1
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Metangle S, Ranjan N. Preferential Binding of a Red Emissive Julolidine Derivative to a Promoter G-Quadruplex. Chembiochem 2024; 25:e202300527. [PMID: 37926689 DOI: 10.1002/cbic.202300527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/23/2023] [Accepted: 11/02/2023] [Indexed: 11/07/2023]
Abstract
The therapeutic potential of G-quadruplexes has increased significantly with the growing understanding of their functional roles in pathogens apart from human diseases such as cancer. Here, we report the synthesis of three julolidine-based molecules and their binding to nucleic acids. Among the synthesized molecules, compound 1 exhibited red emissive fluorescence with a distinct preference for Pu22 G-quadruplex. The binding of compound 1 to Pu22 G-quadruplex, initially identified through a fluorescence-based screening, was further confirmed by UV-vis, fluorescence spectroscopy, and circular dichroism-based experiments. Thermal denaturation of compound 1 in the presence of Pu22 G-quadruplex revealed a concentration-dependent stabilization (~10.0 °C at 1 : 3 stoichiometry). Fluorescence-based experiments revealed 1 : 1 stoichiometry of the interaction and an association constant (Ka ) of 5.67×106 M-1 . CD experiments displayed that the parallel conformation of the G-quadruplex was retained on compound 1's binding and signs of higher order binding/complex formation were observed at high compound 1 to DNA ratio. Molecular docking studies revealed the dominance of stacking and van der Waals interactions in the molecular recognition which was aided by some close-distance interactions involving the quinolinium nitrogen atom.
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Affiliation(s)
- Sachin Metangle
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh, 226002, India
| | - Nihar Ranjan
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh, 226002, India
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2
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Li JH, You PD, Lu F, Tang HY, Guo HY, Zhou CQ. NIR C-Myc Pu22 G-quadruplex probe as a photosensitizer for bioimaging and antitumor study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 294:122533. [PMID: 36842212 DOI: 10.1016/j.saa.2023.122533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 02/05/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
Despite the fact that C-Myc G-quadruplex in the oncogene promoter regions is one of the crucial targets of antitumor drugs, the selectivities and proliferation inhibitions of its probes towards tumor cells remain a big challenge. Until now, no effective C-Myc G-quadruplex probes have been reported as a photosensitizer to increase their antitumor activities. Here, the first NIR C-Myc G-quadruplex probe PDS-SQ has been designed, comprising a G-quadruplex binder PDS and a squaraine dye SQ as a photosensitizer. Conjugate PDS-SQ could selectively NIR image C-Myc Pu22 G-quadruplex in tumor cells, and show stronger antitumor activity in the irradiation by a chemo-photodynamic method than in the dark. The study provides a new way to develop the novel NIR C-Myc G-quadruplex probes with more potent antitumor activities.
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Affiliation(s)
- Jun-Hui Li
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Pei-Dan You
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Fei Lu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Hao-Yun Tang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Hong-Yan Guo
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Chun-Qiong Zhou
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China.
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3
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Mendoza A, Takemoto Y, Cruzado KT, Masoud SS, Nagata A, Tantipanjaporn A, Okuda S, Kawagoe F, Sakamoto R, Odagi M, Mototani S, Togashi M, Kawatani M, Aono H, Osada H, Nakagawa H, Higashi T, Kittaka A, Nagasawa K, Uesugi M. Controlled lipid β-oxidation and carnitine biosynthesis by a vitamin D metabolite. Cell Chem Biol 2021; 29:660-669.e12. [PMID: 34506728 DOI: 10.1016/j.chembiol.2021.08.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 07/20/2021] [Accepted: 08/20/2021] [Indexed: 12/21/2022]
Abstract
Lactone-vitamin D3 is a major metabolite of vitamin D3, a lipophilic vitamin biosynthesized in numerous life forms by sunlight exposure. Although lactone-vitamin D3 was discovered 40 years ago, its biological role remains largely unknown. Chemical biological analysis of its photoaffinity probe identified the hydroxyacyl-CoA dehydrogenase trifunctional multienzyme complex subunit alpha (HADHA), a mitochondrial enzyme that catalyzes β-oxidation of long-chain fatty acids, as its selective binding protein. Intriguingly, the interaction of lactone-vitamin D3 with HADHA does not affect the HADHA enzymatic activity but instead limits biosynthesis of carnitine, an endogenous metabolite required for the transport of fatty acids into the mitochondria for β-oxidation. Lactone-vitamin D3 dissociates the protein-protein interaction of HADHA with trimethyllysine dioxygenase (TMLD), thereby impairing the TMLD enzyme activity essential in carnitine biosynthesis. These findings suggest a heretofore undescribed role of lactone-vitamin D3 in lipid β-oxidation and carnitine biosynthesis, and possibly in sunlight-dependent shifts of lipid metabolism in animals.
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Affiliation(s)
- Aileen Mendoza
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yasushi Takemoto
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Kevin Tan Cruzado
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Shadi Sedghi Masoud
- Department of Biotechnology and Life Sciences, Graduate School of Technology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Akiko Nagata
- Department of Biotechnology and Life Sciences, Graduate School of Technology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | | | - Satoshi Okuda
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Fumihiro Kawagoe
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi, Tokyo 173-8605, Japan
| | - Ryota Sakamoto
- Department of Biotechnology and Life Sciences, Graduate School of Technology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Minami Odagi
- Department of Biotechnology and Life Sciences, Graduate School of Technology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Sayuri Mototani
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi, Tokyo 173-8605, Japan
| | - Moeka Togashi
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Makoto Kawatani
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Harumi Aono
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Hayato Nakagawa
- Department of Gastroenterology, the University of Tokyo, Bunkyo, Tokyo 113-8655, Japan
| | - Tatsuya Higashi
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Atsushi Kittaka
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi, Tokyo 173-8605, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Sciences, Graduate School of Technology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan.
| | - Motonari Uesugi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan; School of Pharmacy, Fudan University, Shanghai 201203, China.
