1
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Clowes SR, Ali Y, Astley OR, Răsădean DM, Pantoş GD. The Influence of Chirality on the β-Amino-Acid Naphthalenediimides/G-Quadruplex DNA Interaction. Molecules 2023; 28:7291. [PMID: 37959711 PMCID: PMC10647805 DOI: 10.3390/molecules28217291] [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: 09/05/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
G-quadruplexes (G4s) have been identified as a potential alternative chemotherapy target. A series of eight β-amino acid derived naphthalenediimides (NDI) were screened against a series of oncogenic G4 sequences: c-KIT1, h-TELO, and TBA. Three sets of enantiomers were investigated to further our understanding of the effect of point chirality on G4 stabilisation. Enantioselective binding behaviour was observed with both c-KIT1 and h-TELO. Docking studies using GNINA and UV-vis titrations were employed to better understand this selective binding behaviour.
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Affiliation(s)
| | | | | | | | - G. Dan Pantoş
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
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2
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Dwivedi A, Kumari A, Aarthy M, Singh SK, Ojha M, Jha S, Jha SK, Jha NS. Spectroscopic and molecular docking studies for the binding and interaction aspects of curcumin-cysteine conjugate and rosmarinic acid with human telomeric G-quadruplex DNA. Int J Biol Macromol 2021; 182:1463-1472. [PMID: 34015406 DOI: 10.1016/j.ijbiomac.2021.05.089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 11/24/2022]
Abstract
The binding and interaction aspects of potential anticancer ligands like: curcumin-cysteine (CC) and rosmarinic acid (RA) with human telomeric G-quadruplex DNA, a novel anticancer target, have been probed by spectroscopic and molecular docking approach. The circular dichroism study unravels the conformational switching from mixed hybrid to parallel structure for the short sequence of human telomeric G-quadruplex structure in the presence of both the ligands. Further a good correlation for binding affinity has been established from the emission and absorption binding spectrum analysis. Further our spectroscopic and molecular docking studies have suggested that the CC having better binding capability than RA to human telomeric G-quadruplex. The presence of L-cysteine moiety in CC ligand is responsible factor for its binding via both minor as well as major groove of human telomeric G-quadruplex DNA where-as RA binds only via minor groove of telomeric G-DNA.
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Affiliation(s)
- Awadesh Dwivedi
- Department of Chemistry, National Institute of Technology, Patna 800005, India
| | - Arya Kumari
- Department of Chemistry, National Institute of Technology, Patna 800005, India
| | - Murali Aarthy
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Karaikudi 630003, Tamil Nadu, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Karaikudi 630003, Tamil Nadu, India
| | - Monalisha Ojha
- Department of Life Science, National Institute of Technology, Rourkela 769008, India
| | - Suman Jha
- Department of Life Science, National Institute of Technology, Rourkela 769008, India
| | | | - Niki Sweta Jha
- Department of Chemistry, National Institute of Technology, Patna 800005, India.
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3
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Aznauryan M, Noer SL, Pedersen CW, Mergny JL, Teulade-Fichou MP, Birkedal V. Ligand Binding to Dynamically Populated G-Quadruplex DNA. Chembiochem 2021; 22:1811-1817. [PMID: 33450114 DOI: 10.1002/cbic.202000792] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/11/2021] [Indexed: 12/14/2022]
Abstract
Several small-molecule ligands specifically bind and stabilize G-quadruplex (G4) nucleic acid structures, which are considered to be promising therapeutic targets. G4s are polymorphic structures of varying stability, and their formation is dynamic. Here, we investigate the mechanisms of ligand binding to dynamically populated human telomere G4 DNA by using the bisquinolinium based ligand Phen-DC3 and a combination of single-molecule FRET microscopy, ensemble FRET and CD spectroscopies. Different cations are used to tune G4 polymorphism and folding dynamics. We find that ligand binding occurs to pre-folded G4 structures and that Phen-DC3 also induces G4 formation in unfolded single strands. Following ligand binding to dynamically populated G4s, the DNA undergoes pronounced conformational redistributions that do not involve direct ligand-induced G4 conformational interconversion. On the contrary, the redistribution is driven by ligand-induced G4 folding and trapping of dynamically populated short-lived conformation states. Thus, ligand-induced stabilization does not necessarily require the initial presence of stably folded G4s.
