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Sharma T, Kundu N, Kaur S, Shankaraswamy J, Saxena S. Why to target G-quadruplexes using peptides: Next-generation G4-interacting ligands. J Pept Sci 2023; 29:e3491. [PMID: 37009771 DOI: 10.1002/psc.3491] [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: 11/18/2022] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 04/04/2023]
Abstract
Guanine-rich oligonucleotides existing in both DNA and RNA are able to fold into four-stranded DNA secondary structures via Hoogsteen type hydrogen-bonding, where four guanines self-assemble into a square planar arrangement, which, when stacked upon each other, results in the formation of higher-order structures called G-quadruplexes. Their distribution is not random; they are more frequently present at telomeres, proto-oncogenic promoters, introns, 5'- and 3'-untranslated regions, stem cell markers, ribosome binding sites and so forth and are associated with various biological functions, all of which play a pivotal role in various incurable diseases like cancer and cellular ageing. Several studies have suggested that G-quadruplexes could not regulate biological processes by themselves; instead, various proteins take part in this regulation and can be important therapeutic targets. There are certain limitations in using whole G4-protein for therapeutics purpose because of its high manufacturing cost, laborious structure prediction, dynamic nature, unavailability for oral administration due to its degradation in the gut and inefficient penetration to reach the target site because of the large size. Hence, biologically active peptides can be the potential candidates for therapeutic intervention instead of the whole G4-protein complex. In this review, we aimed to clarify the biological roles of G4s, how we can identify them throughout the genome via bioinformatics, the proteins interacting with G4s and how G4-interacting peptide molecules may be the potential next-generation ligands for targeting the G4 motifs located in biologically important regions.
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Affiliation(s)
- Taniya Sharma
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Nikita Kundu
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Sarvpreet Kaur
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Jadala Shankaraswamy
- Department of Fruit Science, College of Horticulture, Mojerla, Sri Konda Laxman Telangana State Horticultural University, Budwel, Telangana, India
| | - Sarika Saxena
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
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2
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Ruthenium(II) Polypyridyl Complexes and Their Use as Probes and Photoreactive Agents for G-quadruplexes Labelling. Molecules 2022; 27:molecules27051541. [PMID: 35268640 PMCID: PMC8912042 DOI: 10.3390/molecules27051541] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 02/01/2023] Open
Abstract
Due to their optical and electrochemical properties, ruthenium(II) polypyridyl complexes have been used in a wide array of applications. Since the discovery of the light-switch ON effect of [Ru(bpy)2dppz]2+ when interacting with DNA, the design of new Ru(II) complexes as light-up probes for specific regions of DNA has been intensively explored. Amongst them, G-quadruplexes (G4s) are of particular interest. These structures formed by guanine-rich parts of DNA and RNA may be associated with a wide range of biological events. However, locating them and understanding their implications in biological pathways has proven challenging. Elegant approaches to tackle this challenge relies on the use of photoprobes capable of marking, reversibly or irreversibly, these G4s. Indeed, Ru(II) complexes containing ancillary π-deficient TAP ligands can create a covalently linked adduct with G4s after a photoinduced electron transfer from a guanine residue to the excited complex. Through careful design of the ligands, high selectivity of interaction with G4 structures can be achieved. This allows the creation of specific Ru(II) light-up probes and photoreactive agents for G4 labelling, which is at the core of this review composed of an introduction dedicated to a brief description of G-quadruplex structures and two main sections. The first one will provide a general picture of ligands and metal complexes interacting with G4s. The second one will focus on an exhaustive and comprehensive overview of the interactions and (photo)reactions of Ru(II) complexes with G4s.
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3
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Lejault P, Mitteaux J, Sperti FR, Monchaud D. How to untie G-quadruplex knots and why? Cell Chem Biol 2021; 28:436-455. [PMID: 33596431 DOI: 10.1016/j.chembiol.2021.01.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/08/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022]
Abstract
For over two decades, the prime objective of the chemical biology community studying G-quadruplexes (G4s) has been to use chemicals to interact with and stabilize G4s in cells to obtain mechanistic interpretations. This strategy has been undoubtedly successful, as demonstrated by recent advances. However, these insights have also led to a fundamental rethinking of G4-targeting strategies: due to the prevalence of G4s in the human genome, transcriptome, and ncRNAome (collectively referred to as the G4ome), and their involvement in human diseases, should we continue developing G4-stabilizing ligands or should we invest in designing molecular tools to unfold G4s? Here, we first focus on how, when, and where G4s fold in cells; then, we describe the enzymatic systems that have evolved to counteract G4 folding and how they have been used as tools to manipulate G4s in cells; finally, we present strategies currently being implemented to devise new molecular G4 unwinding agents.
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Affiliation(s)
- Pauline Lejault
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - Jérémie Mitteaux
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - Francesco Rota Sperti
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - David Monchaud
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France.
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Maddah M, Karami L. An atomistic investigation on the interaction of distamycin A and its derivative with the telomeric G-Quadruplex as anticancer agents by molecular dynamics simulation. Arch Biochem Biophys 2021; 701:108797. [PMID: 33607110 DOI: 10.1016/j.abb.2021.108797] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/05/2021] [Accepted: 02/06/2021] [Indexed: 10/22/2022]
Abstract
Human telomerase that activates within cancer cells has a telomeric sequence at the 3' end. Each factor that stabilizes the G-quadruplex in guanine-rich telomeric sequences can inhibit the regular telomerase activity. Therefore, the telomeric G-quadruplex is known as a promising target in cancer treatment. In this work, we studied the binding of positively charged distamycin A and its uncharged derivative to the G-quadruplex in a solution environment by Molecular Dynamics (MD) simulation. The binding mechanism and subtle conformational changes were investigated as a result of the ligand attachment. Moreover, binding free energy and clustering analysis describe the stability and flexibility of G-quadruplexes upon ligand binding. Structural analyses displayed that the favorable binding of both ligands imposes significant stability and rigidity in G-quadruplex conformation compared to free G-quadruplex, especially charged distamycin. Hydration pattern and ion distribution were different for free G-quadruplex and both of the ligand complexes. Energy decomposition reveals the electrostatic effect on the stability of G-quadruplex. The radial distribution function displayed the solvent shell and ion moving away from the groove. The hydrogen bond played an essential role in the binding of both ligands, especially for the charged derivative. van der Waals interaction is the only factor that is more important in binding uncharged distamycin into G-quadruplex than the charged one. The calculated ΔGbind showed the stability of both ligands within grooves and good agreement with the experimental binding free energy data. Finally, the results suggest that ligand modification improves the binding mode toward stabilizing G-quadruplexes.
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Affiliation(s)
- Mina Maddah
- Depatment of Chemistry, K. N. Toosi University of Technology, Tehran, Iran; Super Computing Institute, University of Tehran, Tehran, Iran.
| | - Leila Karami
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran.