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4
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Yasuda M, Ma Y, Okabe S, Wakabayashi Y, Su D, Chang YT, Seimiya H, Tera M, Nagasawa K. Target identification of a macrocyclic hexaoxazole G-quadruplex ligand using post-target-binding visualization. Chem Commun (Camb) 2020; 56:12905-12908. [PMID: 33030187 DOI: 10.1039/d0cc04957c] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Macrocyclic hexaoxazoles (6OTDs) are G-quadruplex (G4) ligands, and some derivatives, such as L2H2-6OTD (1a) bearing two aminobutyl side chains, show cytotoxicity towards cancer cells. To identify the cellular target of 1a, we employed a post-target-binding strategy utilizing click reaction (Huisgen cyclization) between the azide-conjugated ligand L2H2-6OTD-Az (1b) and the cell-permeable dye CO-1 bearing a strained alkyne moiety and the BODIPY fluorophore under Cu-free conditions. We confirmed that introduction of the small azide group did not alter the physical or biological properties, including anti-cancer activity, of 1a, and we also demonstrated bias-free localization of CO-1. The post-binding visualization strategy suggested that L2H2-6OTD (1a) colocalized with RNA G4 in living cells.
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Affiliation(s)
- Mizuho Yasuda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
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5
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6
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Maleki P, Mustafa G, Gyawali P, Budhathoki JB, Ma Y, Nagasawa K, Balci H. Quantifying the impact of small molecule ligands on G-quadruplex stability against Bloom helicase. Nucleic Acids Res 2020; 47:10744-10753. [PMID: 31544934 PMCID: PMC6847008 DOI: 10.1093/nar/gkz803] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 08/28/2019] [Accepted: 09/09/2019] [Indexed: 01/28/2023] Open
Abstract
G-quadruplex (GQ) stabilizing small molecule (SM) ligands have been used to stabilize human telomeric GQ (hGQ) to inhibit telomerase activity, or non-telomeric GQs to manipulate gene expression at transcription or translation level. GQs are known to inhibit DNA replication unless destabilized by helicases, such as Bloom helicase (BLM). Even though the impact of SM ligands on thermal stability of GQs is commonly used to characterize their efficacy, how these ligands influence helicase-mediated GQ unfolding is not well understood. Three prominent SM ligands (an oxazole telomestatin derivative, pyridostatin, and PhenDC3), which thermally stabilize hGQ at different levels, were utilized in this study. How these ligands influence BLM-mediated hGQ unfolding was investigated using two independent single-molecule approaches. While the frequency of dynamic hGQ unfolding events was used as the metric in the first approach, the second approach was based on quantifying the cumulative unfolding activity as a function of time. All three SM ligands inhibited BLM activity at similar levels, 2–3 fold, in both approaches. Our observations suggest that the impact of SM ligands on GQ thermal stability is not an ideal predictor for their inhibition of helicase-mediated unfolding, which is physiologically more relevant.
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Affiliation(s)
- Parastoo Maleki
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | - Golam Mustafa
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | - Prabesh Gyawali
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | | | - Yue Ma
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH 44242, USA
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8
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Pandith A, Siddappa RG, Seo YJ. Recent developments in novel blue/green/red/NIR small fluorescent probes for in cellulo tracking of RNA/DNA G-quadruplexes. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2019. [DOI: 10.1016/j.jphotochemrev.2019.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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9
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Iida K, Tsushima Y, Ma Y, Sedghi Masoud S, Sakuma M, Yokoyama T, Yoshida W, Ikebukuro K, Nagasawa K. Model studies for isolation of G-quadruplex-forming DNA sequences through a pull-down strategy with macrocyclic polyoxazole. Bioorg Med Chem 2019; 27:1742-1746. [PMID: 30842030 DOI: 10.1016/j.bmc.2019.02.056] [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: 12/21/2018] [Revised: 02/18/2019] [Accepted: 02/28/2019] [Indexed: 12/22/2022]
Abstract
G-quadruplexes (G4s) are non-B DNA structures present in guanine-rich regions of gene regulatory areas, promoters and CpG islands, but their occurrence and functions remain incompletely understood. Thus, methodology to identify G4 sequences is needed. Here, we describe the synthesis of a novel cyclic hepta-oxazole compound, L1Bio-7OTD (1), bearing a biotin affinity-tag as a tool to pull down G4 structures from mixtures of G4-forming and non G4-forming DNA sequences. We confirmed that it could pull down G4s associated with telomeres, bcl-2 gene, and c-kit gene.
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Affiliation(s)
- Keisuke Iida
- Department of Chemistry, Chiba University, 1-33 Yayoi, Inage, Chiba 263-8522, Japan.
| | - Yamato Tsushima
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Yue Ma
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Shadi Sedghi Masoud
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Mai Sakuma
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Tomomi Yokoyama
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Wataru Yoshida
- School of Bioscience and Biotechnology, Graduate School of Bionics, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji 192-0982, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
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10
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Abstract
This review describes a selection of macrocyclic natural products and structurally modified analogs containing peptidic and non-peptidic elements as structural features that potentially modulate cellular permeability. Examples range from exclusively peptidic structures like cyclosporin A or phepropeptins to compounds with mostly non-peptidic character, such as telomestatin or largazole. Furthermore, semisynthetic approaches and synthesis platforms to generate general and focused libraries of compounds at the interface of cyclic peptides and non-peptidic macrocycles are discussed.
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11
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Shirinfar B, Seema H, Ahmed N. Charged probes: turn-on selective fluorescence for RNA. Org Biomol Chem 2018; 16:164-168. [DOI: 10.1039/c7ob02423a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Imidazolium-based charged fluorescent probes for the selective in vitro and in vivo recognition of RNA over other biomolecules.