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Affiliation(s)
- Mikayel Aznauryan
- Department of Chemistry and iNANO center, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark.,Present address: Univ. Bordeaux, INSERM, CNRS ARNA, U1212, UMR 5320, IECB, 33600, Pessac, France
| | - Sofie Louise Noer
- Department of Chemistry and iNANO center, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark
| | - Camilla W Pedersen
- Department of Chemistry and iNANO center, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark
| | - Jean-Louis Mergny
- Laboratoire d'Optique et Biosciences (LOB), CNRS UMR7645, INSERM U1182, Ecole Polytechnique, 91128, Palaiseau Cedex, France.,Institute of Biophysics of the CAS, 61265, Brno, Czech Republic
| | - Marie-Paule Teulade-Fichou
- CMBC Laboratory (Chemistry and Modelling for the Biology of Cancer), Institut Curie, Research Center Orsay, CNRS UMR9187, INSERM U1196, Paris-Saclay University, Bât. 110, 91405, Orsay, France
| | - Victoria Birkedal
- Department of Chemistry and iNANO center, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark
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4
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Gao C, Liu Z, Hou H, Ding J, Chen X, Xie C, Song Z, Hu Z, Feng M, Mohamed HI, Xu S, Parkinson GN, Haider S, Wei D. BMPQ-1 binds selectively to (3+1) hybrid topologies in human telomeric G-quadruplex multimers. Nucleic Acids Res 2020; 48:11259-11269. [PMID: 33080032 PMCID: PMC7672424 DOI: 10.1093/nar/gkaa870] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 09/23/2020] [Accepted: 10/14/2020] [Indexed: 12/21/2022] Open
Abstract
A single G-quadruplex forming sequence from the human telomere can adopt six distinct topologies that are inter-convertible under physiological conditions. This presents challenges to design ligands that show selectivity and specificity towards a particular conformation. Additional complexity is introduced in differentiating multimeric G-quadruplexes over monomeric species, which would be able to form in the single-stranded 3′ ends of telomeres. A few ligands have been reported that bind to dimeric quadruplexes, but their preclinical pharmacological evaluation is limited. Using multidisciplinary approaches, we identified a novel quinoline core ligand, BMPQ-1, which bound to human telomeric G-quadruplex multimers over monomeric G-quadruplexes with high selectivity, and induced the formation of G-quadruplex DNA along with the related DNA damage response at the telomere. BMPQ-1 reduced tumor cell proliferation with an IC50 of ∼1.0 μM and decreased tumor growth rate in mouse by half. Biophysical analysis using smFRET identified a mixture of multiple conformations coexisting for dimeric G-quadruplexes in solution. Here, we showed that the titration of BMPQ-1 shifted the conformational ensemble of multimeric G-quadruplexes towards (3+1) hybrid-2 topology, which became more pronounced as further G-quadruplex units are added.