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Zell J, Rota Sperti F, Britton S, Monchaud D. DNA folds threaten genetic stability and can be leveraged for chemotherapy. RSC Chem Biol 2021; 2:47-76. [PMID: 35340894 PMCID: PMC8885165 DOI: 10.1039/d0cb00151a] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/20/2020] [Indexed: 12/22/2022] Open
Abstract
Damaging DNA is a current and efficient strategy to fight against cancer cell proliferation. Numerous mechanisms exist to counteract DNA damage, collectively referred to as the DNA damage response (DDR) and which are commonly dysregulated in cancer cells. Precise knowledge of these mechanisms is necessary to optimise chemotherapeutic DNA targeting. New research on DDR has uncovered a series of promising therapeutic targets, proteins and nucleic acids, with application notably via an approach referred to as combination therapy or combinatorial synthetic lethality. In this review, we summarise the cornerstone discoveries which gave way to the DNA being considered as an anticancer target, and the manipulation of DDR pathways as a valuable anticancer strategy. We describe in detail the DDR signalling and repair pathways activated in response to DNA damage. We then summarise the current understanding of non-B DNA folds, such as G-quadruplexes and DNA junctions, when they are formed and why they can offer a more specific therapeutic target compared to that of canonical B-DNA. Finally, we merge these subjects to depict the new and highly promising chemotherapeutic strategy which combines enhanced-specificity DNA damaging and DDR targeting agents. This review thus highlights how chemical biology has given rise to significant scientific advances thanks to resolutely multidisciplinary research efforts combining molecular and cell biology, chemistry and biophysics. We aim to provide the non-specialist reader a gateway into this exciting field and the specialist reader with a new perspective on the latest results achieved and strategies devised.
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Affiliation(s)
- Joanna Zell
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon France
| | - Francesco Rota Sperti
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon France
| | - Sébastien Britton
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS Toulouse France
- Équipe Labellisée la Ligue Contre le Cancer 2018 Toulouse France
| | - David Monchaud
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon France
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6
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Mal M, Mandal D. Molecular Rotors as Guest Fluorophores Probing the Local Environment inside Host G4 Supramolecular Hydrogels. J Phys Chem B 2021; 125:219-230. [PMID: 33370116 DOI: 10.1021/acs.jpcb.0c07954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Fluorescent molecular rotors with a high binding affinity toward the guanosine quartet (G4) were incorporated as guest fluorophores into host supramolecular hydrogels based on the self-assembly of G4 units, to probe the local environment. Torsional dynamics of the rotors were severely inhibited inside the hydrogels in comparison with aqueous solutions, although the hydrogels were composed of >95% water. Moreover, even though all the gels were rigid bodies with no spontaneous deformation or flow property at room temperature, torsional dynamics in G4 borate gels was found to be consistently several orders of magnitude slower than those in the other G4 gels, irrespective of the identity of the molecular rotor probe. This clear difference in the molecular mobilities of the guest fluorophore could be attributed to systematic differences in the internal structure between the two categories of host G4 hydrogels. In specific terms, the borate groups in G4 borate hydrogels serve as bridging units between separate G4 quadruplex strands, generating additional cross-links that reinforce the network structure of the gel. The results demonstrate that molecular rotors act as efficient fluorescent probes for the quantitative assessment of the molecular-level environment and dynamics inside the hydrogels, an aspect that is missed out by most other analytical methods that are routinely employed for studying them.
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Affiliation(s)
- Madhushree Mal
- Department of Chemistry, University of Calcutta, 92, APC Road, Kolkata 700009, India
| | - Debabrata Mandal
- Department of Chemistry, University of Calcutta, 92, APC Road, Kolkata 700009, India
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8
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Owens EA, Huynh HT, Stroeva EM, Barman A, Ziabrev K, Paul A, Nguyen SV, Laramie M, Hamelberg D, Germann MW, Wilson WD, Henary M. Second Generation G-Quadruplex Stabilizing Trimethine Cyanines. Bioconjug Chem 2019; 30:2647-2663. [PMID: 31518105 DOI: 10.1021/acs.bioconjchem.9b00571] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
G-Quadruplex DNA has been recognized as a highly appealing target for the development of new selective chemotherapeutics, which could result in markedly reduced toxicity toward normal cells. In particular, the cyanine dyes that bind selectively to G-quadruplex structures without targeting duplex DNA have attracted attention due to their high amenability to structural modifications that allows fine-tuning of their biomolecular interactions. We have previously reported pentamethine and symmetric trimethine cyanines designed to effectively bind G-quadruplexes through end stacking interactions. Herein, we are reporting a second generation of drug candidates, the asymmetric trimethine cyanines. These have been synthesized and evaluated for their quadruplex binding properties. Incorporating a benz[c,d]indolenine heterocyclic unit increased overall quadruplex binding, and elongating the alkyl length increases the quadruplex-to-duplex binding specificity.
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Affiliation(s)
- Eric A Owens
- Department of Chemistry , Georgia State University , Petit Science Center, 100 Piedmont Ave SE. Atlanta Georgia 30303 , United States.,Center for Diagnostics and Therapeutics , Georgia State University , Petit Science Center, 100 Piedmont Ave SE , Atlanta , Georgia 30303 , United States
| | - Hang T Huynh
- Department of Chemistry , Georgia State University , Petit Science Center, 100 Piedmont Ave SE. Atlanta Georgia 30303 , United States
| | - Ekaterina M Stroeva
- Department of Chemistry , Georgia State University , Petit Science Center, 100 Piedmont Ave SE. Atlanta Georgia 30303 , United States
| | | | - Kostiantyn Ziabrev
- Department of Chemistry , Georgia State University , Petit Science Center, 100 Piedmont Ave SE. Atlanta Georgia 30303 , United States
| | | | | | | | - Donald Hamelberg
- Department of Chemistry , Georgia State University , Petit Science Center, 100 Piedmont Ave SE. Atlanta Georgia 30303 , United States.,Center for Diagnostics and Therapeutics , Georgia State University , Petit Science Center, 100 Piedmont Ave SE , Atlanta , Georgia 30303 , United States
| | - Markus W Germann
- Department of Chemistry , Georgia State University , Petit Science Center, 100 Piedmont Ave SE. Atlanta Georgia 30303 , United States.,Department of Biology , Georgia State University , Petit Science Center, 100 Piedmont Ave. , Atlanta , Georgia 30303 , United States
| | - W David Wilson
- Department of Chemistry , Georgia State University , Petit Science Center, 100 Piedmont Ave SE. Atlanta Georgia 30303 , United States.,Center for Diagnostics and Therapeutics , Georgia State University , Petit Science Center, 100 Piedmont Ave SE , Atlanta , Georgia 30303 , United States
| | - Maged Henary
- Department of Chemistry , Georgia State University , Petit Science Center, 100 Piedmont Ave SE. Atlanta Georgia 30303 , United States.,Center for Diagnostics and Therapeutics , Georgia State University , Petit Science Center, 100 Piedmont Ave SE , Atlanta , Georgia 30303 , United States
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9
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Chen X, Tang WJ, Shi JB, Liu MM, Liu XH. Therapeutic strategies for targeting telomerase in cancer. Med Res Rev 2019; 40:532-585. [PMID: 31361345 DOI: 10.1002/med.21626] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/12/2019] [Accepted: 07/16/2019] [Indexed: 12/13/2022]
Abstract
Telomere and telomerase play important roles in abnormal cell proliferation, metastasis, stem cell maintenance, and immortalization in various cancers. Therefore, designing of drugs targeting telomerase and telomere is of great significance. Over the past two decades, considerable knowledge regarding telomere and telomerase has been accumulated, which provides theoretical support for the design of therapeutic strategies such as telomere elongation. Therefore, the development of telomere-based therapies such as nucleoside analogs, non-nucleoside small molecules, antisense technology, ribozymes, and dominant negative human telomerase reverse transcriptase are being prioritized for eradicating a majority of tumors. While the benefits of telomere-based therapies are obvious, there is a need to address the limitations of various therapeutic strategies to improve the possibility of clinical applications. In this study, current knowledge of telomere and telomerase is discussed, and therapeutic strategies based on recent research are reviewed.
