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Shiekh S, Kodikara SG, Balci H. Structure, Topology, and Stability of Multiple G-quadruplexes in Long Telomeric Overhangs. J Mol Biol 2024; 436:168205. [PMID: 37481156 PMCID: PMC10799177 DOI: 10.1016/j.jmb.2023.168205] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/05/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023]
Abstract
Telomeres and their single stranded overhangs gradually shorten with successive cell divisions, as part of the natural aging process, but can be elongated by telomerase, a nucleoprotein complex which is activated in the majority of cancers. This prominent implication in cancer and aging has made the repetitive telomeric sequences (TTAGGG repeats) and the G-quadruplex structures that form in their overhangs the focus of intense research in the past several decades. However, until recently most in vitro efforts to understand the structure, stability, dynamics, and interactions of telomeric overhangs had been focused on short sequences that are not representative of longer sequences encountered in a physiological setting. In this review, we will provide a broad perspective about telomeres and associated factors, and introduce the agents and structural characteristics involved in organizing, maintaining, and protecting telomeric DNA. We will also present a summary of recent research performed on long telomeric sequences, nominally defined as those that can form two or more tandem G-quadruplexes, i.e., which contain eight or more TTAGGG repeats. Results of experimental studies using a broad array of experimental tools, in addition to recent computational efforts will be discussed, particularly in terms of their implications for the stability, folding topology, and compactness of the tandem G-quadruplexes that form in long telomeric overhangs.
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Affiliation(s)
- Sajad Shiekh
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | | | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH 44242, USA.
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2
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Sasaki S, Ma Y, Hirokawa T, Ikebukuro K, Tera M, Nagasawa K. Regulation of thrombin activity by ligand-induced topological alteration in a thrombin-binding aptamer. Chem Commun (Camb) 2023. [PMID: 37377065 DOI: 10.1039/d3cc02308g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Thrombin-binding aptamer (TBA), which forms a G-quadruplex (G4) structure with anti-parallel topology, interacts with thrombin to inhibit its enzymatic activity. Here we show that the G4-topology-altering ligand L2H2-2M2EA-6LCO (6LCO) changes the anti-parallel topology of TBA G4 to the parallel topology, thereby abrogating the thrombin-inhibitory activity of TBA. This finding suggests that G4 ligands that alter topology may be promising drug candidates for diseases involving G4-binding proteins.
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Affiliation(s)
- Shogo Sasaki
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Yue Ma
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
- Research Core Center, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Takatsugu Hirokawa
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, 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.
| | - Masayuki Tera
- 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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3
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Iwasaki Y, Ookuro Y, Iida K, Nagasawa K, Yoshida W. Destabilization of DNA and RNA G-quadruplex structures formed by GGA repeat due to N 6-methyladenine modification. Biochem Biophys Res Commun 2022; 597:134-139. [PMID: 35144176 DOI: 10.1016/j.bbrc.2022.01.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 01/30/2022] [Indexed: 11/22/2022]
Abstract
N6-methyladenine (m6A) is the most abundant RNA modification in eukaryotic RNA. Further, m6A has been identified in the genomic DNA of both eukaryotes and prokaryotes. The G-quadruplex (G4) structure is a non-canonical nucleic acid structure formed by the stacking of G:G:G:G tetrads. In this study, we evaluated the effect of m6A modifications on G4 structures formed by GGA repeat oligonucleotides, d(GGA)8, d(GGA)4, and r(GGA)4. The d(GGA)8 forms an intramolecular tetrad:heptad:heptad:tetrad G4 structure, while d(GGA)4 forms a dimerized intermolecular tetrad:heptad:heptad:tetrad G4 structure. r(GGA)4 forms a dimerized intermolecular tetrad:hexad:hexad:tetrad G4 structure. Circular dichroism melting analysis demonstrated that (1) m6A modifications destabilized the G4 structure formed by d(GGA)8, (2) m6A modification at A3 disrupted the G4 structure formed by d(GGA)4, and (3) m6A modification at A3 destabilized the G4 structure formed by r(GGA)4. m6A modifications may be involved in controlling G4 structure formation to regulate biological functions.
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Affiliation(s)
- Yuka Iwasaki
- Graduate School of Bionics, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo, 192-0982, Japan
| | - Yurino Ookuro
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo, 192-0982, Japan
| | - Keisuke Iida
- Department of Chemistry, Chiba University, 1-33 Yayoi, Inage, Chiba, 263-8522, 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
| | - Wataru Yoshida
- Graduate School of Bionics, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo, 192-0982, Japan; School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo, 192-0982, Japan.