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Affiliation(s)
| | - Humaira Seema
- Institute of Chemical Sciences
- University of Peshawar
- Pakistan
| | - Nisar Ahmed
- School of Chemistry
- Cardiff University
- Cardiff
- UK
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12
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Targeting glioma stem cells in vivo by a G-quadruplex-stabilizing synthetic macrocyclic hexaoxazole. Sci Rep 2017; 7:3605. [PMID: 28620243 PMCID: PMC5472576 DOI: 10.1038/s41598-017-03785-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 05/03/2017] [Indexed: 11/15/2022] Open
Abstract
G-quadruplex (G4) is a higher-order nucleic acid structure that is formed by guanine-rich sequences. G4 stabilization by small-molecule compounds called G4 ligands often causes cytotoxicity, although the potential medicinal impact of this effect has not been fully established. Here we demonstrate that a synthetic G4 ligand, Y2H2-6M(4)-oxazole telomestatin derivative (6OTD), limits the growth of intractable glioblastoma (grade IV glioma) and glioma stem cells (GSCs). Experiments involving a human cancer cell line panel and mouse xenografts revealed that 6OTD exhibits antitumor activity against glioblastoma. 6OTD inhibited the growth of GSCs more potently than it did the growth of differentiated non-stem glioma cells (NSGCs). 6OTD caused DNA damage, G1 cell cycle arrest, and apoptosis in GSCs but not in NSGCs. These DNA damage foci tended to colocalize with telomeres, which contain repetitive G4-forming sequences. Compared with temozolomide, a clinical DNA-alkylating agent against glioma, 6OTD required lower concentrations to exert anti-cancer effects and preferentially affected GSCs and telomeres. 6OTD suppressed the intracranial growth of GSC-derived tumors in a mouse xenograft model. These observations indicate that 6OTD targets GSCs through G4 stabilization and promotion of DNA damage responses. Therefore, G4s are promising therapeutic targets for glioblastoma.
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13
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Jiang G, Chen X, Xu L, Cao Y, Hong S, Liu M, Cao W, Pei R. Design and Synthesis of a Dimethylindole Red Trimer: A New Light-Up Red-Emitting Fluorescent Probe for G-Quadruplexes. ChemistrySelect 2017. [DOI: 10.1002/slct.201601889] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Guimei Jiang
- CAS Key Laboratory of Nano-Bio Interface; Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences; Suzhou 215123 China
- Department of Chemistry, College of Sciences; Shanghai University; Shanghai 200444 China
| | - Xing Chen
- Public Health of Guangxi Medical University; Nanning 530021 China
| | - Lijun Xu
- CAS Key Laboratory of Nano-Bio Interface; Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences; Suzhou 215123 China
| | - Yi Cao
- CAS Key Laboratory of Nano-Bio Interface; Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences; Suzhou 215123 China
| | - Shanni Hong
- CAS Key Laboratory of Nano-Bio Interface; Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences; Suzhou 215123 China
| | - Min Liu
- CAS Key Laboratory of Nano-Bio Interface; Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences; Suzhou 215123 China
| | - Weiguo Cao
- Department of Chemistry, College of Sciences; Shanghai University; Shanghai 200444 China
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interface; Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences; Suzhou 215123 China
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14
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Shen G, Zhang H, Yang C, Yang Q, Tang Y. Thrombin Ultrasensitive Detection Based on Chiral Supramolecular Assembly Signal-Amplified Strategy Induced by Thrombin-Binding Aptamer. Anal Chem 2016; 89:548-551. [PMID: 27958723 DOI: 10.1021/acs.analchem.6b04247] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Thrombin plays a critical role in hemostasis and hemolysis. It is of high importance to develop a system toward thrombin detection with high sensitivity and high selectivity for both research and clinical diagnosis applications. In this paper, we developed a thrombin detection assay by taking advantage of the novel signal amplified strategy based on the chiral supramolecular assembly in physiological K+ background. This assay could detect thrombin as low concentration as about 2 pM and provided a highly specific selectivity among several common interferences. Furthermore, the assay can discriminate thrombin from other nonspecific analogous proteins with high selectivity and can be used to detect thrombin in diluted real human serum samples, which suggested its great potential for rapid detection of thrombin in the clinic.
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Affiliation(s)
- Gang Shen
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
| | - Hong Zhang
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
| | - Chunrong Yang
- College of Chemistry, Sichuan University , Chengdu, 610065, China
| | - Qianfan Yang
- College of Chemistry, Sichuan University , Chengdu, 610065, China
| | - Yalin Tang
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
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15
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New pyridinium-based fluorescent dyes: A comparison of symmetry and side-group effects on G-Quadruplex DNA binding selectivity and application in live cell imaging. Biosens Bioelectron 2016; 81:373-381. [PMID: 26994364 DOI: 10.1016/j.bios.2016.03.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 03/07/2016] [Accepted: 03/07/2016] [Indexed: 11/22/2022]
Abstract
A series of C1-, C2-and C3-symmetric pyridinium conjugates with different styrene-like side groups were synthesized and were utilized as G-quadruplex selective fluorescent probes. The new compounds were well-characterized. Their selectivity, sensitivity, and stability towards G-quadruplex were studied by fluorescence titration, native PAGE experiments, FRET and circular dichroism (CD) analyses. These new compounds investigated in the fluorescence assays were preferentially bound with G-quadruplex DNA compared with other type of nucleic acids and it is fascinating to realize the effects of molecular symmetry and associated side groups showing unexpectedly great influence on the fluorescent signal enhancement for the discrimination of G-quadruplexes DNA from other nucleic acids. This may correlate with the pocket symmetry and shape of the G-quadruplex DNA inherently. Among the compounds, a C2-symmetric dye (2,6-bis-((E)-2-(1H-indol-3-yl)-vinyl)-1-methylpyridin-1-ium iodide) with indolyl-groups substituted was screened out from the series giving the best selectivity and sensitivity towards G-quadruplexes DNA, particularly telo21, due to its high equilibrium binding constant (K=2.17×10(5)M(-1)). In addition, the limit of detection (LOD) of the dye to determine telo21 DNA in bioassays was found as low as 33nM. The results of the study give insight and certain crucial factors, such as molecular symmetry and the associated side groups, on developing of effective fluorescent dyes for G-quadruplex DNA applications including G-quadruplex structure stabilization, biosensing and clinical applications. The compound was also demonstrated as a very selective G-quadruplex fluorescent agent for living cell staining and imaging.