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Affiliation(s)
- Xing Chen
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, People's Republic of China
| | - Wen-Jian Tang
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, People's Republic of China
| | - Jing Bo Shi
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, People's Republic of China
| | - Ming Ming Liu
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, People's Republic of China
| | - Xin-Hua Liu
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, People's Republic of China
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10
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McCallum JEB, Coyle CW, Elson RR, Titterington BA. Interactions of 4,4'-diaminoazobenzene derivatives with telomeric G-quadruplex DNA. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2018. [PMID: 29528273 DOI: 10.1080/15257770.2018.1442578] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The development of small molecules to stabilize the G-quadruplex structure has garnered significant attention for anticancer drug discovery. Herein, we report the synthesis of several 4,4'-diaminoazobenzene derivatives containing different substituent groups and their ability to bind and stabilize telomeric G-quadruplex DNA. Circular dichroism (CD) spectroscopy was performed to characterize the quadruplex topologies, measure stabilization effects, and evaluate their capabilities for conformational photoregulation. 4,4'-Diaminoazobenzene derivatives were found to moderately stabilize quadruplex structures but not affect conformational photoregulation. This work further develops the design and general understanding of the stabilization effects of small molecules with telomeric G-quadruplex DNA.
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Affiliation(s)
- Jeremy E B McCallum
- a Department of Chemistry and Biochemistry , Loyola Marymount University , Los Angeles , CA , USA
| | - Christopher W Coyle
- b Molecular and Systems Pharmacology , Emory University , Atlanta , GA , USA
| | - Ryan R Elson
- a Department of Chemistry and Biochemistry , Loyola Marymount University , Los Angeles , CA , USA
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Suseela YV, Narayanaswamy N, Pratihar S, Govindaraju T. Far-red fluorescent probes for canonical and non-canonical nucleic acid structures: current progress and future implications. Chem Soc Rev 2018; 47:1098-1131. [DOI: 10.1039/c7cs00774d] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Our review presents the recent progress on far-red fluorescent probes of canonical and non-canonical nucleic acid (NA) structures, critically discusses the design principles, applications, limitations and outline the future prospects of developing newer probes with target-specificity for different NA structures.
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Affiliation(s)
- Y. V. Suseela
- Bioorganic Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
| | - Nagarjun Narayanaswamy
- Bioorganic Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
| | - Sumon Pratihar
- Bioorganic Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
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12
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Ma DL, Wu C, Dong ZZ, Tam WS, Wong SW, Yang C, Li G, Leung CH. The Development of G-Quadruplex-Based Assays for the Detection of Small Molecules and Toxic Substances. Chem Asian J 2017; 12:1851-1860. [PMID: 28470784 DOI: 10.1002/asia.201700533] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Indexed: 11/12/2022]
Abstract
G-Quadruplexes can be induced to form guanine-rich DNA sequences by certain small molecules or metal ions. In concert with an appropriate signal transducer, such as a fluorescent dye or a phosphorescent metal complex, the ligand-recognition event can be transduced into a luminescent response. This focus review aims to highlight recent examples of aptamer-based and metal-mediated G-quadruplex assays for the detection of small molecules and toxic substances in the last three years. We discuss the mechanisms and features of the different assays and present an outlook and a perspective for the future of this field.
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Affiliation(s)
- Dik-Lung Ma
- Department of Chemistry, Faculty of Science, Hong Kong Baptist University
| | - Chun Wu
- Department of Chemistry, Faculty of Science, Hong Kong Baptist University
| | - Zhen-Zhen Dong
- Department of Chemistry, Faculty of Science, Hong Kong Baptist University
| | - Wing-Sze Tam
- Department of Chemistry, Faculty of Science, Hong Kong Baptist University
| | - Sze-Wan Wong
- Department of Chemistry, Faculty of Science, Hong Kong Baptist University
| | - Chao Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau
| | - Guodong Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau
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Buchholz I, Karg B, Dickerhoff J, Sievers-Engler A, Lämmerhofer M, Weisz K. Selective Targeting of G-Quadruplex Structures by a Benzothiazole-Based Binding Motif. Chemistry 2017; 23:5814-5823. [PMID: 28276093 DOI: 10.1002/chem.201700298] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Indexed: 12/28/2022]
Abstract
A benzothiazole derivative was identified as potent ligand for DNA G-quadruplex structures. Fluorescence titrations revealed selective binding to quadruplexes of different topologies including parallel, antiparallel, and (3+1) hybrid structures. The parallel c-MYC sequence was found to constitute the preferred target with dissociation constants in the micromolar range. Binding of the benzothiazole-based ligand to c-MYC was structurally and thermodynamically characterized in detail by employing a comprehensive set of spectroscopic and calorimetric techniques. Job plot analyses and mass spectral data indicate noncooperative ligand binding to form complexes with 1:1 and 2:1 stoichiometries. Whereas stacking interactions are suggested by optical methods, NMR chemical shift perturbations also indicate significant rearrangements of both 5'- and 3'-flanking sequences upon ligand binding. Additional isothermal calorimetry studies yield a thermodynamic profile of the ligand-quadruplex association and reveal enthalpic contributions to be the major driving force for binding. Structural and thermodynamic information obtained in the present work provides the basis for the rational development of benzothiazole derivatives as promising quadruplex binding agents.
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Affiliation(s)
- Ina Buchholz
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Beatrice Karg
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Jonathan Dickerhoff
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Adrian Sievers-Engler
- Institute of Pharmaceutical Sciences, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Klaus Weisz
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
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14
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Ranjan N, Arya DP. Linker dependent intercalation of bisbenzimidazole-aminosugars in an RNA duplex; selectivity in RNA vs. DNA binding. Bioorg Med Chem Lett 2016; 26:5989-5994. [PMID: 27884695 PMCID: PMC6201841 DOI: 10.1016/j.bmcl.2016.10.076] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Revised: 10/24/2016] [Accepted: 10/25/2016] [Indexed: 01/08/2023]
Abstract
Neomycin and Hoechst 33258 are two well-known nucleic acid binders that interact with RNA and DNA duplexes with high affinities respectively. In this manuscript, we report that covalent attachment of bisbenzimidazole unit derived from Hoechst 33258 to neomycin leads to intercalative binding of the bisbenzimidazole unit (oriented at 64-74° with respected to the RNA helical axis) in a linker length dependent manner. The dual binding and intercalation of conjugates were supported by thermal denaturation, CD, LD and UV-Vis absorption experiments. These studies highlight the importance of linker length in dual recognition by conjugates, for effective RNA recognition, which can lead to novel ways of recognizing RNA structures. Additionally, the ligand library screens also identify DNA and RNA selective compounds, with compound 9, containing a long linker, showing a 20.3°C change in RNA duplex Tm with only a 13.0°C change in Tm for the corresponding DNA duplex. Significantly, the shorter linker in compound 3 shows almost the reverse trend, a 23.8°C change in DNA Tm, with only a 9.1°C change in Tm for the corresponding RNA duplex.