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4
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Mendes E, Aljnadi IM, Bahls B, Victor BL, Paulo A. Major Achievements in the Design of Quadruplex-Interactive Small Molecules. Pharmaceuticals (Basel) 2022; 15:300. [PMID: 35337098 PMCID: PMC8953082 DOI: 10.3390/ph15030300] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/17/2022] Open
Abstract
Organic small molecules that can recognize and bind to G-quadruplex and i-Motif nucleic acids have great potential as selective drugs or as tools in drug target discovery programs, or even in the development of nanodevices for medical diagnosis. Hundreds of quadruplex-interactive small molecules have been reported, and the challenges in their design vary with the intended application. Herein, we survey the major achievements on the therapeutic potential of such quadruplex ligands, their mode of binding, effects upon interaction with quadruplexes, and consider the opportunities and challenges for their exploitation in drug discovery.
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Affiliation(s)
- Eduarda Mendes
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
| | - Israa M. Aljnadi
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Bárbara Bahls
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Bruno L. Victor
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Alexandra Paulo
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
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5
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Pal S, Fatma K, Ravichandiran V, Dash J. Triazolyl Dibenzo[ a,c]phenazines Stabilize Telomeric G-quadruplex and Inhibit Telomerase. ASIAN J ORG CHEM 2021; 10:2921-2926. [PMID: 37823002 PMCID: PMC7614908 DOI: 10.1002/ajoc.202100468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Indexed: 11/10/2022]
Abstract
We herein report the synthesis and biophysical evaluation of triazolyl dibenzo[a,c]phenazine derivatives as a novel class of G-quadruplex ligands. The aromatic core facilitates π-π interaction and the flexible, protonatable side chains interact with the phosphate backbone of DNA via electrostatic interactions. Förster resonance energy transfer (FRET) melting assay and isothermal titration calorimetry (ITC) studies suggest that these ligands show binding preference for the hTELO G-quadruplex over G-quadruplexes found in the promoter region of various oncogenes and duplex DNA. The in vitro telomeric repeat amplification protocol (Q-TRAP) assay reveals that these ligands reduce telomerase activity in cancer cells.
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Affiliation(s)
- Sarmistha Pal
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
- Department of Medicinal Chemistry, NIPER-KOLKATA, Chunilal Bhawan (Adjacent to BCPL), 168, Maniktala Main Road P.O. Bengal Chemicals, P.S. Phoolbagan, Kolkata – 700054, West Bengal
| | - Khushnood Fatma
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Velayutham Ravichandiran
- Department of Medicinal Chemistry, NIPER-KOLKATA, Chunilal Bhawan (Adjacent to BCPL), 168, Maniktala Main Road P.O. Bengal Chemicals, P.S. Phoolbagan, Kolkata – 700054, West Bengal
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
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6
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Ishikawa R, Yasuda M, Sasaki S, Ma Y, Nagasawa K, Tera M. Stabilization of telomeric G-quadruplex by ligand binding increases susceptibility to S1 nuclease. Chem Commun (Camb) 2021; 57:7236-7239. [PMID: 34263271 DOI: 10.1039/d1cc03294a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The extent of thermodynamic stabilization of telomeric G-quadruplex (G4) by isomers of G4 ligand L2H2-6OTD, a telomestatin analog, is inversely correlated with susceptibility to S1 nuclease. L2H2-6OTD facilitated the S1 nuclease activities through the base flipping in G4, unlike the conventional role of G4 ligands which inhibit the protein binding to DNA/RNA upon ligand interactions.
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Affiliation(s)
- Ryo Ishikawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Mizuho Yasuda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Shogo Sasaki
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Yue Ma
- Institute of Global Innovation Research, 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.
| | - Masayuki Tera
- 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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7
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Wang Y, Li C, Hao X, Wang L, Ma X, Jin R, Kang C, Gao L. Hydrogen-bond-driven dimers of naphthyridine derivatives for selective identification of DNA G-quadruplexes. Org Biomol Chem 2021; 19:4768-4774. [PMID: 33978052 DOI: 10.1039/d1ob00651g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
G-quadruplex (GQ) ligands as potential anti-cancer drugs have received extensive attention. Large aromatic systems are usually considered in the design of the ligands to improve the binding with GQs, which are typically constructed by the combination of small modules with covalent bonds. In this study, we presented a non-covalent bond approach to construct GQ ligands with an extended planar structure. The ligands were stable dimers assembled through quadruplex intermolecular hydrogen bonds between two molecules of naphthyridine derivatives. Spectroscopic analyses showed that dimeric ligands could stabilize GQs with an increase of the melting temperature up to 12 °C and induced conformational conversion of hybrid GQs. Confocal fluorescence microscopy confirmed the enrichment of naphthyridine ligands in the nucleus. The ligands showed moderate cytotoxicity against HeLa cells with an IC50 value of 7.5 μg mL-1 and effectively induced growth inhibition and apoptosis in HeLa cells. These results confirmed the feasibility of the quick building of GQ ligands through intermolecular interactions of simple molecules that are easily obtained during synthesis, which is helpful for GQ ligand design and quick establishment of a ligand library through the self-assembly of easily available molecular components.