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Affiliation(s)
- Chao Gao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong AgriculturalUniversity, Wuhan, 430070, China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhu Liu
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haitao Hou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Jieqin Ding
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Congbao Xie
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Zibing Song
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhe Hu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Mingqian Feng
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hany I Mohamed
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Chemistry Department, Faculty of Science, Benha University, Benha 13518, Egypt
| | - Shengzhen Xu
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Gary N Parkinson
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Shozeb Haider
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Dengguo Wei
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong AgriculturalUniversity, Wuhan, 430070, China
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5
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Xiao CD, He ZY, Guo CX, Shen XC, Xu Y. Conformation of G-quadruplex Controlled by Click Reaction. Molecules 2020; 25:molecules25184339. [PMID: 32971833 PMCID: PMC7570587 DOI: 10.3390/molecules25184339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/18/2020] [Accepted: 09/19/2020] [Indexed: 11/16/2022] Open
Abstract
G-quadruplexes are non-canonical four stranded secondary structures possessing great biological importance. Controlling G-quadruplex conformation for further regulating biological processes is both exciting and challenging. In this study, we described a method for regulating G-quadruplex conformation by click chemistry for the first time. 8-ethynyl-2'-deoxyguanosine was synthesized and incorporated into a 12-nt telomere DNA sequence. Such a sequence, at first, formed mixed parallel/anti-parallel G-quadruplexes, while it changed to anti-parallel after reaction with azidobenzene. Meanwhile, the click reaction can give the sequence intense fluorescence.
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Affiliation(s)
- Chao-Da Xiao
- State Key Laboratory of Functions and Applications of Medicinal Plants, School of Pharmaceutical Sciences, Guizhou Medical University, University Town, Guian New District, Guiyang 550025, China;
- Correspondence: (C.-D.X.); (Y.X.); Tel.: +86-0851-88416160 (C.-D.X.); +81-985-85-0993 (Y.X.)
| | - Zhi-Yong He
- Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyo-take, Miyazaki 889-1692, Japan;
| | - Chuan-Xin Guo
- Nucleic Acid Division, Shanghai Cell Therapy Group Co. Ltd., Jiading, Shanghai 201805, China;
| | - Xiang-Chun Shen
- State Key Laboratory of Functions and Applications of Medicinal Plants, School of Pharmaceutical Sciences, Guizhou Medical University, University Town, Guian New District, Guiyang 550025, China;
| | - Yan Xu
- Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyo-take, Miyazaki 889-1692, Japan;
- Correspondence: (C.-D.X.); (Y.X.); Tel.: +86-0851-88416160 (C.-D.X.); +81-985-85-0993 (Y.X.)
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6
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Cao Y, Li W, Gao T, Ding P, Pei R. One Terminal Guanosine Flip of Intramolecular Parallel G-Quadruplex: Catalytic Enhancement of G-Quadruplex/Hemin DNAzymes. Chemistry 2020; 26:8631-8638. [PMID: 32428287 DOI: 10.1002/chem.202001462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/13/2020] [Indexed: 11/09/2022]
Abstract
Numerous studies have shown compelling evidence that incorporation of an inversion of polarity site (IPS) in G-rich sequences can affect the topological and structural characteristics of G-quadruplexes (G4s). Herein, the influence of IPS on the formation of a previously studied intramolecular parallel G4 of d(G3 TG3 TG3 TG3 ) (TTT) and its stacked higher-order structures is explored. Insertion of 3'-3' or 5'-5' IPS did not change the parallel folding pattern of TTT. However, both the species and position of the IPS in TTT have a significant impact on the G4 stability and end-stacking through the alteration of G4-G4 interfaces properties. The data demonstrate that one base flip in each terminal G-tetrad can stabilize parallel G4s and facilitate intermolecular packing of monomeric G4s. Such modifications can also enhance the fluorescence and enzymatic performances by promoting interactions between parallel G4s with N-methyl mesoporphyrin IX (NMM) and hemin, respectively.