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Affiliation(s)
- Nihar Ranjan
- Laboratory of Bioorganic and Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, United States
| | - Dev P Arya
- Laboratory of Bioorganic and Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, United States.
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15
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Sheu SY, Huang CH, Zhou JK, Yang DY. Relative stability of G-quadruplex structures: Interactions between the human Bcl2 promoter region and derivatives of carbazole and diphenylamine. Biopolymers 2016; 101:1038-50. [PMID: 24723333 DOI: 10.1002/bip.22497] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 04/07/2014] [Accepted: 04/07/2014] [Indexed: 01/24/2023]
Abstract
The bcl2 promoter region forms a G-quadruplex structure, which is a crucial target for anticancer drug development. In this study, we provide theoretical predictions of the stability of different G-quadruplex folds of the 23-mer bcl2 promoter region and G-quadruplex ligand. We take into account the whole G-quadruplex structure, including bound-cations and solvent effects, in order to compute the ligand binding free energy using molecular dynamics simulation. Two series of the carbazole and diphenylamine derivatives are used to screen for the most potent drug in terms of stabilization. The energy analysis identifies the predominant energy components affecting the stability of the various different G-quadruplex folds. The energy associated with the stability of the G-quadruplex-K(+) structures obtained displays good correlation with experimental Tm measurements. We found that loop orientation has an intrinsic influence on G-quadruplex stability and that the basket structure is the most stable. Furthermore, parallel loops are the most effective drug binding site. Our studies also demonstrate that rigidity and planarity are the key structural elements of a drug that stabilizes the G-quadruplex structure. BMVC-4 is the most potential G-quadruplex ligand. This approach demonstrates significant promise and should benefit drug design.
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Affiliation(s)
- Sheh-Yi Sheu
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, 112, Taiwan; Institute of Biomedical informatics, National Yang-Ming University, Taipei, 112, Taiwan
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16
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Rizeq N, Georgiades SN. Linear and Branched Pyridyl-Oxazole Oligomers: Synthesis and Circular Dichroism Detectable Effect on c-Myc G-Quadruplex Helicity. European J Org Chem 2015. [DOI: 10.1002/ejoc.201501269] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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17
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Karg B, Funke A, Ficht A, Sievers-Engler A, Lämmerhofer M, Weisz K. Molecular Recognition and Visual Detection of G-Quadruplexes by a Dicarbocyanine Dye. Chemistry 2015; 21:13802-11. [DOI: 10.1002/chem.201502118] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Indexed: 11/12/2022]
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18
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Ren J, Wang T, Wang E, Wang J. Versatile G-quadruplex-mediated strategies in label-free biosensors and logic systems. Analyst 2015; 140:2556-72. [DOI: 10.1039/c4an02282c] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This review addresses how G-quadruplex (G4)-mediated biosensors convert the events of target recognition into a measurable physical signal. The application of label-free G4-strategies in the construction of logic systems is also discussed.
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Affiliation(s)
- Jiangtao Ren
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Tianshu Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
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19
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Laguerre A, Chang Y, Pirrotta M, Desbois N, Gros CP, Lesniewska E, Monchaud D. Surface-promoted aggregation of amphiphilic quadruplex ligands drives their selectivity for alternative DNA structures. Org Biomol Chem 2015; 13:7034-9. [DOI: 10.1039/c5ob00692a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The surface-promoted aggregation of a structurally fine-tuned TMPyP4 derivative allows for the straightforward visualization of the quadruplex/ligand interactionsviahigh-speed AFM.
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Affiliation(s)
| | - Yi Chang
- Institute of Molecular Chemistry
- Dijon
- France
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20
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Ilyinsky NS, Varizhuk AM, Beniaminov AD, Puzanov MA, Shchyolkina AK, Kaluzhny DN. G-quadruplex ligands: Mechanisms of anticancer action and target binding. Mol Biol 2014. [DOI: 10.1134/s0026893314060077] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Müller S, Laxmi-Reddy K, Jena PV, Baptiste B, Dong Z, Godde F, Ha T, Rodriguez R, Balasubramanian S, Huc I. Targeting DNA G-quadruplexes with helical small molecules. Chembiochem 2014; 15:2563-70. [PMID: 25256604 PMCID: PMC4284101 DOI: 10.1002/cbic.201402439] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Indexed: 11/08/2022]
Abstract
We previously identified quinoline-based oligoamide helical foldamers and a trimeric macrocycle as selective ligands of DNA quadruplexes. Their helical structures might permit targeting of the backbone loops and grooves of G-quadruplexes instead of the G-tetrads. Given the vast array of morphologies G-quadruplex structures can adopt, this might be a way to achieve sequence selective binding. Here, we describe the design and synthesis of molecules based on macrocyclic and helically folded oligoamides. We tested their ability to interact with the human telomeric G-quadruplex and an array of promoter G-quadruplexes by using FRET melting assay and single-molecule FRET. Our results show that they constitute very potent ligands--comparable to the best so far reported. Their modes of interaction differ from those of traditional tetrad binders, thus opening avenues for the development of molecules specific for certain G-quadruplex conformations.
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Affiliation(s)
- Sebastian Müller
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge CB2 1EW (UK)
- Cambridge Institute, Cancer Research UK, Li Ka Shing CenterCambridge CB2 0RE (UK)
| | - Katta Laxmi-Reddy
- Université de Bordeaux, CBMN, UMR 5248, Institut Européen de Chimie Biologie2 rue Escarpit, 33607 Pessac (France) and CNRS, CBMN, UMR 5248 (France)
| | - Prakrit V Jena
- Department of Physics, Howard Hughes Medical Institute, University of Illinois at Urbana–ChampaignUrbana, IL 61801 (USA)
| | - Benoit Baptiste
- Université de Bordeaux, CBMN, UMR 5248, Institut Européen de Chimie Biologie2 rue Escarpit, 33607 Pessac (France) and CNRS, CBMN, UMR 5248 (France)
| | - Zeyuan Dong
- Université de Bordeaux, CBMN, UMR 5248, Institut Européen de Chimie Biologie2 rue Escarpit, 33607 Pessac (France) and CNRS, CBMN, UMR 5248 (France)
| | - Frédéric Godde
- Université de Bordeaux, CBMN, UMR 5248, Institut Européen de Chimie Biologie2 rue Escarpit, 33607 Pessac (France) and CNRS, CBMN, UMR 5248 (France)
| | - Taekjip Ha
- Department of Physics, Howard Hughes Medical Institute, University of Illinois at Urbana–ChampaignUrbana, IL 61801 (USA)
| | - Raphaël Rodriguez
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge CB2 1EW (UK)
- Cambridge Institute, Cancer Research UK, Li Ka Shing CenterCambridge CB2 0RE (UK)
| | - Shankar Balasubramanian
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge CB2 1EW (UK)
- Cambridge Institute, Cancer Research UK, Li Ka Shing CenterCambridge CB2 0RE (UK)
| | - Ivan Huc
- Université de Bordeaux, CBMN, UMR 5248, Institut Européen de Chimie Biologie2 rue Escarpit, 33607 Pessac (France) and CNRS, CBMN, UMR 5248 (France)
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22
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Mohammed HS, Delos Santos JO, Armitage BA. Noncovalent binding and fluorogenic response of cyanine dyes to DNA homoquadruplex and PNA-DNA heteroquadruplex structures. ARTIFICIAL DNA, PNA & XNA 2014; 2:43-49. [PMID: 21912726 DOI: 10.4161/adna.2.2.16339] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 05/10/2011] [Indexed: 12/18/2022]
Abstract
Two symmetrical cyanine dyes based on benzothiazole heterocycles and a trimethine bridge were found to bind to a parallel-stranded DNA guanine quadruplex based on the MYC oncogene promoter sequence with high nanomolar affinity and 1:1 stoichiometry. The dyes exhibited substantial fluorescence enhancements upon binding. In the presence of homologous guanine-rich peptide nucleic acid oligomers, PNA-DNA heteroquadruplexes were formed. The dyes retained their ability to bind to the heteroquadruplexes at low micromolar concentrations and with varying fluorescence enhancements, although indeterminate stoichiometries preclude quantitative comparison of the affinities with the DNA homoquadruplex precursor. The difference in fluorescence enhancement between DNA homoquadruplex and PNA-DNA heteroquadruplex allows the dyes to be used as fluorogenic indicators of hybridization in a facile method for determining PNA-DNA stoichiometry.