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16
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Hu MH, Chen SB, Guo RJ, Ou TM, Huang ZS, Tan JH. Development of a highly sensitive fluorescent light-up probe for G-quadruplexes. Analyst 2016; 140:4616-25. [PMID: 26027520 DOI: 10.1039/c5an00761e] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
G-quadruplexes are higher-order nucleic acid structures that have attracted extensive attention because of their biological significance and potential applications in supramolecular chemistry. An ever-increasing interest in G-quadruplexes has promoted the development of selective and sensitive fluorescent probes as research tools for these structures. However, most current studies primarily focus on the improved selectivity of probes for G-quadruplexes. Their detection limits or ways to improve their detection limits are rarely described. In this study, a new set of di-substituted triarylimidazole fluorescent probes were designed and synthesized, with the aim of upgrading the detection limit of a lead triarylimidazole IZCM-1 for G-quadruplexes. Among these compounds, IZCM-7 was the most promising candidate. The limit of detection (LOD) value of IZCM-7 for the G-quadruplex was up to 3 nM in solution and up to 5 ng in a gel matrix. These values were significantly improved in comparison with those of IZCM-1. Further biophysical studies revealed that the fluorescence quantum yield and binding affinity of IZCM-7 for G-quadruplexes were markedly increased, and these two factors might be responsible for the significantly improved detection limit of IZCM-7. In addition, the sensitive and selective fluorescence performance of IZCM-7 for G-quadruplexes remained the same even in the presence of large amounts of non-G-quadruplex competitors, suggesting its promising application prospect.
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Affiliation(s)
- Ming-Hao Hu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
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17
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Wachter E, Moyá D, Parkin S, Glazer EC. Ruthenium Complex "Light Switches" that are Selective for Different G-Quadruplex Structures. Chemistry 2016; 22:550-9. [PMID: 26560887 PMCID: PMC4703525 DOI: 10.1002/chem.201503203] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Indexed: 01/03/2023]
Abstract
Recognition and regulation of G-quadruplex nucleic acid structures is an important goal for the development of chemical tools and medicinal agents. The addition of a bromo-substituent to the dipyridylphenazine (dppz) ligands in the photophysical "light switch", [Ru(bpy)2 dppz](2+) , and the photochemical "light switch", [Ru(bpy)2 dmdppz](2+) , creates compounds with increased selectivity for an intermolecular parallel G-quadruplex and the mixed-hybrid G-quadruplex, respectively. When [Ru(bpy)2 dppz-Br](2+) and [Ru(bpy)2 dmdppz-Br](2+) are incubated with the G-quadruplexes, they have a stabilizing effect on the DNA structures. Activation of [Ru(bpy)2 dmdppz-Br](2+) with light results in covalent adduct formation with the DNA. These complexes demonstrate that subtle chemical modifications of Ru(II) complexes can alter G-quadruplex selectivity, and could be useful for the rational design of in vivo G-quadruplex probes.
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Affiliation(s)
- Erin Wachter
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, KY 40506 (USA)
| | - Diego Moyá
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, KY 40506 (USA)
| | - Sean Parkin
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, KY 40506 (USA)
| | - Edith C Glazer
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, KY 40506 (USA).
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18
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Nagasawa K, Ma Y, Iida K, Nakamura T, Seimiya H, Ohtake T. Design, Synthesis and Evaluation of an L-Dopa-Derived Macrocyclic Hexaoxazole (6otd) as a G-Quadruplex-Selective Ligand. HETEROCYCLES 2016. [DOI: 10.3987/com-15-13383] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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19
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Dang DT, Phan AT. Development of Fluorescent Protein Probes Specific for Parallel DNA and RNA G-Quadruplexes. Chembiochem 2015; 17:42-5. [DOI: 10.1002/cbic.201500503] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Indexed: 12/16/2022]
Affiliation(s)
- Dung Thanh Dang
- School of Physical and Mathematical Sciences; Nanyang Technological University; 21 Nanyang Link Singapore 637371 Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences; Nanyang Technological University; 21 Nanyang Link Singapore 637371 Singapore
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20
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Lu YJ, Deng Q, Hu DP, Wang ZY, Huang BH, Du ZY, Fang YX, Wong WL, Zhang K, Chow CF. A molecular fluorescent dye for specific staining and imaging of RNA in live cells: a novel ligand integration from classical thiazole orange and styryl compounds. Chem Commun (Camb) 2015; 51:15241-4. [PMID: 26329127 DOI: 10.1039/c5cc05551b] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A new RNA-selective fluorescent dye integrated with a thiazole orange and a p-(methylthio)styryl moiety shows better nucleolus RNA staining and imaging performance in live cells than the commercial stains. It also exhibits excellent photostability, cell tolerance, and counterstain compatibility with 4',6-diamidino-2-phenylindole for specific RNA-DNA colocalization in bioassays.
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Affiliation(s)
- Yu-Jing Lu
- Institute of Natural Medicine and Green Chemistry, School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou 510006, P. R. China.