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Affiliation(s)
- Yu Wang
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. and University of Science and Technology of China, Hefei 230026, China
| | - Chunjie Li
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
| | - Xueyu Hao
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. and University of Science and Technology of China, Hefei 230026, China
| | - Liangpeng Wang
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
| | - Xiaoye Ma
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
| | - Rizhe Jin
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
| | - Chuanqing Kang
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China. and University of Science and Technology of China, Hefei 230026, China
| | - Lianxun Gao
- Laboratory of Polymer Composite and Engineering, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
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8
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Sasaki S, Ma Y, Ishizuka T, Bao HL, Hirokawa T, Xu Y, Tera M, Nagasawa K. Linear consecutive hexaoxazoles as G4 ligands inducing chair-type anti-parallel topology of a telomeric G-quadruplex. RSC Adv 2020; 10:43319-43323. [PMID: 35519695 PMCID: PMC9058415 DOI: 10.1039/d0ra09413g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022] Open
Abstract
G-quadruplex structures (G4s) in guanine-rich regions of DNA play critical roles in various biological phenomena, including replication, translation, and gene expression. There are three types of G4 topology, i.e., parallel, anti-parallel, and hybrid, and ligands that selectively interact with or stabilize a specific topology have been extensively explored to enable studies of topology-related functions. Here, we describe the synthesis of a new series of G4 ligands based on 6LCOs (6-linear consecutive oxazoles), i.e., L2H2-2M2EA-6LCO (2), L2A2-2M2EAc-6LCO (3), and L2G2-2M2EG-6LCO (4), which bear four aminoalkyl, acetamidealkyl, and guanidinylalkyl side chains, respectively. Among them, ligand 2 stabilized telomeric G4 and induced anti-parallel topology independently of the presence of cations. The anti-parallel topology induced by 2 was identified as chair-type by means of 19F NMR spectroscopy and fluorescence experiments with 2-aminopurine-labeled DNA.
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Affiliation(s)
- Shogo Sasaki
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology 2-24-16 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Yue Ma
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology 2-24-16 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Takumi Ishizuka
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazak 5200 Kihara, Kiyotake Miyazaki 889-1692 Japan
| | - Hong-Liang Bao
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazak 5200 Kihara, Kiyotake Miyazaki 889-1692 Japan
| | - Takatsugu Hirokawa
- Transborder Medical Research Center, University of Tsukuba 1-1-1 Tennodai Tsukuba, 305-8575 Japan
- Division of Biomedical Science, University of Tsukuba 1-1-1 Tennodai Tsukuba, 305-8575 Japan
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology 2-4-7 Aomi, Koto-ward Tokyo 135-0064 Japan
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazak 5200 Kihara, Kiyotake Miyazaki 889-1692 Japan
| | - Masayuki Tera
- 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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9
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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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10
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Ma Y, Iida K, Nagasawa K. Topologies of G-quadruplex: Biological functions and regulation by ligands. Biochem Biophys Res Commun 2020; 531:3-17. [PMID: 31948752 DOI: 10.1016/j.bbrc.2019.12.103] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 12/20/2019] [Accepted: 12/28/2019] [Indexed: 01/06/2023]
Abstract
G-Quadruplex (G4) is one of the higher-order structures occurring in guanine-rich sequences of nucleic acids, and plays critical roles in biological processes. The G4-forming sequences can generate three kinds of topologies, i.e., parallel, anti-parallel, and hybrid, and these polymorphic structures have an important influence on G4-related biological functions. In this review, we highlight variety of structures generated by G4s containing various sequences and under diverse conditions. We also discuss the G4 ligands which induce specific topologies and/or conversion between different topologies.
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Affiliation(s)
- Yue Ma
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Japan.
| | - Keisuke Iida
- Department of Chemistry, Chiba University, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Japan.
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11
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Gyawali P, Gc K, Ma Y, Abeysirigunawardena S, Nagasawa K, Balci H. Impact of Small Molecules on Intermolecular G-Quadruplex Formation. Molecules 2019; 24:molecules24081570. [PMID: 31010019 PMCID: PMC6514588 DOI: 10.3390/molecules24081570] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 04/18/2019] [Accepted: 04/19/2019] [Indexed: 11/24/2022] Open
Abstract
We performed single molecule studies to investigate the impact of several prominent small molecules (the oxazole telomestatin derivative L2H2-6OTD, pyridostatin, and Phen-DC3) on intermolecular G-quadruplex (i-GQ) formation between two guanine-rich DNA strands that had 3-GGG repeats in one strand and 1-GGG repeat in the other (3+1 GGG), or 2-GGG repeats in each strand (2+2 GGG). Such structures are not only physiologically significant but have recently found use in various biotechnology applications, ranging from DNA-based wires to chemical sensors. Understanding the extent of stability imparted by small molecules on i-GQ structures, has implications for these applications. The small molecules resulted in different levels of enhancement in i-GQ formation, depending on the small molecule and arrangement of GGG repeats. The largest enhancement we observed was in the 3+1 GGG arrangement, where i-GQ formation increased by an order of magnitude, in the presence of L2H2-6OTD. On the other hand, the enhancement was limited to three-fold with Pyridostatin (PDS) or less for the other small molecules in the 2+2 GGG repeat case. By demonstrating detection of i-GQ formation at the single molecule level, our studies illustrate the feasibility to develop more sensitive sensors that could operate with limited quantities of materials.
