1
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Abe K, Hirose Y, Kumagai T, Hashiya K, Hidaka K, Emura T, Bando T, Takeda K, Sugiyama H. Structural Studies of a Complex of a CAG/CTG Repeat Sequence-Specific Binding Molecule and A-A-Mismatch-Containing DNA. JACS AU 2024; 4:1801-1810. [PMID: 38818057 PMCID: PMC11134352 DOI: 10.1021/jacsau.3c00830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/04/2024] [Accepted: 03/06/2024] [Indexed: 06/01/2024]
Abstract
Triplet repeat diseases are caused by the abnormal elongation of repeated sequences comprising three bases. In particular, the elongation of CAG/CTG repeat sequences is thought to result in conditions such as Huntington's disease and myotonic dystrophy type 1. Although the causes of these diseases are known, fundamental treatments have not been established, and specific drugs are expected to be developed. Pyrrole imidazole polyamide (PIP) is a class of molecules that binds to the minor groove of the DNA duplex in a sequence-specific manner; because of this property, it shows promise in drug discovery applications. Earlier, it was reported that PIP designed to bind CAG/CTG repeat sequences suppresses the genes that cause triplet repeat diseases. In this study, we performed an X-ray crystal structure analysis of a complex of double-stranded DNA containing A-A mismatched base pairs and a cyclic-PIP that binds specifically to CAG/CTG sequences. Furthermore, the validity and characteristics of this structure were analyzed using in silico molecular modeling, ab initio energy calculations, gel electrophoresis, and surface plasmon resonance. With our direct observation using atomic force microscopy and DNA origami, we revealed that the PIP caused structural changes in the DNA strands carrying the expanded CAG/CTG repeat. Overall, our study provides new insight into PIP from a structural perspective.
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Affiliation(s)
- Katsuhiko Abe
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Yuki Hirose
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Tomotaka Kumagai
- 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
| | - Kumi Hidaka
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Tomoko Emura
- 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
| | - Kazuki Takeda
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Institute
for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
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2
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Hidaka T, Sugiyama H. Chemical Approaches to the Development of Artificial Transcription Factors Based on Pyrrole-Imidazole Polyamides. CHEM REC 2020; 21:1374-1384. [PMID: 33332727 DOI: 10.1002/tcr.202000158] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 12/19/2022]
Abstract
To maintain the functions of living organisms, cells have developed complex gene regulatory networks. Transcription factors have a central role in spatiotemporal control of gene expression and this has motivated us to develop artificial transcription factors that mimic their function. We found that three functions could be mimicked by applying our chemical approaches: i) efficient delivery into organelles that contain target DNA, ii) specific DNA binding to the target genomic region, and iii) regulation of gene expression by interaction with other transcription coregulators. We chose pyrrole-imidazole polyamides (PIPs), sequence-selective DNA binding molecules, as DNA binding domains, and have achieved each of the required functions by introducing other functional moieties. The developed artificial transcription factors have potential as chemical tools that can be used to artificially modulate gene expression to enable cell fate control and to correct abnormal gene regulation for therapeutic purposes.