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21
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Tera M, Hirokawa T, Okabe S, Sugahara K, Seimiya H, Shimamoto K. Design and synthesis of a berberine dimer: a fluorescent ligand with high affinity towards G-quadruplexes. Chemistry 2015; 21:14519-28. [PMID: 26272465 DOI: 10.1002/chem.201501693] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Indexed: 12/20/2022]
Abstract
G-quadruplexes (G4) are thought to be important factors for telomerase inhibition and transcriptional/translational modulations. Bioinformatic analyses imply that the human genome and mRNA contain a multitude of G4-forming sequences; however, their analysis requires selective and detectable ligands. Given that two molecules of fluorescent berberine (BBR) coordinate to telomeric G4 in their co-crystals, we designed hydrocarbon-linked BBR-analogue dimers because we expected the alignment of two BBR chromophores would avoid Watson-Crick base pair intercalation, which should result in high selectivity towards G4. An alkene-cis-C2 BBR dimer showed the highest affinity (Kd ≤2.6 nM) and selectivity (ca. 900-fold vs. duplex) towards G4. The intrinsic "light-up" fluorescence properties of this BBR dimer, derived from its conformational switching by G4, allowed a selective visualization of various G4 in the gel without using additional bulky fluorescence dyes, which, combined with the observed lack of conformational change of the ligand, suggested future applications in in vitro detection systems.
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Affiliation(s)
- Masayuki Tera
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seikacho, Soraku, Kyoto 619-0284 (Japan).
| | - Takatsugu Hirokawa
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ward, Tokyo, 135-0064 (Japan)
| | - Sachiko Okabe
- Division of Molecular Biotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ward, Tokyo, 135-8550 (Japan)
| | - Kohtaro Sugahara
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seikacho, Soraku, Kyoto 619-0284 (Japan)
| | - Hiroyuki Seimiya
- Division of Molecular Biotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ward, Tokyo, 135-8550 (Japan)
| | - Keiko Shimamoto
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seikacho, Soraku, Kyoto 619-0284 (Japan)
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22
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Hsu YL, Nandakumar M, Lai HY, Chou TC, Chu CY, Lin CH, Lo LC. Development of Activity-Based Probes for Imaging Human α-l-Fucosidases in Cells. J Org Chem 2015; 80:8458-63. [DOI: 10.1021/acs.joc.5b01204] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yu-Ling Hsu
- Department
of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Manjula Nandakumar
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Chemical
Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, No.128, Academia Road Section 2, Nan-Kang, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Hsin-Yi Lai
- Department
of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Tzyy-Chao Chou
- Department
of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Chi-Yuan Chu
- Department
of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Chun-Hung Lin
- Department
of Chemistry, National Taiwan University, Taipei 10617, Taiwan
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Chemical
Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, No.128, Academia Road Section 2, Nan-Kang, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Lee-Chiang Lo
- Department
of Chemistry, National Taiwan University, Taipei 10617, Taiwan
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23
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Das RN, Debnath M, Gaurav A, Dash J. Environment-Sensitive Probes Containing a 2,6-Diethynylpyridine Motif for Fluorescence Turn-On Detection and Induction of Nanoarchitectures of Human Telomeric Quadruplex. Chemistry 2014; 20:16688-93. [DOI: 10.1002/chem.201404795] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Indexed: 12/24/2022]
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24
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Ni Y, Zeng L, Kang NY, Huang KW, Wang L, Zeng Z, Chang YT, Wu J. meso-Ester and carboxylic acid substituted BODIPYs with far-red and near-infrared emission for bioimaging applications. Chemistry 2014; 20:2301-10. [PMID: 24515608 DOI: 10.1002/chem.201303868] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Indexed: 12/26/2022]
Abstract
A series of meso-ester-substituted BODIPY derivatives 1-6 are synthesized and characterized. In particular, dyes functionalized with oligo(ethylene glycol) ether styryl or naphthalene vinylene groups at the α positions of the BODIPY core (3-6) become partially soluble in water, and their absorptions and emissions are located in the far-red or near-infrared region. Three synthetic approaches are attempted to access the meso-carboxylic acid (COOH)-substituted BODIPYs 7 and 8 from the meso-ester-substituted BODIPYs. Two feasible synthetic routes are developed successfully, including one short route with only three steps. The meso-COOH-substituted BODIPY 7 is completely soluble in pure water, and its fluorescence maximum reaches around 650 nm with a fluorescence quantum yield of up to 15 %. Time-dependent density functional theory calculations are conducted to understand the structure-optical properties relationship, and it is revealed that the Stokes shift is dependent mainly on the geometric change from the ground state to the first excited singlet state. Furthermore, cell staining tests demonstrate that the meso-ester-substituted BODIPYs (1 and 3-6) and one of the meso-COOH-substituted BODIPYs (8) are very membrane-permeable. These features make these meso-ester- and meso-COOH-substituted BODIPY dyes attractive for bioimaging and biolabeling applications in living cells.
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Affiliation(s)
- Yong Ni
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543 (Singapore), Fax: (+65) 6779-1691; NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, 02-01, Singapore 117411 (Singapore)
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25
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Naud-Martin D, Martin-Benlloch X, Poyer F, Mahuteau-Betzer F, Teulade-Fichou MP. Acri-2,7-Py, a bright red-emitting DNA probe identified through screening of a distyryl dye library. Biotechnol J 2014; 9:301-10. [DOI: 10.1002/biot.201300197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 10/17/2013] [Accepted: 12/09/2013] [Indexed: 12/23/2022]
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26
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Maji B, Bhattacharya S. Advances in the molecular design of potential anticancer agents via targeting of human telomeric DNA. Chem Commun (Camb) 2014; 50:6422-38. [DOI: 10.1039/c4cc00611a] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Telomerase is an attractive drug target to develop new generation drugs against cancer.