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Affiliation(s)
- Halimatu S Mohammed
- Department of Chemistry and Center for Nucleic Acids Science and Technology; Carnegie Mellon University; Pittsburgh, PA USA
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23
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Chen BJ, Wu YL, Tanaka Y, Zhang W. Small molecules targeting c-Myc oncogene: promising anti-cancer therapeutics. Int J Biol Sci 2014; 10:1084-96. [PMID: 25332683 PMCID: PMC4202025 DOI: 10.7150/ijbs.10190] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 08/25/2014] [Indexed: 02/07/2023] Open
Abstract
The nuclear transcription factor c-Myc is a member of the Myc gene family with multiple functions and located on band q24.1 of chromosome 8. The c-Myc gene is activated by chromosomal translocation, rearrangement, and amplification. Its encoded protein transduces intracellular signals to the nucleus, resulting in the regulation of cell proliferation, differentiation, and apoptosis, and has the ability to transform cells and bind chromosomal DNA. c-Myc also plays a critical role in malignant transformation. The abnormal over-expression of c-Myc is frequently observed in some tumors, including carcinomas of the breast, colon, and cervix, as well as small-cell lung cancer, osteosarcomas, glioblastomas, and myeloid leukemias, therefore making it a possible target for anticancer therapy. In this minireview, we summarize unique characteristics of c-Myc and therapeutic strategies against cancer using small molecules targeting the oncogene, and discuss the prospects in the development of agents targeting c-Myc, in particular G-quadruplexes formed in c-Myc promoter and c-Myc/Max dimerization. Such information will be of importance for the research and development of c-Myc-targeted drugs.
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Affiliation(s)
- Bing-Jia Chen
- 1. Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, China
| | - Yan-Ling Wu
- 2. Lab of Molecular Immunology, Virus Inspection Department, Zhejiang Provincial Center for Disease Control and Prevention, 630 Xincheng Road, Hangzhou, 310051, China. ; 1. Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, China
| | - Yoshimasa Tanaka
- 3. Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Wen Zhang
- 1. Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, China
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24
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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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25
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Biver T. Stabilisation of non-canonical structures of nucleic acids by metal ions and small molecules. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2013.04.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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26
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Zhuang XY, Yao YG. Mitochondrial dysfunction and nuclear-mitochondrial shuttling of TERT are involved in cell proliferation arrest induced by G-quadruplex ligands. FEBS Lett 2013; 587:1656-62. [PMID: 23603390 DOI: 10.1016/j.febslet.2013.04.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 04/08/2013] [Accepted: 04/08/2013] [Indexed: 02/01/2023]
Abstract
G-quadruplex ligands DODC and TMPyP4 have different binding modes to quadruplex structure and cause cell proliferation arrest. Here we showed that DODC was more efficient in cell growth inhibition than TMPyP4. Both G-quadruplex ligands induced nuclear-cytoplasmic shuttling and accumulation of TERT in mitochondria. This effect was not fully dependent on cellular oxidative stress. DODC induced robust cell apoptosis by perturbing mitochondrial function intensively. Overexpression of TERT could not counteract the effects of DODC on mitochondrial respiratory function. Taken together, our results suggest that interference of mitochondrial function by DODC is one of main targets for its anti-tumor ability.
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Affiliation(s)
- Xin-Ying Zhuang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
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27
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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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28
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Gai W, Yang Q, Xiang J, Jiang W, Li Q, Sun H, Yu L, Shang Q, Guan A, Zhang H, Tang Y. A novel signal-amplified strategy based on assembly reactivation for highly specific and sensitive detection of chair-like antiparallel G-quadruplex. Analyst 2012. [PMID: 23207802 DOI: 10.1039/c2an36557j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Specific and sensitive identification of special G-quadruplex structures is an important issue and attracts increasing interest. In this paper, a novel, signal-amplified strategy is proposed for the specific detection of G-quadruplexes, which is very different from those currently-dominating methods based on single-molecular fluorescent probes. In this strategy, a 'special designed' cyanine dye loses the ability of self-assembly in solution but still keeps its assembly potential. When the G-quadruplex with a specific structure is present, the assembly potential of the dye is reactivated so that it can assemble to J-aggregates. Other DNA motifs without this specific structure cannot activate its assembly potential no matter if they are double-stranded or quadruplex DNA. Since the assembly is quite specific to structure, the induced procedure of the aggregates provides high specificity for this strategy. In addition, the attached aggregates exponentially amplify the signal due to the signal stacking of those monomers within the aggregates, which then significantly enhances the sensitivity of this strategy. As a result, this strategy exhibits a highly specific and sensitive detection ability for specific G-quadruplex structures both between quadruplexes and non-quadruplexes and among diverse quadruplex motifs.
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Affiliation(s)
- Wei Gai
- Beijing National Laboratory for Molecular Sciences (BNLMS), Centre for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing, 100190, PR China
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29
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Abstract
The interactions of a triangle-shaped [2.2.2]heptamethinecyanine dye 1, namely 1,5,7-tris-[3-methylbenzothiazol-2-yl]-[2.2.2]heptamethindiium, with quadruplex DNA were studied with photometric and fluorimetric titrations, thermal DNA denaturation, CD and (1)H-NMR spectroscopy. The ligand binds to the quadruplex DNA with moderate affinity (K = 8 × 10(5) M(-1)), mainly by terminal π stacking. Remarkably, the ligand 1 exhibits a selectivity for quadruplex DNA relative to duplex DNA. Whereas the cyanine dye is very weakly fluorescent in aqueous solution, the emission intensity increases by a factor of >100 upon association with quadruplex DNA. Thus, it is shown that trinuclear cyanine derivatives may be employed as selective probes for the fluorimetric detection of quadruplex DNA.
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Affiliation(s)
- Heiko Ihmels
- University of Siegen, Organic Chemistry II, Adolf-Reichwein-Str. 2, D-57068, Siegen, Germany.