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Affiliation(s)
- Takuya Hidaka
- 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, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomaecho, Sakyo-ku, Kyoto, 606-8501, Japan
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3
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Zhang M, Liang J, Jiang SK, Xu L, Wu YL, Awadasseid A, Zhao XY, Xiong XQ, Sugiyama H, Zhang W. Design, synthesis and anti-cancer activity of pyrrole-imidazole polyamides through target-downregulation of c-kit gene expression. Eur J Med Chem 2020; 207:112704. [DOI: 10.1016/j.ejmech.2020.112704] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/12/2020] [Accepted: 07/28/2020] [Indexed: 12/18/2022]
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4
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Lee JA, An J, Taniguchi J, Kashiwazaki G, Pandian GN, Parveen N, Kang TM, Sugiyama H, De D, Kim KK. Targeted epigenetic modulation using a DNA-based histone deacetylase inhibitor enhances cardiomyogenesis in mouse embryonic stem cells. J Cell Physiol 2020; 236:3946-3962. [PMID: 33164232 DOI: 10.1002/jcp.30140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 09/25/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022]
Abstract
The epigenome has an essential role in orchestrating transcriptional activation and modulating key developmental processes. Previously, we developed a library of pyrrole-imidazole polyamides (PIPs) conjugated with suberoylanilide hydroxamic acid (SAHA), a histone deacetylase (HDAC) inhibitor, for the purpose of sequence-specific modification of epigenetics. Based on the gene expression profile of SAHA-PIPs and screening studies using the α-myosin heavy chain promoter-driven reporter and SAHA-PIP library, we identified that SAHA-PIP G activates cardiac-related genes. Studies in mouse ES cells showed that SAHA-PIP G could enhance the generation of spontaneous beating cells, which is consistent with upregulation of several cardiac-related genes. Moreover, ChIP-seq results confirmed that the upregulation of cardiac-related genes is highly correlated with epigenetic activation, relevant to the sequence-specific binding of SAHA-PIP G. This proof-of-concept study demonstrating the applicability of SAHA-PIP not only improves our understanding of epigenetic alterations involved in cardiomyogenesis but also provides a novel chemical-based strategy for stem cell differentiation.
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Affiliation(s)
- Jin-A Lee
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Jieun An
- Department of Physiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Junichi Taniguchi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto, Japan
| | - Gengo Kashiwazaki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto, Japan
| | - Ganesh N Pandian
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto, Japan
| | - Nazia Parveen
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Tong Mook Kang
- Department of Physiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto, Japan
| | - Debojyoti De
- Department of Biotechnology, National Institute of Technology, Durgapur, Burdwan, West Bengal, India
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
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5
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Bando T, Sugiyama H. Epigenetic Drug Discovery by Artificial Genetic Switches. J SYN ORG CHEM JPN 2020. [DOI: 10.5059/yukigoseikyokaishi.78.476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science Kyoto University
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6
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Bando T, Sugiyama H. Sequence-Specific PI Polyamides Make It Possible to Regulate DNA Structure and Function. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20190311] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- 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, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomaecho, Sakyo-ku, Kyoto 606-8501, Japan
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7
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Heinrich B, Vázquez O. 4-Methyltrityl-Protected Pyrrole and Imidazole Building Blocks for Solid Phase Synthesis of DNA-Binding Polyamides. Org Lett 2020; 22:533-536. [PMID: 31904984 DOI: 10.1021/acs.orglett.9b04288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA-binding polyamides are synthetic oligomers of pyrrole/imidazole units with high specificity and affinity for double-stranded DNA. To increase their synthetic diversity, we report a mild methodology based on 4-methyltrityl (Mtt) solid phase peptide synthesis (SPPS), whose building blocks are more accessible than the standard Fmoc and Boc SPPS ones. We demonstrate the robustness of the approach by preparing and studying a hairpin with all precursors. Importantly, our strategy is orthogonal and compatible with sensitive molecules and could be readily automated.
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Affiliation(s)
- Benedikt Heinrich
- Fachbereich Chemie , Philipps-Universität Marburg , Hans-Meerwein-Straße 4 , 35043 Marburg , Germany
| | - Olalla Vázquez
- Fachbereich Chemie , Philipps-Universität Marburg , Hans-Meerwein-Straße 4 , 35043 Marburg , Germany
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8
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Yu Z, Ai M, Samanta SK, Hashiya F, Taniguchi J, Asamitsu S, Ikeda S, Hashiya K, Bando T, Pandian GN, Isaacs L, Sugiyama H. A synthetic transcription factor pair mimic for precise recruitment of an epigenetic modifier to the targeted DNA locus. Chem Commun (Camb) 2020; 56:2296-2299. [DOI: 10.1039/c9cc09608f] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
ePIP–HoGu not only mimics the transcription factor operation as pairs but is also capable of recruiting the epigenetic modifiers to a particular DNA locus.
