizaki
- Department of Science; Graduate School of Science; Kyoto University; Sakyo Kyoto 606-8501 Japan
| | - Ganesh N. Pandian
- Institute for Integrated Cell-Material Sciences (iCeMS); Kyoto University; Yoshida Ushinomiya-cho Sakyo Kyoto 606-8502 Japan
| | - Hiroshi Sugiyama
- Department of Science; Graduate School of Science; Kyoto University; Sakyo Kyoto 606-8501 Japan
- Institute for Integrated Cell-Material Sciences (iCeMS); Kyoto University; Yoshida Ushinomiya-cho Sakyo Kyoto 606-8502 Japan
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8
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Jewginski M, Fischer L, Colombo C, Huc I, Mackereth CD. Solution Observation of Dimerization and Helix Handedness Induction in a Human Carbonic Anhydrase-Helical Aromatic Amide Foldamer Complex. Chembiochem 2016; 17:727-36. [PMID: 26807531 DOI: 10.1002/cbic.201500619] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Indexed: 12/18/2022]
Abstract
The design of synthetic foldamers to selectively bind proteins is currently hindered by the limited availability of molecular data to establish key features of recognition. Previous work has described dimerization of human carbonic anhydrase II (HCA) through self-association of a quinoline oligoamide helical foldamer attached to a tightly binding HCA ligand. A crystal structure of the complex provided atomic details to explain the observed induction of single foldamer helix handedness and revealed an unexpected foldamer-mediated dimerization. Here, we investigated the detailed behavior of the HCA-foldamer complex in solution by using NMR spectroscopy. We found that the ability to dimerize is buffer-dependent and uses partially distinct intermolecular contacts. The use of a foldamer variant incapable of self-association confirmed the ability to induce helix handedness separately from dimer formation and provided insight into the dynamics of enantiomeric selection.
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Affiliation(s)
- Michal Jewginski
- University of Bordeaux, CBMN (UMR 5248), Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France.,CNRS, CBMN (UMR 5248).,Bordeaux Institut National Polytechnique, CBMN (UMR 5248).,Wrocław University of Technology, Faculty of Chemistry, Wrocław, Poland
| | - Lucile Fischer
- University of Bordeaux, CBMN (UMR 5248), Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France.,CNRS, CBMN (UMR 5248).,Bordeaux Institut National Polytechnique, CBMN (UMR 5248)
| | - Cinzia Colombo
- University of Bordeaux, CBMN (UMR 5248), Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France.,CNRS, CBMN (UMR 5248).,Bordeaux Institut National Polytechnique, CBMN (UMR 5248)
| | - Ivan Huc
- University of Bordeaux, CBMN (UMR 5248), Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France. .,CNRS, CBMN (UMR 5248). .,Bordeaux Institut National Polytechnique, CBMN (UMR 5248).
| | - Cameron D Mackereth
- University of Bordeaux, ARNA (U1212), Institut Européen de Chimie et Biologie. .,INSERM, ARNA (U1212). .,CNRS, ARNA (UMR 5320), 2 rue Escarpit, 33600, Pessac, France.
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9
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Kawamoto Y, Sasaki A, Hashiya K, Ide S, Bando T, Maeshima K, Sugiyama H. Tandem trimer pyrrole-imidazole polyamide probes targeting 18 base pairs in human telomere sequences. Chem Sci 2015; 6:2307-2312. [PMID: 29308145 PMCID: PMC5645774 DOI: 10.1039/c4sc03755c] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 01/20/2015] [Indexed: 01/06/2023] Open
Abstract
The novel tandem trimer pyrrole-imidazole polyamide probe targeting 18 bp in telomeric repeats visualized telomeres in human cells selectively.