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30
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Ma DL, Chan DSH, Fu WC, He HZ, Yang H, Yan SC, Leung CH. Discovery of a natural product-like c-myc G-quadruplex DNA groove-binder by molecular docking. PLoS One 2012; 7:e43278. [PMID: 22912844 PMCID: PMC3422278 DOI: 10.1371/journal.pone.0043278] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 07/18/2012] [Indexed: 11/18/2022] Open
Abstract
The natural product-like carbamide (1) has been identified as a stabilizer of the c-myc G-quadruplex through high-throughput virtual screening. NMR and molecular modeling experiments revealed a groove-binding mode for 1. The biological activity of 1 against the c-myc G-quadruplex was confirmed by its ability to inhibit Taq polymerase-mediated DNA extension and c-myc expression in vitro, demonstrating that 1 is able to control c-myc gene expression at the transcriptional level presumably through the stabilization of the c-myc promoter G-quadruplex. Furthermore, the interaction between carbamide analogues and the c-myc G-quadruplex was also investigated by in vitro experiments in order to generate a brief structure-activity relationship (SAR) for the observed potency of carbamide 1.
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Affiliation(s)
- Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
- * E-mail: (DLM); (CHL)
| | - Daniel Shiu-Hin Chan
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Wai-Chung Fu
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Hong-Zhang He
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Hui Yang
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Siu-Cheong Yan
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
| | - Chung-Hang Leung
- Institute of Chinese Medical Sciences, University of Macau, Macao SAR, China
- State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macao SAR, China
- * E-mail: (DLM); (CHL)
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31
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Nanjunda R, Musetti C, Kumar A, Ismail MA, Farahat AA, Wang S, Sissi C, Palumbo M, Boykin DW, Wilson WD. Heterocyclic dications as a new class of telomeric G-quadruplex targeting agents. Curr Pharm Des 2012; 18:1934-47. [PMID: 22380518 DOI: 10.2174/138161212799958422] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 11/28/2011] [Indexed: 11/22/2022]
Abstract
Small molecules that can induce and stabilize G-quadruplex DNA structures represent a novel approach for anti-cancer and anti-parasitic therapy and extensive efforts have been directed towards discovering lead compounds that are capable of stabilizing quadruplexes. The purpose of this study is to explore conformational modifications in a series of heterocyclic dications to discover structural motifs that can selectively bind and stabilize specific G-quadruplexes, such as those present in the human telomere. The G-quadruplex has various potential recognition sites for small molecules; however, the primary interaction site of most of these ligands is the terminal tetrads. Similar to duplex-DNA groove recognition, quadruplex groove recognition by small molecules offers the potential for enhanced selectivity that can be developed into a viable therapeutic strategy. The compounds investigated were selected based on preliminary studies with DB832, a bifuryl-phenyl diamidine with a unique telomere interaction. This compound provides a paradigm that can help in understanding the optimum compound-DNA interactions that lead to quadruplex groove recognition. DNA recognition by the DB832 derivatives was investigated by biophysical experiments such as thermal melting, circular dichroism, mass spectrometry and NMR. Biological studies were also performed to complement the biophysical data. The results suggest a complex binding mechanism which involves the recognition of grooves for some ligands as well as stacking at the terminal tetrads of the human telomeric G-quadruplex for most of the ligands. These molecules represent an excellent starting point for further SAR analysis for diverse modes of quadruplex recognition and subsequent structure optimization for drug development.
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Affiliation(s)
- Rupesh Nanjunda
- Dept. of Chemistry, Georgia State University, Atlanta GA 30303, USA
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32
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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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33
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Jain AK, Bhattacharya S. Interaction of G-Quadruplexes with Nonintercalating Duplex-DNA Minor Groove Binding Ligands. Bioconjug Chem 2011; 22:2355-68. [DOI: 10.1021/bc200268a] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Akash K. Jain
- Department
of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Santanu Bhattacharya
- Department
of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India
- Chemical Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560 012, India
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34
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Chu JF, Wang ZF, Tseng TY, Chang TC. A Novel Method for Screening G-quadruplex Stabilizers to Human Telomeres. J CHIN CHEM SOC-TAIP 2011. [DOI: 10.1002/jccs.201190028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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35
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Zhang H, Xiang JF, Hu HY, Li L, Jin X, Liu Y, Li PF, Tang Y, Chen CF. Stabilizing G-Quadruplex DNA by a Scissors-Shaped Binaphthyl Derivative through the Entangling Mode: Cooperation of Binaphthylene and the Ethoxy Chain. Biochemistry 2010; 49:10351-3. [DOI: 10.1021/bi1001773] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Hong Zhang
- Beijing National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Graduate University of the Chinese Academy of Sciences, Institute of Chemistry
| | - Jun-feng Xiang
- Beijing National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species
| | - Hai-yu Hu
- National Laboratory for Molecular Sciences, Center for Chemical Biology
- Graduate University of the Chinese Academy of Sciences, Institute of Chemistry
| | - Lin Li
- Beijing National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Graduate University of the Chinese Academy of Sciences, Institute of Chemistry
| | - Xue Jin
- Beijing National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species
| | - Yan Liu
- Beijing National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species
| | - Peng-fei Li
- National Laboratory for Molecular Sciences, Center for Chemical Biology
- Graduate University of the Chinese Academy of Sciences, Institute of Chemistry
| | - Yalin Tang
- Beijing National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species
| | - Chuan-feng Chen
- National Laboratory for Molecular Sciences, Center for Chemical Biology
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36
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Yang Q, Xiang JF, Yang S, Li Q, Zhou Q, Guan A, Li L, Zhang Y, Zhang X, Zhang H, Tang Y, Xu G. Verification of Intramolecular Hybrid/Parallel G-Quadruplex Structure under Physiological Conditions Using Novel Cyanine Dye H-Aggregates: Both in Solution and on Au Film. Anal Chem 2010; 82:9135-7. [DOI: 10.1021/ac1017716] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Qianfan Yang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry for Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing, 100190, P. R. China, and Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Jun-Feng Xiang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry for Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing, 100190, P. R. China, and Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Shu Yang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry for Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing, 100190, P. R. China, and Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Qian Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry for Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing, 100190, P. R. China, and Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Qiuju Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry for Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing, 100190, P. R. China, and Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Aijiao Guan
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry for Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing, 100190, P. R. China, and Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Lin Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry for Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing, 100190, P. R. China, and Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yanxia Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry for Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing, 100190, P. R. China, and Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Xiufeng Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry for Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing, 100190, P. R. China, and Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Hong Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry for Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing, 100190, P. R. China, and Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yalin Tang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry for Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing, 100190, P. R. China, and Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Guangzhi Xu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry for Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing, 100190, P. R. China, and Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
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Yang Q, Xiang J, Yang S, Zhou Q, Li Q, Guan A, Zhang X, Zhang H, Tang Y, Xu G. Recognizing Hybrid/Mixed G-quadruplex in Human Telomeres by Using a Cyanine Dye Supramolecule with Confocal Laser Scanning Microscopy. CHINESE J CHEM 2010. [DOI: 10.1002/cjoc.201090196] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Murat P, Bonnet R, Van der Heyden A, Spinelli N, Labbé P, Monchaud D, Teulade-Fichou MP, Dumy P, Defrancq E. Template-assembled synthetic G-quadruplex (TASQ): a useful system for investigating the interactions of ligands with constrained quadruplex topologies. Chemistry 2010; 16:6106-14. [PMID: 20397247 DOI: 10.1002/chem.200903456] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A new biomolecular device for investigating the interactions of ligands with constrained DNA quadruplex topologies, using surface plasmon resonance (SPR), is reported. Biomolecular systems containing an intermolecular-like G-quadruplex motif 1 (parallel G-quadruplex conformation), an intramolecular G-quadruplex 2, and a duplex DNA 3 have been designed and developed. The method is based on the concept of template-assembled synthetic G-quadruplex (TASQ), whereby quadruplex DNA structures are assembled on a template that allows precise control of the parallel G-quadruplex conformation. Various known G-quadruplex ligands have been used to investigate the affinities of ligands for intermolecular 1 and intramolecular 2 DNA quadruplexes. As anticipated, ligands displaying a pi-stacking binding mode showed a higher binding affinity for intermolecular-like G-quadruplexes 1, whereas ligands with other binding modes (groove and/or loop binding) showed no significant difference in their binding affinities for the two quadruplexes 1 or 2. In addition, the present method has also provided information about the selectivity of ligands for G-quadruplex DNA over the duplex DNA. A numerical parameter, termed the G-quadruplex binding mode index (G4-BMI), has been introduced to express the difference in the affinities of ligands for intermolecular G-quadruplex 1 against intramolecular G-quadruplex 2. The G-quadruplex binding mode index (G4-BMI) of a ligand is defined as follows: G4-BMI=K(D)(intra)/K(D)(inter), where K(D)(intra) is the dissociation constant for intramolecular G-quadruplex 2 and K(D)(inter) is the dissociation constant for intermolecular G-quadruplex 1. In summary, the present work has demonstrated that the use of parallel-constrained quadruplex topology provides more precise information about the binding modes of ligands.