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Affiliation(s)
- Yanwei Cao
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionic, Chinese Academy of Sciences, Suzhou, 215123, P. R. China
| | - Wenjing Li
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionic, Chinese Academy of Sciences, Suzhou, 215123, P. R. China
| | - Tian Gao
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionic, Chinese Academy of Sciences, Suzhou, 215123, P. R. China
| | - Pi Ding
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionic, Chinese Academy of Sciences, Suzhou, 215123, P. R. China
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionic, Chinese Academy of Sciences, Suzhou, 215123, P. R. China
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7
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Musumeci D, Mokhir A, Roviello GN. Synthesis and nucleic acid binding evaluation of a thyminyl l-diaminobutanoic acid-based nucleopeptide. Bioorg Chem 2020; 100:103862. [PMID: 32428744 DOI: 10.1016/j.bioorg.2020.103862] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 04/01/2020] [Accepted: 04/16/2020] [Indexed: 01/09/2023]
Abstract
Herein we present the synthesis of a l-diaminobutanoic acid (DABA)-based nucleopeptide (3), with an oligocationic backbone, realized by solid phase peptide synthesis using thymine-bearing DABA moieties alternating in the sequence with free ones. CD studies evidenced the ability of this oligothymine nucleopeptide, well soluble in aqueous solution, to alter the secondary structure particularly of complementary RNA (poly rA vs poly rU) and inosine-rich RNAs, like poly rI and poly rIC, and showed its preference in binding double vs single-stranded DNAs. Furthermore, ESI mass spectrometry revealed that 3 bound also G-quadruplex (G4) DNAs, with either parallel or antiparallel topologies (adopted in our experimental conditions by c-myc and tel22, respectively). However, it caused detectable changes only in the CD of c-myc (whose parallel G4 structure was also thermally stabilized by ~3 °C), while leaving unaltered the antiparallel structure of tel22. Interestingly, CD and UV analyses suggested that 3 induced a hybrid mixed parallel/antiparallel G4 DNA structure in a random-coil tel22 DNA obtained under salt-free buffer conditions. Titration of the random-coil telomeric DNA with 3 gave quantitative information on the stoichiometry of the obtained complex. Overall, the findings of this work suggest that DABA-based nucleopeptides are synthetic nucleic acid analogues potentially useful in antigene and antisense strategies. Nevertheless, the hexathymine DABA-nucleopeptide shows an interesting behaviour as molecular tool per se thanks to its efficacy in provoking G4 induction in random coil G-rich DNA, as well as for the possibility to bind and stabilize c-myc oncogene in a G4 structure.
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Affiliation(s)
- Domenica Musumeci
- Department of Chemical Sciences, Federico II University, Via Cintia 21, 80126 Naples, Italy; Istituto di Biostrutture e Bioimmagini IBB - CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Andriy Mokhir
- Department of Chemistry and Pharmacy, Friedrich Alexander University, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Giovanni N Roviello
- Istituto di Biostrutture e Bioimmagini IBB - CNR, Via Mezzocannone 16, 80134 Naples, Italy.
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8
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Qi Q, Yang C, Xia Y, Guo S, Song D, Su H. Preferential Binding of π-Ligand Porphyrin Targeting 5'-5' Stacking Interface of Human Telomeric RNA G-Quadruplex Dimer. J Phys Chem Lett 2019; 10:2143-2150. [PMID: 30995046 DOI: 10.1021/acs.jpclett.9b00637] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Human telomeric RNA (TERRA) containing thousands of G-rich repeats has the propensity to form parallel-stranded G-quadruplexes. The emerging crucial roles of TERRA G-quadruplexes in RNA biology fuel increasing attention for studying anticancer ligand binding with such structures, which, however, remains scarce. Here we utilized multiple steady-state and time-resolved spectroscopy analyses in conjunction with NMR methods and investigated thoroughly the binding behavior of TMPyP4 to a TERRA G-quadruplex dimer formed by the 10-nucleotide sequence r(GGGUUAGGGU). It is clearly identified that TMPyP4 intercalates into the 5'-5' stacking interface of two G-quadruplex blocks with a binding stoichiometry of 1:1 and binding constant of 1.92 × 106 M-1. This is consistent with the unique TERRA structural features of the enlarged π-π stacking plane of the A·(G·G·G·G)·A hexad at 5'-ends of each G-quadruplex block. The preferential binding of π-ligand porphyrin to the 5'-5' stacking interface of the native TERRA G-quadruplex dimer is first ascertained by the combination of dynamics and structural characterization.