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Affiliation(s)
- Basudeb Maji
- Department of Organic Chemistry
- Indian Institute of Science
- Bangalore-560012, India
| | - Santanu Bhattacharya
- Department of Organic Chemistry
- Indian Institute of Science
- Bangalore-560012, India
- Chemical Biology Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
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27
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Shibata K, Yoshida M, Takahashi T, Takagi M, Shin-ya K, Doi T. Synthesis of Heptaoxazole Macrocyclic Analogues of Telomestatin and Evaluation of Their Telomerase Inhibitory Activities. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2013. [DOI: 10.1246/bcsj.20130198] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kazuaki Shibata
- Department of Applied Chemistry, Tokyo Institute of Technology
| | | | | | - Motoki Takagi
- Biomedicinal Information Research Center (BIRC), Japan Biological Informatics Consortium (JBIC)
| | - Kazuo Shin-ya
- National Institute of Advanced Industrial Science and Technology (AIST)
| | - Takayuki Doi
- Graduate School of Pharmaceutical Sciences, Tohoku University
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28
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Iida K, Nagasawa K. Macrocyclic Polyoxazoles as G-Quadruplex Ligands. CHEM REC 2013; 13:539-48. [DOI: 10.1002/tcr.201300015] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Indexed: 01/11/2023]
Affiliation(s)
- Keisuke Iida
- Tokyo University of Agriculture and Technology; 2-24-16 Naka-cho Koganei Tokyo 184-8588 Japan
| | - Kazuo Nagasawa
- Tokyo University of Agriculture and Technology; 2-24-16 Naka-cho Koganei Tokyo 184-8588 Japan
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29
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Iida K, Nakamura T, Yoshida W, Tera M, Nakabayashi K, Hata K, Ikebukuro K, Nagasawa K. Fluorescent-ligand-mediated screening of G-quadruplex structures using a DNA microarray. Angew Chem Int Ed Engl 2013; 52:12052-5. [PMID: 24150845 DOI: 10.1002/anie.201305366] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 09/10/2013] [Indexed: 01/13/2023]
Affiliation(s)
- Keisuke Iida
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei city, 184-8588 Tokyo (Japan)
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30
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Iida K, Nakamura T, Yoshida W, Tera M, Nakabayashi K, Hata K, Ikebukuro K, Nagasawa K. Fluorescent-Ligand-Mediated Screening of G-Quadruplex Structures Using a DNA Microarray. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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31
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Savory N, Takahashi Y, Tsukakoshi K, Hasegawa H, Takase M, Abe K, Yoshida W, Ferri S, Kumazawa S, Sode K, Ikebukuro K. Simultaneous improvement of specificity and affinity of aptamers against Streptococcus mutans by in silico maturation for biosensor development. Biotechnol Bioeng 2013; 111:454-61. [PMID: 24018905 DOI: 10.1002/bit.25111] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Revised: 08/27/2013] [Accepted: 09/03/2013] [Indexed: 01/23/2023]
Abstract
In silico evolution with an in vitro system can facilitate the development of functional aptamers with high specificity and affinity. Although a general technique known as systematic evolution of ligand by exponential enrichment (SELEX) is an efficient method for aptamer selection, it sometimes fails to identify aptamers with sufficient binding properties. We have previously developed in silico maturation (ISM) to improve functions of aptamers based on genetic algorithms. ISM represents an intelligent exploitation of a random search within a defined sequence space to optimize aptamer sequences and improve their function of interest. Here we demonstrated a successful application of ISM of aptamers to simultaneously improve specificity and affinity for Streptococcus mutans with discovery of a core sequence, which was required to form a polymerized guanine quadruplex structure for target binding. We applied ISM to aptamers selected by whole-cell SELEX and identified an aptamer with up to 16-fold improvement in affinity compared to its parent aptamers, and specificity was increased to show 12-fold more binding to S. mutans than to Lactobacillus acidophilus. Furthermore, we demonstrated a specific flow-through detection of S. mutans at a concentration range of 1 × 10(5) -10(8) CFU/mL using the evolved aptamer immobilized on gold colloids.
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Affiliation(s)
- Nasa Savory
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
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32
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Iida K, Majima S, Nakamura T, Seimiya H, Nagasawa K. Evaluation of the interaction between long telomeric DNA and macrocyclic hexaoxazole (6OTD) dimer of a G-quadruplex ligand. Molecules 2013; 18:4328-41. [PMID: 23584054 PMCID: PMC6269967 DOI: 10.3390/molecules18044328] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 04/02/2013] [Accepted: 04/09/2013] [Indexed: 11/19/2022] Open
Abstract
Macrocyclic hexaoxazole dimer of L2H2-6OTD-dimer (3) was newly synthesized as a telomeric G-quadruplex (G4) ligand, and interaction with long telomeric DNAs telo48, 72, and 96 was evaluated by means of electrophoresis mobility shift assay, CD spectra analysis, and CD melting experiments. The L2H2-6OTD-dimer (3) interacted with the long telomeric DNAs by inducing anti-parallel type G4 structure of each unit of 24 bases, i.e., (TTAGGG)₄ sequences. Dimer 3 stabilizes long telomeric DNAs more efficiently than the corresponding monomer of L2H2-6OTD (2). It showed potent inhibitory activity against telomerase, with an IC₅₀ value of 7.5 nm.