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Affiliation(s)
- Pierre Murat
- Département de Chimie Moléculaire, UMR CNRS 5250, Université Joseph Fourier, BP 53, 38041 Grenoble cedex 9, France
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Chang TC, Chang CC. Detection of G-quadruplexes in cells and investigation of G-quadruplex structure of d(T2AG3)4 in K+ solution by a carbazole derivative: BMVC. Methods Mol Biol 2010; 608:183-206. [PMID: 20012423 DOI: 10.1007/978-1-59745-363-9_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Verification of the existence of quadruplex structure in native human telomeres and determination of the major structure of d(T(2)AG(3))(4) (H24) in K(+) solution are the major questions regarding the structure of human telomeres. We have synthesized a fluorescent probe of 3,6-bis(1-methyl-4-vinylpyridinium)carbazole diiodide (BMVC) that has a very high binding affinity for G-quadruplex H24. BMVC stabilizes quadruplex structures and acts as a sensitive probe to the local environment. Although the circular dichroism patterns of H24 are different in Na(+) and K(+) solutions, similar binding behaviors of BMVC to H24 in these solutions led us to suggest that the major G-quadruplex structure of H24 in K(+) solution is very likely similar to that in Na(+) solution. Of particular interest is the fluorescent band detected at -575 nm in quadruplex H24 and at -545 nm in duplex DNA. In addition, the intensity of BMVC fluorescence increases by two orders of magnitudes upon interaction with either duplex or G-quadruplex DNA. BMVC has a greater binding preference for G-quadruplex H24 than for duplex DNA. Analyzing the BMVC fluorescence at the ends of metaphase chromosomes and other regions of chromosomes allowed us to verify the presence of G-quadruplex structure in human telomeres for the first time. Using fluorescence lifetime imaging microscopy, the longer decay time of BMVC in G-quadruplex H24 than in duplex DNA allowed us to map the G-quadruplex structure in human metaphase chromosomes.
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Affiliation(s)
- Ta-Chau Chang
- Institute of Atomic and Molecular Sciences, and Genomic Research Center, Academia Sinica, Taipei, Taiwan, Republic of China
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40
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Yang Q, Xiang J, Yang S, Li Q, Zhou Q, Guan A, Zhang X, Zhang H, Tang Y, Xu G. Verification of specific G-quadruplex structure by using a novel cyanine dye supramolecular assembly: II. The binding characterization with specific intramolecular G-quadruplex and the recognizing mechanism. Nucleic Acids Res 2009; 38:1022-33. [PMID: 19933263 PMCID: PMC2817466 DOI: 10.1093/nar/gkp1045] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The supramolecular assembly of a novel cyanine dye, 3,3′-di(3-sulfopropyl)-4,5,4′,5′-dibenzo-9-ethyl-thiacarbocyanine triethylammonium salt (ETC) was designed to verify specific intramolecular G-quadruplexes from duplex and single-strand DNAs. Spectral results have shown that ETC presented two major distinct signatures with specific intramolecular G-quadruplexes in vitro: (i) dramatic changes in the absorption spectra (including disappearance of absorption peak around 660 nm and appearance of independent new peak around 584 nm); (ii) ∼70 times enhancement of fluorescence signal at 600 nm. Furthermore, based on 1H-nuclear magnetic resonance and circular dichroism results, the preferring binding of ETC to specific intramolecular G-quadruplexes probably result from end-stacking, and the loop structure nearby also plays an important role.
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Affiliation(s)
- Qianfan Yang
- Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, People's Republic of China
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41
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Amato J, Oliviero G, De Pauw E, Gabelica V. Hybridization of short complementary PNAs to G-quadruplex forming oligonucleotides: An electrospray mass spectrometry study. Biopolymers 2009; 91:244-55. [PMID: 19065573 DOI: 10.1002/bip.21124] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We investigated the interaction of the short peptide nucleic acid (PNA) strand [acccca]-PNA with oligodeoxynucleotides containing one, two, or four tracts of TGGGGT units. Electrospray ionization mass spectrometry allowed exploring the wide variety of complex stoichiometries that were found to coexist in solution. In water, the PNA strand forms short heteroduplexes with the complementary DNA sequences, but higher-order structures are also found, with PNA(2n).DNA(n) triplex units, culminating in precipitation at very low ionic strength. In the presence of ammonium acetate, there is a competition between PNA.DNA heteroduplex formation and DNA G-quadruplex formation. Heteroduplex formation is favored when the PNA + DNA mixture in ammonium acetate is heated and cooled at room temperature, but not if the PNA is added at room temperature to the preformed G-quadruplex. We also found that the short [acccca]-PNA strand binds to G-quadruplexes.
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Affiliation(s)
- Jussara Amato
- Dipartimento di Chimica delle Sostanze Naturali, Facoltà di Scienze Biotecnologiche, Università di Napoli Federico II, Italy
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Owen EA, Keniry MA. Exploring the Binding of Calothrixin A to the G-Quadruplex from the c-myc Oncogene Promotor. Aust J Chem 2009. [DOI: 10.1071/ch09169] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Calothrixin A, a bioactive pentacyclic metabolite from the cyanobacteria Calothrix, has potent antiproliferative behaviour against several cancer cell lines. The in vitro binding of calothrixin A to the DNA quadruplex formed at the promotor region of c-myc was investigated by monitoring changes in the fluorescence emission of 2-aminopurine (2Ap)-substituted analogues of the native Pu22 sequence d(TGAGGGTGGGGAGGGTGGGGAA) on titration with calothrixin A and N-methoxymethyl-calothrixin B. Calothrixin A binds to Pu22 and its constituent loop isomers with a micromolar dissociation constant whereas N-methoxymethyl-calothrixin B has over an order of magnitude lower affinity. Competitive displacement experiments with double-stranded DNA showed preferential binding of calothrixin A to the Pu22 quadruplex compared with double-stranded DNA. The association of calothrixin A with DNA quadruplexes is the first direct evidence that calothrixin A binds to DNA and may aid in the understanding of the bioactivity of the calothrixins.