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Affiliation(s)
- Qige Qi
- Beijing National Laboratory for Molecular Science, Institute of Chemistry , Chinese Academy of Science , Beijing 100190 , China
- University of Chinese Academy of Science , Beijing 100049 , China
| | - Chunfan Yang
- College of Chemistry , Beijing Normal University , Beijing 100875 , China
| | - Ye Xia
- College of Chemistry , Beijing Normal University , Beijing 100875 , China
| | - Shaoshi Guo
- College of Chemistry , Beijing Normal University , Beijing 100875 , China
| | - Di Song
- Beijing National Laboratory for Molecular Science, Institute of Chemistry , Chinese Academy of Science , Beijing 100190 , China
| | - Hongmei Su
- College of Chemistry , Beijing Normal University , Beijing 100875 , China
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9
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Verma S, Ghuge SA, Ravichandiran V, Ranjan N. Spectroscopic studies of Thioflavin-T binding to c-Myc G-quadruplex DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 212:388-395. [PMID: 30703662 DOI: 10.1016/j.saa.2018.12.044] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 11/16/2018] [Accepted: 12/22/2018] [Indexed: 05/29/2023]
Abstract
G-quadruplexes are well-known DNA secondary structures which can be formed both within the DNA and the RNA sequences of the human genome. While many functions of G-quadruplex during cell regulatory events are still unknown, a number of reports have established their role in finding new cancer therapies. In this report, we provide a detailed account of Thioflavin T (ThT) interacting with a promoter gene (c-Myc) which has relevance in several types of human cancers. Using a variety of spectroscopic techniques, we have shown that the binding of ThT is selective to c-Myc G-quadruplex only, having poor interactions with the duplex DNA sequences. UV-Visible titration experiments show that binding involves stacking interactions which were further corroborated by CD experiments. Fluorescence studies showed that the binding of ThT to c-Myc G-quadruplex results in a large increase in the fluorescence emission spectrum of c-Myc G-quadruplex while the same to duplex DNAs was much poor. Binding of ThT to c-Myc G-quadruplex results in thermal stabilization of the quadruplex DNA by up to 7.4 °C and Job plot experiments demonstrated the presence of 1:1 and 2:1 ligand to quadruplex complexes. Finally, the docking study suggested that ThT stacks with the guanine bases in one of the grooves which is in agreement with the CD studies. These results are expected to provide leads into the design of new ThT analogs and derivatives for enhancing the stability and selectivity of new G-quadruplex targeting ligands.
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Affiliation(s)
- Smita Verma
- National Institute of Pharmaceutical Education and Research, ITI Compound, Raebareli 229010, India; National Institute of Pharmaceutical Education and Research, Kolkata, Maniktala Main Road, Kolkata 700054, India
| | - Sandip A Ghuge
- TERI-Deakin Nanobiotechnology Research Center, Sustainable Agriculture Division, The Energy and Resources Institute, New Delhi 110003, India
| | - V Ravichandiran
- National Institute of Pharmaceutical Education and Research, Kolkata, Maniktala Main Road, Kolkata 700054, India
| | - Nihar Ranjan
- National Institute of Pharmaceutical Education and Research, ITI Compound, Raebareli 229010, India.