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Affiliation(s)
- Prabesh Gyawali
- Department of Physics, Kent State University, Kent, OH 44242, USA.
| | - Keshav Gc
- Department of Chemistry and Biochemistry, 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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12
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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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13
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Ma Y, Iida K, Sasaki S, Hirokawa T, Heddi B, Phan AT, Nagasawa K. Synthesis and Telomeric G-Quadruplex-Stabilizing Ability of Macrocyclic Hexaoxazoles Bearing Three Side Chains. Molecules 2019; 24:molecules24020263. [PMID: 30642002 PMCID: PMC6358838 DOI: 10.3390/molecules24020263] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/04/2019] [Accepted: 01/10/2019] [Indexed: 01/02/2023] Open
Abstract
G-quadruplexes (G4s), which are structures formed in guanine-rich regions of DNA, are involved in a variety of significant biological functions, and therefore “sequence-dependent” selective G4-stabilizing agents are required as tools to investigate and modulate these functions. Here, we describe the synthesis of a new series of macrocyclic hexaoxazole-type G4 ligand (6OTD) bearing three side chains. One of these ligands, 5b, stabilizes telomeric G4 preferentially over the G4-forming DNA sequences of c-kit and K-ras, due to the interaction of its piperazinylalkyl side chain with the groove of telomeric G4.
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Affiliation(s)
- Yue Ma
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Keisuke Iida
- Department of Chemistry, Chiba University, 1-33 Yayoi, Inage, Chiba 263-8522, Japan.
| | - Shogo Sasaki
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Takatsugu Hirokawa
- Transborder Medical Reserch Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan.
- Division of Biomedical Science, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan.
- 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.
| | - Brahim Heddi
- Laboratoire de Biologie et Pharmacologie appliquée, CNRS UMR 8113, ENS paris-saclay 60 avenue du president Wilson, 94230 Cachan, France.
- Division of Physics and Applied Physics, Nanyang Technological University, Singapore 637371, Singapore.
| | - Anh Tuân Phan
- Division of Physics and Applied Physics, Nanyang Technological University, Singapore 637371, Singapore.
| | - 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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14
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Sedghi Masoud S, Nagasawa K. i-Motif-Binding Ligands and Their Effects on the Structure and Biological Functions of i-Motif. Chem Pharm Bull (Tokyo) 2018; 66:1091-1103. [DOI: 10.1248/cpb.c18-00720] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Shadi Sedghi Masoud
- Department of Life Science and Biotechnology, Faculty of Technology, Tokyo University of Agriculture and Technology
| | - Kazuo Nagasawa
- Department of Life Science and Biotechnology, Faculty of Technology, Tokyo University of Agriculture and Technology
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15
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Sedghi Masoud S, Yamaoki Y, Ma Y, Marchand A, Winnerdy FR, Gabelica V, Phan AT, Katahira M, Nagasawa K. Analysis of Interactions between Telomeric i-Motif DNA and a Cyclic Tetraoxazole Compound. Chembiochem 2018; 19:2268-2272. [PMID: 30160816 DOI: 10.1002/cbic.201800425] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Indexed: 12/31/2022]
Abstract
The interaction of a macrocyclic tetraoxazole compound, L2H2-4OTD (1), with two aminoalkyl side chains and telomeric i-motif, was investigated by means of electrophoretic mobility shift assay, circular dichroism spectroscopy, mass spectrometry and NMR spectroscopy analyses. The results indicate that 1 interacts with the i-motif structure at two preferred binding sites.