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Yang Q, Xiang J, Yang S, Zhou Q, Li Q, Tang Y, Xu G. Verification of specific G-quadruplex structure by using a novel cyanine dye supramolecular assembly: I. Recognizing mixed G-quadruplex in human telomeres. Chem Commun (Camb) 2009:1103-5. [DOI: 10.1039/b820101c] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Chen B, Liang J, Tian X, Liu X. G-quadruplex structure: a target for anticancer therapy and a probe for detection of potassium. BIOCHEMISTRY (MOSCOW) 2008; 73:853-61. [PMID: 18774931 DOI: 10.1134/s0006297908080026] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
G-Quadruplexes are four-stranded DNA structures that play important regulatory roles in the maintenance of telomere length by inhibiting telomerase activity. Telomeres are specialized functional DNA-protein structures consisting of a variable number of tandem G-rich repeats together with a group of specific proteins. Telomere losses during cell replication are compensated by telomerase, which adds telomeric repeats onto the chromosome ends in the presence of its substrate--the 3'-overhang. Recently, quadruplexes have been considered as a potential therapeutic target for human cancer because they can inhibit telomerase activity, and some quadruplex-interacting drugs can induce senescence and apoptosis of cancer cells. In addition, due to the potassium preference to the other cations, especially sodium ions, quadruplexes have been suggested for developing potassium detection probes with higher sensitivity and selectivity. This review will illustrate these two aspects to provide further understanding of G-quadruplex structures.
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Affiliation(s)
- Bo Chen
- Bioengineering Institute of Life Science Department, Zhejiang Sci-Tech University, Hangzhou, China
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The biological activity of G-quadruplex DNA binding papaverine-derived ligand in breast cancer cells. Invest New Drugs 2008; 27:289-96. [DOI: 10.1007/s10637-008-9173-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2008] [Accepted: 08/18/2008] [Indexed: 11/30/2022]
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Paramasivan S, Bolton PH. Mix and measure fluorescence screening for selective quadruplex binders. Nucleic Acids Res 2008; 36:e106. [PMID: 18663011 PMCID: PMC2553591 DOI: 10.1093/nar/gkn487] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The human genome contains thousands of regions, including that of the telomere, that have the potential to form quadruplex structures. Many of these regions are potential targets for therapeutic intervention. There are many different folding patterns for quadruplex DNAs and the loops exhibit much more variation than do the quartets. The successful targeting of a particular quadruplex structure requires distinguishing that structure from all of the other quadruplex structures that may be present. A mix and measure fluorescent screening method has been developed, that utilizes multiple reporter molecules that bind to different features of quadruplex DNA. The reporter molecules are used in combination with DNAs that have a variety of quadruplex structures. The screening is based on observing the increase or decrease in the fluorescence of the reporter molecules. The selectivity of a set of test molecules has been determined by this approach.
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Ou TM, Lu YJ, Tan JH, Huang ZS, Wong KY, Gu LQ. G-quadruplexes: targets in anticancer drug design. ChemMedChem 2008; 3:690-713. [PMID: 18236491 DOI: 10.1002/cmdc.200700300] [Citation(s) in RCA: 408] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
G-quadruplexes are special secondary structures adopted in some guanine-rich DNA sequences. As guanine-rich sequences are present in important regions of the eukaryotic genome, such as telomeres and the regulatory regions of many genes, such structures may play important roles in the regulation of biological events in the body. G-quadruplexes have become valid targets for new anticancer drugs in the past few decades. Many leading compounds that target these structures have been reported, and a few of them have entered preclinical or clinical trials. Nonetheless, the selectivity of this kind of antitumor compound has yet to be improved in order to suppress the side effects caused by nonselective binding. As drug design targets, the topology and structural characteristics of quadruplexes, their possible biological roles, and the modes and sites of small-ligand binding to these structures should be understood clearly. Herein we provide a summary of published research that has set out to address the above problem to provide useful information on the design of small ligands that target G-quadruplexes. This review also covers research methodologies that have been developed to study the binding of ligands to G-quadruplexes.
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Affiliation(s)
- Tian-miao Ou
- School of Pharmaceutical Science, Sun Yat-sen University, Guangzhou 510080, People's Republic of China
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Arora A, Balasubramanian C, Kumar N, Agrawal S, Ojha RP, Maiti S. Binding of berberine to human telomeric quadruplex - spectroscopic, calorimetric and molecular modeling studies. FEBS J 2008; 275:3971-83. [DOI: 10.1111/j.1742-4658.2008.06541.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Monchaud D, Allain C, Teulade-Fichou MP. Thiazole orange: a useful probe for fluorescence sensing of G-quadruplex-ligand interactions. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 26:1585-8. [PMID: 18066832 DOI: 10.1080/15257770701548212] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Fluorimetric titrations were performed to gain insight into parameters that govern the association of thiazole orange (TO) and G-quadruplex-DNA (G4-DNA). Use of loop-containing and loop-lacking quadruplexes evidenced the critical influence of the loops on the stoichiometry of the association and on the fluorescence exaltation of TO. We subsequently tried to benefit from this sensitivity to evaluate the influence of G4-DNA cationic environment on ligand binding via a recently reported G4-FID assay.
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Affiliation(s)
- D Monchaud
- Section Richerche, Institut Curie, CNRS UMR 176, Centre Universitaire Paris XI, 91405 Orsay, France
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50
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Ragazzon P, Chaires JB. Use of competition dialysis in the discovery of G-quadruplex selective ligands. Methods 2008; 43:313-23. [PMID: 17967701 DOI: 10.1016/j.ymeth.2007.08.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2007] [Revised: 05/23/2007] [Accepted: 08/02/2007] [Indexed: 10/22/2022] Open
Abstract
G-quadrplex DNA can exist in a rich variety of structural forms, ranging from unimolecular folded structures containing diverse types of loops and strand oreintations, to bimolecular dimeric structures, and finally to tetramolecular parallel-stranded structures. These diverse structures present numerous potential small molecule binding sites with distinctive properties. There is mounting evidence for important functional roles for G-quadruplex structures in biology. G-quadruplexes may participate in the maintenance of telomeres, in transcriptional regulation and, in mRNA, may act to modulate translation. G-quadruplexes thus represent an attractive target for new small-molecule therapeutic agents. Competition dialysis provides a useful tool for the discovery of small molecules that selectively recognize the unique structural features of G-quadruplexes. The principles and practice of the competition dialysis experiment are described here.
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Affiliation(s)
- Patricia Ragazzon
- James Graham Brown Cancer Center, University of Louisville, 529 S. Jackson St., Louisville, KY 40202, USA
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