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9
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Yu Z, Pandian GN, Hidaka T, Sugiyama H. Therapeutic gene regulation using pyrrole-imidazole polyamides. Adv Drug Deliv Rev 2019; 147:66-85. [PMID: 30742856 DOI: 10.1016/j.addr.2019.02.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/22/2018] [Accepted: 02/04/2019] [Indexed: 12/13/2022]
Abstract
Recent innovations in cutting-edge sequencing platforms have allowed the rapid identification of genes associated with communicable, noncommunicable and rare diseases. Exploitation of this collected biological information has facilitated the development of nonviral gene therapy strategies and the design of several proteins capable of editing specific DNA sequences for disease control. Small molecule-based targeted therapeutic approaches have gained increasing attention because of their suggested clinical benefits, ease of control and lower costs. Pyrrole-imidazole polyamides (PIPs) are a major class of DNA minor groove-binding small molecules that can be predesigned to recognize specific DNA sequences. This programmability of PIPs allows the on-demand design of artificial genetic switches and fluorescent probes. In this review, we detail the progress in the development of PIP-based designer ligands and their prospects as advanced DNA-based small-molecule drugs for therapeutic gene modulation.
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10
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Sato S, Asamitsu S, Bando T, Sugiyama H. Orientation preferences of hairpin pyrrole-imidazole polyamides toward mCGG site. Bioorg Med Chem 2019; 27:2167-2171. [PMID: 31000407 DOI: 10.1016/j.bmc.2019.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/02/2019] [Accepted: 04/04/2019] [Indexed: 11/16/2022]
Abstract
Hairpin pyrrole-imidazole (Py-Im) polyamides are promising medium-sized molecules that bind sequence-specifically to the minor groove of B-form DNA. Here, we synthesized a series of hairpin Py-Im polyamides and explored their binding affinities and orientation preferences to methylated DNA with the mCGG target sequence. Thermal denaturation assays revealed that the five hairpin Py-Im polyamides, which were anticipated to recognize mCGG in a forward orientation, bind to nontarget DNA, GGmC, in a reverse orientation. Therefore, we designed five Py-Im polyamides that could recognize mCGG in a reverse orientation. We found that the two Py-Im polyamides containing Im/β pairs preferentially bound to mCGG in a reverse orientation. The reverse binding Py-Im polyamide successfully inhibited TET1 binding on the methylated DNA. Taken together, this study illustrated the importance of designing reverse binding Py-Im polyamides for the target sequence, mCGG, which paved the way for Py-Im polyamides that can be used with otherwise difficult to access DNA with CG sequences.
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Affiliation(s)
- Shinsuke Sato
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Sefan Asamitsu
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan.
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan; Institute for Integrated Cell-Materials Science (WPI-iCeMS), Kyoto University, Sakyo-Ku, Kyoto 606-8501, Japan.