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Affiliation(s)
- Shadi Sedghi Masoud
- Department of Life Science and Biotechnology, Faculty of Technology, Tokyo University of Agriculture and Technology, Koganei, Tokyo, 184-8588, Japan
| | - Yudai Yamaoki
- Institute of Advanced Energy, Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Yue Ma
- Department of Life Science and Biotechnology, Faculty of Technology, Tokyo University of Agriculture and Technology, Koganei, Tokyo, 184-8588, Japan
| | - Adrien Marchand
- Université de Bordeaux, INSERM, CNRS, Acides Nucléiques, Régulations Naturelle et Artificielle (ARNA, U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33607, Pessac, France
| | - Fernaldo Richtia Winnerdy
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, SPMS PAP 05-04, 637371, Singapore, Singapore
| | - Valérie Gabelica
- Université de Bordeaux, INSERM, CNRS, Acides Nucléiques, Régulations Naturelle et Artificielle (ARNA, U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33607, Pessac, France
| | - Anh Tuân Phan
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, SPMS PAP 05-04, 637371, Singapore, Singapore
| | - Masato Katahira
- Institute of Advanced Energy, Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Kazuo Nagasawa
- Department of Life Science and Biotechnology, Faculty of Technology, Tokyo University of Agriculture and Technology, Koganei, Tokyo, 184-8588, Japan
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16
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Mustafa G, Chuang CY, Roy WA, Farhath MM, Pokhrel N, Ma Y, Nagasawa K, Antony E, Comstock MJ, Basu S, Balci H. A force sensor that converts fluorescence signal into force measurement utilizing short looped DNA. Biosens Bioelectron 2018; 121:34-40. [PMID: 30195120 DOI: 10.1016/j.bios.2018.08.073] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/13/2018] [Accepted: 08/30/2018] [Indexed: 01/27/2023]
Abstract
A force sensor concept is presented where fluorescence signal is converted into force information via single-molecule Förster resonance energy transfer (smFRET). The basic design of the sensor is a ~100 base pair (bp) long double stranded DNA (dsDNA) that is restricted to a looped conformation by a nucleic acid secondary structure (NAS) that bridges its ends. The looped dsDNA generates a tension across the NAS and unfolds it when the tension is high enough. The FRET efficiency between donor and acceptor (D&A) fluorophores placed across the NAS reports on its folding state. Three dsDNA constructs with different lengths were bridged by a DNA hairpin and KCl was titrated to change the applied force. After these proof-of-principle measurements, one of the dsDNA constructs was used to maintain the G-quadruplex (GQ) construct formed by thrombin binding aptamer (TBA) under tension while it interacted with a destabilizing protein and stabilizing small molecule. The force required to unfold TBA-GQ was independently investigated with high-resolution optical tweezers (OT) measurements that established the relevant force to be a few pN, which is consistent with the force generated by the looped dsDNA. The proposed method is particularly promising as it enables studying NAS, protein, and small molecule interactions using a highly-parallel FRET-based assay while the NAS is kept under an approximately constant force.
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Affiliation(s)
- Golam Mustafa
- Department of Physics, Kent State University, Kent, OH 44242, United States
| | - Cho-Ying Chuang
- Department of Physics, Michigan State University, East Lansing, MI 48824, United States
| | - William A Roy
- Department of Physics, Kent State University, Kent, OH 44242, United States
| | - Mohamed M Farhath
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, United States
| | - Nilisha Pokhrel
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, United States
| | - 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
| | - Edwin Antony
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, United States
| | - Matthew J Comstock
- Department of Physics, Michigan State University, East Lansing, MI 48824, United States
| | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, United States
| | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH 44242, United States.
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17
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Abstract
Guanine-rich nucleic acid sequences able to form four-stranded structures (G-quadruplexes, G4) play key cellular regulatory roles and are considered as promising drug targets for anticancer therapy. On the basis of the organization of their structural elements, G4 ligands can be divided into three major families: one, fused heteroaromatic polycyclic systems; two, macrocycles; three, modular aromatic compounds. The design of modular G4 ligands emerged as the answer to achieve not only more drug-like compounds but also more selective ligands by targeting the diversity of the G4 loops and grooves. The rationale behind the design of a very comprehensive set of ligands, with particular focus on the structural features required for binding to G4, is discussed and combined with the corresponding biochemical/biological data to highlight key structure-G4 interaction relationships. Analysis of the data suggests that the shape of the ligand is the major factor behind the G4 stabilizing effect of the ligands. The information here critically reviewed will certainly contribute to the development of new and better G4 ligands with application either as therapeutics or probes.
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Affiliation(s)
- Ana Rita Duarte
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Enrico Cadoni
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Ana S Ressurreição
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Rui Moreira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Alexandra Paulo
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
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18
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Yoshida W, Saikyo H, Nakabayashi K, Yoshioka H, Bay DH, Iida K, Kawai T, Hata K, Ikebukuro K, Nagasawa K, Karube I. Identification of G-quadruplex clusters by high-throughput sequencing of whole-genome amplified products with a G-quadruplex ligand. Sci Rep 2018; 8:3116. [PMID: 29449667 PMCID: PMC5814564 DOI: 10.1038/s41598-018-21514-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 02/05/2018] [Indexed: 12/31/2022] Open
Abstract
G-quadruplex (G4) is a DNA secondary structure that has been found to play regulatory roles in the genome. The identification of G4-forming sequences is important to study the specific structure-function relationships of such regions. In the present study, we developed a method for identification of G4 clusters on genomic DNA by high-throughput sequencing of genomic DNA amplified via whole-genome amplification (WGA) in the presence of a G4 ligand. The G4 ligand specifically bound to G4 structures on genomic DNA; thus, DNA polymerase was arrested on the G4 structures stabilised by G4 ligand. We utilised the telomestatin derivative L1H1-7OTD as a G4 ligand and demonstrated that the efficiency of amplification of the G4 cluster regions was lower than that of the non-G4-forming regions. By high-throughput sequencing of the WGA products, 9,651 G4 clusters were identified on human genomic DNA. Among these clusters, 3,766 G4 clusters contained at least one transcriptional start site, suggesting that genes are regulated by G4 clusters rather than by one G4 structure.