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Affiliation(s)
- Keisuke Iida
- Faculty of Technology, Tokyo University of Agriculture and Technology (TUAT), 2-24-16 Naka-cho, Koganei-shi, Tokyo 185-0031, Japan
| | - Satoki Majima
- Faculty of Technology, Tokyo University of Agriculture and Technology (TUAT), 2-24-16 Naka-cho, Koganei-shi, Tokyo 185-0031, Japan
| | - Takahiro Nakamura
- Faculty of Technology, Tokyo University of Agriculture and Technology (TUAT), 2-24-16 Naka-cho, Koganei-shi, Tokyo 185-0031, Japan
| | - Hiroyuki Seimiya
- Cancer Chemotherapy Center, Japanese Foundation for Cancer Research (JFCR), 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Kazuo Nagasawa
- Faculty of Technology, Tokyo University of Agriculture and Technology (TUAT), 2-24-16 Naka-cho, Koganei-shi, Tokyo 185-0031, Japan
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33
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Vummidi BR, Alzeer J, Luedtke NW. Fluorescent Probes for G-Quadruplex Structures. Chembiochem 2013; 14:540-58. [DOI: 10.1002/cbic.201200612] [Citation(s) in RCA: 197] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Indexed: 12/19/2022]
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34
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Nikan M, Di Antonio M, Abecassis K, McLuckie K, Balasubramanian S. An acetylene-bridged 6,8-purine dimer as a fluorescent switch-on probe for parallel G-quadruplexes. Angew Chem Int Ed Engl 2013; 52:1428-31. [PMID: 23238938 PMCID: PMC3652027 DOI: 10.1002/anie.201207075] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 11/15/2012] [Indexed: 11/14/2022]
Affiliation(s)
- Mehran Nikan
- Department of Chemistry, The University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK)
- Cambridge Research Institute, Cancer Research UK, Li Ka Shing CenterCambridge, CB2 0RE (UK)
| | - Marco Di Antonio
- Department of Chemistry, The University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK)
| | - Keren Abecassis
- Department of Chemistry, The University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK)
| | - Keith McLuckie
- Cambridge Research Institute, Cancer Research UK, Li Ka Shing CenterCambridge, CB2 0RE (UK)
| | - Shankar Balasubramanian
- Department of Chemistry, The University of CambridgeLensfield Road, Cambridge, CB2 1EW (UK)
- Cambridge Research Institute, Cancer Research UK, Li Ka Shing CenterCambridge, CB2 0RE (UK)
- School of Clinical Medicine, The University of Cambridge, Addenbrooke's HospitalHills Road, Cambridge, CB2 0SP (UK)
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35
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Xie X, Choi B, Largy E, Guillot R, Granzhan A, Teulade-Fichou MP. Asymmetric Distyrylpyridinium Dyes as Red-Emitting Fluorescent Probes for Quadruplex DNA. Chemistry 2013; 19:1214-26. [DOI: 10.1002/chem.201203710] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Indexed: 11/06/2022]
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36
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Iida K, Tsubouchi G, Nakamura T, Majima S, Seimiya H, Nagasawa K. Interaction of long telomeric DNAs with macrocyclic hexaoxazole as a G-quadruplex ligand. MEDCHEMCOMM 2013. [DOI: 10.1039/c2md20234d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interactions of long telomeric DNAs, which mimic telomeres in living cells, with a macrocyclic hexaoxazole ligand L2H2-6OTD (2) were investigated by means of electrophoresis mobility shift assay, circular dichroism (CD) titration analysis, and DNA melting measurements.
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Affiliation(s)
- Keisuke Iida
- Faculty of Technology
- Tokyo University of Agriculture and Technology (TUAT)
- Koganei-shi
- Japan
| | - Gen Tsubouchi
- Faculty of Technology
- Tokyo University of Agriculture and Technology (TUAT)
- Koganei-shi
- Japan
| | - Takahiro Nakamura
- Faculty of Technology
- Tokyo University of Agriculture and Technology (TUAT)
- Koganei-shi
- Japan
| | - Satoki Majima
- Faculty of Technology
- Tokyo University of Agriculture and Technology (TUAT)
- Koganei-shi
- Japan
| | - Hiroyuki Seimiya
- Cancer Chemotherapy Center
- Japanese Foundation for Cancer Research (JFCR)
- Koto-ku
- Japan
| | - Kazuo Nagasawa
- Faculty of Technology
- Tokyo University of Agriculture and Technology (TUAT)
- Koganei-shi
- Japan
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37
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Chung CYS, Yam VWW. Selective label-free detection of G-quadruplex structure of human telomere by emission spectral changes in visible-and-NIR region under physiological condition through the FRET of a two-component PPE-SO3−–Pt(ii) complex ensemble with Pt⋯Pt, electrostatic and π–π interactions. Chem Sci 2013. [DOI: 10.1039/c2sc20897k] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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38
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Nikan M, Di Antonio M, Abecassis K, McLuckie K, Balasubramanian S. An Acetylene-Bridged 6,8-Purine Dimer as a Fluorescent Switch-On Probe for Parallel G-Quadruplexes. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201207075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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39
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Petenzi M, Verga D, Largy E, Hamon F, Doria F, Teulade-Fichou MP, Guédin A, Mergny JL, Mella M, Freccero M. Cationic pentaheteroaryls as selective G-quadruplex ligands by solvent-free microwave-assisted synthesis. Chemistry 2012; 18:14487-96. [PMID: 22996572 DOI: 10.1002/chem.201202097] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Indexed: 12/15/2022]
Abstract
We report herein a solvent-free and microwaved-assisted synthesis of several water soluble acyclic pentaheteroaryls containing 1,2,4-oxadiazole moieties (1-7). Their binding interactions with DNA quadruplex structures were thoroughly investigated by FRET melting, fluorescent intercalator displacement assay (G4-FID) and CD spectroscopy. Among the G-quadruplexes considered, attention was focused on telomeric repeats together with the proto-oncogenic c-kit sequences and the c-myc oncogene promoter. Compound 1, and to a lesser extent 2 and 5, preferentially stabilise an antiparallel structure of the telomeric DNA motif, and exhibit an opposite binding behaviour to structurally related polyoxazole (TOxaPy), and do not bind duplex DNA. The efficiency and selectivity of the binding process was remarkably controlled by the structure of the solubilising moieties.