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11
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Yao X, Huang P, Nie Z. Cyclodextrin-based polymer materials: From controlled synthesis to applications. Prog Polym Sci 2019. [DOI: 10.1016/j.progpolymsci.2019.03.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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12
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Yu Z, Chen Z, Su Q, Ye S, Yuan H, Kuai M, Lv M, Tu Z, Yang X, Liu R, Hu G, Li Q. Dual inhibitors of RAF-MEK-ERK and PI3K-PDK1-AKT pathways: Design, synthesis and preliminary anticancer activity studies of 3-substituted-5-(phenylamino) indolone derivatives. Bioorg Med Chem 2019; 27:944-954. [PMID: 30777660 DOI: 10.1016/j.bmc.2019.01.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 01/21/2019] [Accepted: 01/23/2019] [Indexed: 12/31/2022]
Abstract
The dysfunction and mutual compensatory activation of RAF-MEK-ERK and PI3K-PDK1-AKT pathways have been demonstrated as the hallmarks in several primary and recurrent cancers. The strategy of concurrent blocking of these two pathways shows clinical merits on effective cancer therapy, such as combinatory treatments and dual-pathway inhibitors. Herein, we report a novel prototype of dual-pathway inhibitors by means of merging the core structural scaffolds of a MEK1 inhibitor and a PDK1 inhibitor. A library of 43 compounds that categorized into three series (Series I-III) was synthesized and tested for antitumor activity in lung cancer cells. The results from structure-activity relationship (SAR) analysis showed the following order of antitumor activity that 3-hydroxy-5-(phenylamino) indolone (Series III) > 3-alkenyl-5-(phenylamino) indolone (Series I) > 3-alkyl-5-(phenylamino) indolone (Series II). A lead compound 9za in Series III showed most potent antitumor activity with IC50 value of 1.8 ± 0.8 µM in A549 cells. Moreover, antitumor mechanism study demonstrated that 9za exerted significant apoptotic effect, and cellular signal pathway analysis revealed the potent blockage of phosphorylation levels of ERK and AKT in RAF-MEK-ERK and PI3K-PDK1-AKT pathways, respectively. The results reported here provide robust experimental basis for the discovery and optimization of dual pathway agents for anti-lung cancer therapy.
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Affiliation(s)
- Zutao Yu
- Department of Medicinal Chemistry, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, PR China
| | - Zhuo Chen
- Department of Medicinal Chemistry, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, PR China
| | - Qiongli Su
- Department of Pharmacy, School of Medicine, Hunan Normal University, Changsha 410013, Hunan, PR China
| | - Shiqi Ye
- School of Medicine, Shenzhen University, Shenzhen 518060, Guangdong, PR China
| | - Hongbo Yuan
- Hunan Qianjin Xiangjiang Pharmaceutical Co., Ltd, Changsha 410013, Hunan, PR China
| | - Mengni Kuai
- Department of Medicinal Chemistry, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, PR China; Department of Pharmacy, School of Medicine, Hunan Normal University, Changsha 410013, Hunan, PR China
| | - Meng Lv
- Department of Medicinal Chemistry, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, PR China
| | - Zhijun Tu
- Department of Medicinal Chemistry, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, PR China
| | - Xiaoping Yang
- Department of Pharmacy, School of Medicine, Hunan Normal University, Changsha 410013, Hunan, PR China
| | - RangRu Liu
- Key Laboratory of Tropical Diseases and Translational Medicine of the Ministry of Education & Hainan Provincial Key Laboratory of Tropical Medicine, Hainan Medical College, Haikou, PR China
| | - Gaoyun Hu
- Department of Medicinal Chemistry, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, PR China
| | - Qianbin Li
- Department of Medicinal Chemistry, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, PR China.
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13
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Han JH, Park S, Hashiya F, Sugiyama H. Approach to the Investigation of Nucleosome Structure by Using the Highly Emissive Nucleobase
th
dG–tC FRET Pair. Chemistry 2018; 24:17091-17095. [DOI: 10.1002/chem.201803382] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/07/2018] [Indexed: 01/27/2023]
Affiliation(s)
- Ji Hoon Han
- Department of ChemistryGraduate School of ScienceKyoto University Kitashirakawa-Oiwakecho Sakyo-ku Kyoto 606–8502 Japan
| | - Soyoung Park
- Department of ChemistryGraduate School of ScienceKyoto University Kitashirakawa-Oiwakecho Sakyo-ku Kyoto 606–8502 Japan
| | - Fumitaka Hashiya
- Department of ChemistryGraduate School of ScienceKyoto University Kitashirakawa-Oiwakecho Sakyo-ku Kyoto 606–8502 Japan
| | - Hiroshi Sugiyama
- Department of ChemistryGraduate School of ScienceKyoto University Kitashirakawa-Oiwakecho Sakyo-ku Kyoto 606–8502 Japan
- Institute for Integrated Cell-Material Sciences (iCeMS)Kyoto University Yoshida-ushinomiyacho Sakyo-ku Kyoto 606–8501 Japan
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14
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Zhou X, Pathak P, Jayawickramarajah J. Design, synthesis, and applications of DNA-macrocyclic host conjugates. Chem Commun (Camb) 2018; 54:11668-11680. [PMID: 30255866 DOI: 10.1039/c8cc06716c] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
With this Feature Article we review, for the first time, the development of DNA-host conjugates-a nascent yet rapidly growing research focus within the ambit of DNA supramolecular chemistry. Synthetic hosts (such as cyclodextrins, cucurbiturils, and calixarenes) are well-suited to be partnered with DNA, since DNA assembly and host-guest binding both thrive in aqueous media, are largely orthogonal, and exhibit controllable and input-responsive properties. The covalent braiding of these two supramolecular synthons thus leads to advanced self-assemblies and nanostructures with exciting function that range from drug delivery agents to input-triggered switches. The latter class of DNA-host conjugates have been demonstrated to precisely control protein activity, and have also been used as modulable catalysts and versatile biosensors.