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Affiliation(s)
- Wataru Yoshida
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura-machi, Hachioji, Tokyo, 192-0982, Japan.
| | - Hiroki Saikyo
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura-machi, Hachioji, Tokyo, 192-0982, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Ookura, Setagaya, Tokyo, 157-0074, Japan
| | - Hitomi Yoshioka
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura-machi, Hachioji, Tokyo, 192-0982, Japan
| | - Daniyah Habiballah Bay
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura-machi, Hachioji, Tokyo, 192-0982, Japan.,Biology Department, Umm Al-Qura University, P.O. Box 715, Makkah, 21955, Saudi Arabia
| | - Keisuke Iida
- Molecular Chirality Research Center, Synthetic Organic Chemistry, Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi, Inage, Chiba, 263-8522, Japan
| | - Tomoko Kawai
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Ookura, Setagaya, Tokyo, 157-0074, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Ookura, Setagaya, Tokyo, 157-0074, 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
| | - Isao Karube
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura-machi, Hachioji, Tokyo, 192-0982, Japan
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19
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Ma Y, Tsushima Y, Sakuma M, Sasaki S, Iida K, Okabe S, Seimiya H, Hirokawa T, Nagasawa K. Development of G-quadruplex ligands for selective induction of a parallel-type topology. Org Biomol Chem 2018; 16:7375-7382. [DOI: 10.1039/c8ob01702f] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Parallel type of topology in G4 is selectively induced by tetra-guanidinylalkyl substituted 6OTD derivative.
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Affiliation(s)
- Yue Ma
- Department of Life Science and Biotechnology
- Faculty of Technology
- Tokyo University of Agriculture and Technology
- Koganei
- Japan
| | - Yamato Tsushima
- Department of Life Science and Biotechnology
- Faculty of Technology
- Tokyo University of Agriculture and Technology
- Koganei
- Japan
| | - Mai Sakuma
- Department of Life Science and Biotechnology
- Faculty of Technology
- Tokyo University of Agriculture and Technology
- Koganei
- Japan
| | - Shogo Sasaki
- Department of Life Science and Biotechnology
- Faculty of Technology
- Tokyo University of Agriculture and Technology
- Koganei
- Japan
| | - Keisuke Iida
- Department of Chemistry
- Faculty of Science
- Chiba University
- Chiba 263-8522
- Japan
| | - Sachiko Okabe
- Division of Molecular Biotherapy
- Cancer Chemotherapy Center
- Japanese Foundation for Cancer Research
- Koto-ward
- Tokyo 135-8550
| | - Hiroyuki Seimiya
- Division of Molecular Biotherapy
- Cancer Chemotherapy Center
- Japanese Foundation for Cancer Research
- Koto-ward
- Tokyo 135-8550
| | - Takatsugu Hirokawa
- Transborder Medical Research Center
- University of Tsukuba
- Tsukuba, 305-8575
- Japan
- Division of Biomedical Science
| | - Kazuo Nagasawa
- Department of Life Science and Biotechnology
- Faculty of Technology
- Tokyo University of Agriculture and Technology
- Koganei
- Japan
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20
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Bay DH, Busch A, Lisdat F, Iida K, Ikebukuro K, Nagasawa K, Karube I, Yoshida W. Identification of G-quadruplex structures that possess transcriptional regulating functions in the Dele and Cdc6 CpG islands. BMC Mol Biol 2017; 18:17. [PMID: 28655335 PMCID: PMC5488298 DOI: 10.1186/s12867-017-0094-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 06/23/2017] [Indexed: 12/29/2022] Open
Abstract
Background G-quadruplex is a DNA secondary structure that has been shown to play an important role in biological systems. In a previous study, we identified 1998 G-quadruplex-forming sequences using a mouse CpG islands DNA microarray with a fluorescent-labeled G-quadruplex ligand. Among these putative G-quadruplex-forming sequences, G-quadruplex formation was verified for 10 randomly selected sequences by CD spectroscopy and DMS footprinting analysis. In this study, the biological function of the 10 G-quadruplex-forming sequences in the transcriptional regulation has been analyzed using a reporter assay. Results When G-quadruplex-forming sequences from the Dele and Cdc6 genes have been cloned in reporter vectors carrying a minimal promoter and the luciferase gene, luciferase expression is activated. This has also been detected in experiments applying a promoterless reporter vector. Mutational analysis reveals that guanine bases, which form the G-tetrads, are important in the activation. In addition, the activation has been found to decrease by the telomestatin derivative L1H1-7OTD which can bind to the G-quadruplex DNA. When Dele and Cdc6 CpG islands, containing the G-quadruplex-forming sequence, have been cloned in the promoterless reporter vector, the luciferase expression is activated. Mutational analysis reveals that the expression level is decreased by mutation on Dele G-quadruplex; however, increased by mutation on Cdc6 G-quadruplex. Conclusion Dele and Cdc6 G-quadruplex formation is significant in the transcriptional regulation. Dele and Cdc6 G-quadruplex DNA alone possess enhancer and promotor function. When studied in more complex CpG islands Dele G-quadruplex also demonstrates promotor activity, whereas Cdc6 G-quadruplex may possess a dual function of transcriptional regulation. Electronic supplementary material The online version of this article (doi:10.1186/s12867-017-0094-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniyah H Bay