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Affiliation(s)
- Michele Petenzi
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli 10, 27100 Pavia, Italy
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40
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Hayakawa I, Ikedo A, Chinen T, Usui T, Kigoshi H. Design, synthesis, and biological evaluation of the analogues of glaziovianin A, a potent antitumor isoflavone. Bioorg Med Chem 2012; 20:5745-56. [PMID: 22921744 DOI: 10.1016/j.bmc.2012.08.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 08/07/2012] [Accepted: 08/08/2012] [Indexed: 02/08/2023]
Abstract
Various analogues of glaziovianin A, an antitumor isoflavone, were synthesized, and their biological activities were evaluated. O(7)-modified glaziovianin A showed strong cytotoxicity against HeLa S(3) cells. Compared to glaziovianin A, the O(7)-benzyl and O(7)-propargyl analogues were more cytotoxic against HeLa S(3) cells and more potent M-phase inhibitors. Furthermore, O(7)-modified molecular probes of glaziovianin A were synthesized for biological studies.
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Affiliation(s)
- Ichiro Hayakawa
- Department of Chemistry, Graduate School of Pure and Applied Sciences, University of Tsukuba, Tennodai, Tsukuba 305-8571, Japan.
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41
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Nakamura T, Iida K, Tera M, Shin-ya K, Seimiya H, Nagasawa K. A caged ligand for a telomeric G-quadruplex. Chembiochem 2012; 13:774-7. [PMID: 22438312 DOI: 10.1002/cbic.201200013] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Indexed: 12/31/2022]
Affiliation(s)
- Takahiro Nakamura
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho Koganei, Tokyo 184-8588, Japan
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Largy E, Hamon F, Teulade-Fichou MP. A streptavidin paramagnetic-particle based competition assay for the evaluation of the optical selectivity of quadruplex nucleic acid fluorescent probes. Methods 2012; 57:129-37. [PMID: 22406492 DOI: 10.1016/j.ymeth.2012.02.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 02/18/2012] [Accepted: 02/20/2012] [Indexed: 01/29/2023] Open
Abstract
Although quadruplex nucleic acids are thought to be involved in many biological processes, they are massively overwhelmed by duplex DNA in the cell. Small molecules, able to probe quadruplex nucleic acids with high optical selectivity, could possibly achieve the visualization of these processes. The aim of the method described herein is to evaluate quickly the optical selectivity of quadruplex nucleic acid probes, in isothermal conditions, using widely available materials, small quantities of oligonucleotides and virtually any kind and quantity of biological competitor. The assay relies on the use of streptavidin-coated paramagnetic particles and biotinylated quadruplex forming oligonucleotides, allowing a quick and easy separation of the quadruplex target from the competitor. In the present study, two quadruplex nucleic acids (the DNA and RNA human telomeric repeats) have been used as targets while a duplex DNA oligonucleotide, total DNA, total RNA, another quadruplex nucleic acid and a protein have been used as competitors. The optical selectivity of various probes, displaying different photophysical properties and binding selectivities, has been successfully examined, allowing the identification of a best candidate for further cell microscopy experiments. This assay allows a quick and reliable assessment of the labeling properties of a quadruplex binder in cellular environment conditions. It is an interesting alternative to gel electrophoresis experiments since it is performed in solution, has a well-resolved separation system and allows easy quantifications.
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Affiliation(s)
- Eric Largy
- UMR 176 - Synthèse et Vectorisation de Biomolécules, Institut Curie, Bât. 110-112, Université Paris-Sud, 91405 Orsay, France.
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Visualizing the Quadruplex: From Fluorescent Ligands to Light-Up Probes. Top Curr Chem (Cham) 2012; 330:111-77. [DOI: 10.1007/128_2012_346] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Hamon F, Largy E, Guédin-Beaurepaire A, Rouchon-Dagois M, Sidibe A, Monchaud D, Mergny JL, Riou JF, Nguyen CH, Teulade-Fichou MP. An Acyclic Oligoheteroaryle That Discriminates Strongly between Diverse G-Quadruplex Topologies. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103422] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Hamon F, Largy E, Guédin-Beaurepaire A, Rouchon-Dagois M, Sidibe A, Monchaud D, Mergny JL, Riou JF, Nguyen CH, Teulade-Fichou MP. An Acyclic Oligoheteroaryle That Discriminates Strongly between Diverse G-Quadruplex Topologies. Angew Chem Int Ed Engl 2011; 50:8745-9. [DOI: 10.1002/anie.201103422] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Indexed: 11/09/2022]
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Lu YJ, Yan SC, Chan FY, Zou L, Chung WH, Wong WL, Qiu B, Sun N, Chan PH, Huang ZS, Gu LQ, Wong KY. Benzothiazole-substituted benzofuroquinolinium dye: a selective switch-on fluorescent probe for G-quadruplex. Chem Commun (Camb) 2011; 47:4971-3. [PMID: 21431154 DOI: 10.1039/c1cc00020a] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A new switch-on fluorescent probe containing the natural product cryptolepine analogue benzofuroquinolinium moiety (binding scaffold) and a benzothiazole moiety (signalling unit) shows a remarkable fluorescence enhancement selective for the G-quadruplex nucleic acid structure. Binding studies revealed that the highly selective response of the fluorescent probe arises from end-stack binding to G-quadruplex.
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Affiliation(s)
- Yu-Jing Lu
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
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Tera M, Iida K, Shin-ya K, Nagasawa K. Development of Macrocyclic Polyoxazoles and Evaluation of Their G-Quadruplex Stabilizing Activities. J SYN ORG CHEM JPN 2011. [DOI: 10.5059/yukigoseikyokaishi.69.129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Xu Y. Chemistry in human telomere biology: structure, function and targeting of telomere DNA/RNA. Chem Soc Rev 2011; 40:2719-40. [DOI: 10.1039/c0cs00134a] [Citation(s) in RCA: 249] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Nagasawa K, Majima S, Tera M, Iida K, Shin-ya K. Design and Synthesis of Telomestatin Derivatives Containing Methyl Oxazole and Their G-Quadruplex Stabilizing Activities. HETEROCYCLES 2010. [DOI: 10.3987/com-10-s(e)85] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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