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Affiliation(s)
- X Zhou
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, USA.
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15
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Yu Z, Hsieh WC, Asamitsu S, Hashiya K, Bando T, Ly DH, Sugiyama H. Orthogonal γPNA Dimerization Domains Empower DNA Binders with Cooperativity and Versatility Mimicking that of Transcription Factor Pairs. Chemistry 2018; 24:14183-14188. [PMID: 30003621 PMCID: PMC9724550 DOI: 10.1002/chem.201801961] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/26/2018] [Indexed: 12/21/2022]
Abstract
Synthetic molecules capable of DNA binding and mimicking cooperation of transcription factor (TF) pairs have long been considered a promising tool for manipulating gene expression. Our previously reported Pip-HoGu system, a programmable DNA binder pyrrole-imidazole polyamides (PIPs) conjugated to host-guest moiety, defined a general framework for mimicking cooperative TF pair-DNA interactions. Here, we supplanted the cooperation modules with left-handed (LH) γPNA modules: i.e., PIPs conjugated with nucleic acid-based cooperation system (Pip-NaCo). LH γPNA was chosen because of its bioorthogonality, sequence-specific interaction, and high binding affinity toward the partner strand. From the results of the Pip-NaCo system, cooperativity is highly comparable to the natural TF pair-DNA system, with a minimum energetics of cooperation of -3.27 kcal mol-1 . Moreover, through changing the linker conjugation site, binding mode, and the length of γPNAs sequence, the cooperative energetics of Pip-NaCo can be tuned independently and rationally. The current Pip-NaCo platform might also have the potential for precise manipulation of biological processes through the construction of triple to multiple heterobinding systems.
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Affiliation(s)
- Zutao Yu
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Wei-Che Hsieh
- Institute for Biomolecular Design and Discovery (IBD), Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania, 15213, USA
| | - Sefan Asamitsu
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kaori Hashiya
- 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
| | - Danith H Ly
- Institute for Biomolecular Design and Discovery (IBD), Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania, 15213, USA
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
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16
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Wu C, Wang W, Fang L, Su W. Programmable pyrrole-imidazole polyamides: A potent tool for DNA targeting. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2018.05.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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17
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Taniguchi J, Feng Y, Pandian GN, Hashiya F, Hidaka T, Hashiya K, Park S, Bando T, Ito S, Sugiyama H. Biomimetic Artificial Epigenetic Code for Targeted Acetylation of Histones. J Am Chem Soc 2018; 140:7108-7115. [DOI: 10.1021/jacs.8b01518] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Junichi Taniguchi
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Yihong Feng
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Ganesh N. Pandian
- Institute for Integrated Cell-Material Sciences, Institute for Advanced Study, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Fumitaka Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Takuya Hidaka
- 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
| | - Soyoung Park
- 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
| | - Shinji Ito
- Medical Research Support Center, Graduate School of Medicine, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Sciences, Institute for Advanced Study, Kyoto University, Sakyo, Kyoto 606-8501, Japan
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