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan.,Biology Department, Umm Al-Qura University, Makkah, Kingdom of Saudi Arabia
| | - Annika Busch
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan.,Biosystems Technology, Institute of Applied Life Sciences, Technical University of Applied Sciences Wildau, Wildau, Germany
| | - Fred Lisdat
- Biosystems Technology, Institute of Applied Life Sciences, Technical University of Applied Sciences Wildau, Wildau, Germany
| | - Keisuke Iida
- Graduate School of Science and Engineering, Saitama University, c/o Saitama Cancer Center, Saitama, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Isao Karube
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan
| | - Wataru Yoshida
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan.
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21
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Liu X, Ishizuka T, Bao HL, Wada K, Takeda Y, Iida K, Nagasawa K, Yang D, Xu Y. Structure-Dependent Binding of hnRNPA1 to Telomere RNA. J Am Chem Soc 2017; 139:7533-7539. [PMID: 28510424 DOI: 10.1021/jacs.7b01599] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Telomeric repeat-containing RNA is a new noncoding RNA molecule that performs various biofunctions. Heterogeneous nuclear ribonucleoprotein (hnRNP) A1 is an RNA-binding protein involved in the telomere maintenance machinery. To date, little is known about how hnRNPA1 binds to telomeric RNA. In this study, we investigated the binding affinity and recognition mechanism of telomere RNA with the RNA recognition motif of hnRNPA1. Using the photochemical cross-linking method, we showed that the telomere RNA G-quadruplex with loops is important in the interaction of telomere RNA with hnRNPA1. Using small-molecule probes, we directly visualized the complex formed by the telomere RNA G-quadruplex and hnRNPA1 in vitro and in live cells. The results suggested that the structure-dependent binding of hnRNPA1 to telomere RNA regulates the telomere function. Therefore, our study provides new insights into the interactions between the RNA G-quadruplex and proteins at the telomere.
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Affiliation(s)
- Xiao Liu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki , 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Takumi Ishizuka
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki , 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Hong-Liang Bao
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki , 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Kei Wada
- Organization for Promotion of Tenure Track, University of Miyazaki , 1-1 Gakuenkibanadai-nishi, Kiyotake, Miyazaki 889-2192, Japan
| | - Yuma Takeda
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki , 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Keisuke Iida
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology , 2-24-16 Naka-cho, Koganei City, Tokyo 184-8588, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology , 2-24-16 Naka-cho, Koganei City, Tokyo 184-8588, Japan
| | - Danzhou Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University , 201 South University Street, West Lafayette, Indiana 47907, United States
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki , 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
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22
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A G-quadruplex structure at the 5' end of the H19 coding region regulates H19 transcription. Sci Rep 2017; 8:45815. [PMID: 28367967 PMCID: PMC5377947 DOI: 10.1038/srep45815] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 03/06/2017] [Indexed: 12/15/2022] Open
Abstract
The H19 gene, one of the best known imprinted genes, encodes a long non-coding RNA that regulates cell proliferation and differentiation. H19 RNA is widely expressed in embryonic tissues, but its expression is restricted in only a few tissues after birth. However, regulation of H19 gene expression remains poorly understood outside the context of genomic imprinting. Here we identified evolutionarily conserved guanine (G)-rich repeated motifs at the 5′ end of the H19 coding region that are consistent with theoretically deduced G-quadruplex sequences. Circular dichroism spectroscopy and electrophoretic mobility shift assays with G-quadruplex-specific ligands revealed that the G-rich motif, located immediately downstream of the transcription start site (TSS), forms a G-quadruplex structure in vitro. By using a series of mutant forms of H19 harboring deletion or G-to-A substitutions, we found that the H19-G-quadruplex regulates H19 gene expression. We further showed that transcription factors Sp1 and E2F1 were associated with the H19-G-quadruplex to either suppress or promote the H19 transcription, respectively. Moreover, H19 expression during differentiation of mouse embryonic stem cells appears to be regulated by a genomic H19 G-quadruplex. These results demonstrate that the G-quadruplex structure immediately downstream of the TSS functions as a novel regulatory element for H19 gene expression.