The binding of molecules to specific DNA sequences is important for imaging genome DNA and for studying gene expression. Increasing the number of base pairs targeted by these molecules would provide greater specificity. N-Methylpyrrole–N-methylimidazole (Py–Im) polyamides are one type of such molecules and can bind to the minor groove of DNA in a sequence-specific manner without causing denaturation of DNA. Our recent work has demonstrated that tandem hairpin Py–Im polyamides conjugated with a fluorescent dye can be synthesized easily and can serve as new probes for studying human telomeres under mild conditions. Herein, to improve their selectivities to telomeres by targeting longer sequences, we designed and synthesized a fluorescent tandem trimer Py–Im polyamide probe, comprising three hairpins and two connecting regions (hinges). The new motif bound to 18 bp dsDNA in human telomeric repeats (TTAGGG)n, the longest sequence for specific binding reported for Py–Im polyamides. We compared the binding affinities and the abilities to discriminate mismatch, the UV-visible absorption and fluorescence spectra, and telomere staining in human cells between the tandem trimer and a previously developed tandem hairpin. We found that the tandem trimer Py–Im polyamide probe has higher ability to recognize telomeric repeats and stains telomeres in chemically fixed cells with lower background signal.
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Affiliation(s)
- Yusuke Kawamoto
- Department of Chemistry , Graduate School of Science , Kyoto University , Kyoto 606-8502 , Sakyo , Japan . ;
| | - Asuka Sasaki
- Biological Macromolecules Laboratory , Structural Biology Center , National Institute of Genetics, and Department of Genetics , School of Life Science , Graduate University for Advanced Studies (Sokendai) , Mishima , Shizuoka 411-8540 , Japan .
| | - Kaori Hashiya
- Department of Chemistry , Graduate School of Science , Kyoto University , Kyoto 606-8502 , Sakyo , Japan . ;
| | - Satoru Ide
- Biological Macromolecules Laboratory , Structural Biology Center , National Institute of Genetics, and Department of Genetics , School of Life Science , Graduate University for Advanced Studies (Sokendai) , Mishima , Shizuoka 411-8540 , Japan .
| | - Toshikazu Bando
- Department of Chemistry , Graduate School of Science , Kyoto University , Kyoto 606-8502 , Sakyo , Japan . ;
| | - Kazuhiro Maeshima
- Biological Macromolecules Laboratory , Structural Biology Center , National Institute of Genetics, and Department of Genetics , School of Life Science , Graduate University for Advanced Studies (Sokendai) , Mishima , Shizuoka 411-8540 , Japan .
| | - Hiroshi Sugiyama
- Department of Chemistry , Graduate School of Science , Kyoto University , Kyoto 606-8502 , Sakyo , Japan . ; .,Institute for Integrated Cell-Material Science (WPI-iCeMS) , Kyoto University , Kyoto 606-8501 , Sakyo , Japan
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10
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Guo C, Kawamoto Y, Asamitsu S, Sawatani Y, Hashiya K, Bando T, Sugiyama H. Rational design of specific binding hairpin Py-Im polyamides targeting human telomere sequences. Bioorg Med Chem 2014; 23:855-60. [PMID: 25614111 DOI: 10.1016/j.bmc.2014.12.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 12/12/2014] [Accepted: 12/13/2014] [Indexed: 02/03/2023]
Abstract
N-Methylpyrrole (Py)-N-methylimidazole (Im) polyamides are organic molecules that can recognize predetermined DNA sequences in a sequence-specific manner. Human telomeres contain regions of (TTAGGG)n repetitive nucleotide sequences at each end of chromosomes, and these regions protect the chromosome from deterioration or from fusion with neighboring chromosomes. The telomeres are disposable buffers at the ends of chromosomes that are truncated during cell division. Tandem hairpin Py-Im polyamide TH59, which recognizes human telomere sequences, was reported by Laemmli's group in 2001. Here, we synthesized three types of Py-Im polyamides 1-3 based on TH59 for specific recognition of human telomere repeat sequences. Thermal melting temperature (Tm) measurements and surface plasmon resonance analysis were used to evaluate the abilities of the three types of Py-Im polyamides to discriminate between three kinds of DNA sequences. Significantly, the results showed that polyamides 1 and 2 have better affinities to TTAAGG than to TTAGGG. In contrast, polyamide 3 displayed good specificity to human telomere sequence, TTAGGG, as expected on the basis of Py-Im binding rules.
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Affiliation(s)
- Chuanxin Guo
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Yusuke Kawamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Sefan Asamitsu
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Yoshito Sawatani
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan.
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan; Institute for Integrated Cell-Materials Science (iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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