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23
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Maleki P, Ma Y, Iida K, Nagasawa K, Balci H. A single molecule study of a fluorescently labeled telomestatin derivative and G-quadruplex interactions. Nucleic Acids Res 2016; 45:288-295. [PMID: 27899628 PMCID: PMC5224478 DOI: 10.1093/nar/gkw1090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/10/2016] [Accepted: 10/25/2016] [Indexed: 02/03/2023] Open
Abstract
The potential use of G-quadruplex (GQ) stabilizing small molecules as anti-cancer drugs has created a flurry of activity on various aspects of these molecules. Telomestatin and oxazole telomestatin derivatives (OTD) are some of the most prominent of such molecules, yet the underlying dynamics of their interactions with GQ and the extent of heterogeneities in these interactions are not known. We performed single molecule measurements to study binding kinetics, rotational freedom, and dwell time distributions of a Cy5-labeled OTD (L1Cy5–7OTD) as it interacted with several different GQ structures. Our measurements show that L1Cy5–7OTD dwells on more stable GQ for longer times and binds to such GQ with higher frequency. The dwell times showed a broad distribution, but were longer than a minute for a significant fraction of molecules (characteristic dwell time τ = 192 ± 15 s and τ = 98 ± 15 s for the more and less stable GQ, respectively). In addition, L1Cy5–7OTD might be able to bind to GQ in at least two different primary orientations and occasionally transition between these orientations. The dwell time in one of these orientations was significantly longer than that in the other one, suggesting different stabilities for different binding orientations.
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Affiliation(s)
- Parastoo Maleki
- Department of Physics, Kent State University, Kent, OH 44240, USA
| | - Yue Ma
- Department of Biotechnology and Life Science, Graduate School of Technology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Keisuke Iida
- Department of Biotechnology and Life Science, Graduate School of Technology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Graduate School of Technology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH 44240, USA
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24
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Selective recognition and stabilization of new ligands targeting the potassium form of the human telomeric G-quadruplex DNA. Sci Rep 2016; 6:31019. [PMID: 27511133 PMCID: PMC4980623 DOI: 10.1038/srep31019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 07/12/2016] [Indexed: 02/02/2023] Open
Abstract
The development of a ligand that is capable of distinguishing among the wide variety of G-quadruplex structures and targeting telomeres to treat cancer is particularly challenging. In this study, the ability of two anthraquinone telomerase inhibitors (NSC749235 and NSC764638) to target telomeric G-quadruplex DNA was probed. We found that these ligands specifically target the potassium form of telomeric G-quadruplex DNA over the DNA counterpart. The characteristic interaction with the telomeric G-quadruplex DNA and the anticancer activities of these ligands were also explored. The results of this present work emphasize our understanding of the binding selectivity of anthraquinone derivatives to G-quadruplex DNA and assists in future drug development for G-quadruplex-specific ligands.
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Sakuma M, Ma Y, Tsushima Y, Iida K, Hirokawa T, Nagasawa K. Design and synthesis of unsymmetric macrocyclic hexaoxazole compounds with an ability to induce distinct G-quadruplex topologies in telomeric DNA. Org Biomol Chem 2016; 14:5109-16. [PMID: 27181296 DOI: 10.1039/c6ob00437g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
New macrocyclic hexaoxazole compounds bearing two side chains on an unsymmetrical macrocyclic ring system, i.e., 4,2-L2H2-6OTD (2) and 5,1-L2H2-6OTD (3), were designed as candidate G-quadruplex (G4) ligands and synthesized. These G4 ligands 2 and 3 induced an anti-parallel topology and a hybrid-type topology of telomeric DNA, respectively, in contrast to the previously reported symmetrical macrocycle 3,3-L2H2-6OTD (1), which induces a typical anti-parallel structure. Molecular mechanics calculations and docking studies indicate that these differences arise from the different directions of the side chains in these L2H2-6OTD derivatives, and provide an explanation for the weaker stabilization of telomeric DNA by 2 and 3, compared with 1.
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Affiliation(s)
- Mai Sakuma
- Department of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology (TUAT), Koganei, Tokyo 184-8588, Japan.
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Nagasawa K, Sedghi Masoud S, Tsushima Y, Iida K. Synthesis of Macrocyclic Penta- and Tetraoxazoles as G-Quadruplex Ligands. HETEROCYCLES 2015. [DOI: 10.3987/com-14-s(k)90] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Small-molecule quadruplex-targeted drug discovery. Bioorg Med Chem Lett 2014; 24:2602-12. [DOI: 10.1016/j.bmcl.2014.04.029] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/06/2014] [Accepted: 04/08/2014] [Indexed: 01/24/2023]
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