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10
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Mandal P, Sahoo D, Saha S, Chowdhury J. Sensing of Different Human Telomeric G-Quadruplex DNA Topologies by Natural Alkaloid Allocryptopine Using Spectroscopic Techniques. J Phys Chem B 2018; 122:10279-10290. [PMID: 30346761 DOI: 10.1021/acs.jpcb.8b07856] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Paulami Mandal
- Department of Physics, Jadavpur University, 188, Raja S. C. Mallick Road, Kolkata, West Bengal 700032, India
| | - Dibakar Sahoo
- School of Physics, Sambalpur University, Jyoti Vihar, Burla, Odisha 768 019, India
| | - Saumen Saha
- Department of Physics, Jadavpur University, 188, Raja S. C. Mallick Road, Kolkata, West Bengal 700032, India
| | - Joydeep Chowdhury
- Department of Physics, Jadavpur University, 188, Raja S. C. Mallick Road, Kolkata, West Bengal 700032, India
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11
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Wang S, Qu F, Han W, You J. A resonance Rayleigh scattering sensor for sensitive differentiation of telomere DNA length and monitoring special motifs (G-quadruplex and i-motif) based on the Ag nanoclusters and NAND logic gate responding to chemical input signals. J Nanobiotechnology 2018; 16:78. [PMID: 30301461 PMCID: PMC6176526 DOI: 10.1186/s12951-018-0407-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 10/03/2018] [Indexed: 12/04/2022] Open
Abstract
Background Differentiation of telomere length is of vital importance because telomere length is closely related with several deadly diseases such as cancer. Additionally, G-quadruplex and i-motif formation in telomeric DNA have been shown to act as a negative regulator of telomere elongation by telomerase in vivo and are considered as an attractive drug target for cancer chemotherapy. Results In this assay, Ag nanoclusters templated by hyperbranched polyethyleneimine (PEI–Ag NCs) are designed as a new novel resonance Rayleigh scattering (RRS) probe for sensitive differentiation of telomere length and monitoring special motifs (G-quadruplex and i-motif). In this assay, free PEI–Ag NC probe or DNA sequence alone emits low intensities of RRS, while the formation of PEI–Ag NCs/DNA complexes yields greatly enhanced RRS signals; however, when PEI–Ag NCs react with G-quadruplex or i-motif, the intensities of RRS exhibit slight changes. At the same concentration, the enhancement of RRS signal is directly proportional to the length of telomere, and the sensitivity of 64 bases is the highest with the linear range of 0.3–50 nM (limit of detection 0.12 nM). On the other hand, due to the conversion of telomere DNA molecules among multiple surrounding conditions, a DNA logic gate is developed on the basis of two chemical input signals (K+ and H+) and a change in RRS intensity as the output signal. Conclusion Our results indicate that PEI–Ag NCs can serve as a novel RRS probe to identify DNA length and monitor G-quadruplex/i-motif through the different increasing degrees of RRS intensity. Meanwhile, the novel attributes of the nanoprobe stand superior to those involving dyes or labeled DNA because of no chemical modification, low cost, green, and high efficiency. Electronic supplementary material The online version of this article (10.1186/s12951-018-0407-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shuai Wang
- The Key Laboratory of Life-Organic Analysis, Qufu Normal University, Qufu, 273165, Shandong, China.,The Key Laboratory for Colloid and Interface Chemistry of Education Ministry, Shandong University, Jinan, 250100, Shandong, China
| | - Fei Qu
- The Key Laboratory of Life-Organic Analysis, Qufu Normal University, Qufu, 273165, Shandong, China.
| | - Wenli Han
- Laboratory Animal Center, Chongqing Medical University, Chongqing, China
| | - Jinmao You
- The Key Laboratory of Life-Organic Analysis, Qufu Normal University, Qufu, 273165, Shandong, China.,Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China
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12
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Halder D, Purkayastha P. A flavonol that acts as a potential DNA minor groove binder as also an efficient G-quadruplex loop binder. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.05.117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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13
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Chen SB, Liu GC, Gu LQ, Huang ZS, Tan JH. Identification of small molecules capable of regulating conformational changes of telomeric G-quadruplex. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.09.114] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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14
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Deiana M, Mettra B, Martinez-Fernandez L, Mazur LM, Pawlik K, Andraud C, Samoc M, Improta R, Monnereau C, Matczyszyn K. Specific Recognition of G-Quadruplexes Over Duplex-DNA by a Macromolecular NIR Two-Photon Fluorescent Probe. J Phys Chem Lett 2017; 8:5915-5920. [PMID: 29148817 DOI: 10.1021/acs.jpclett.7b02547] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The implication of guanine-rich DNA sequences in biologically important roles such as telomerase dysfunction and the regulation of gene expression has prompted the search for structure-specific G-quadruplex agents for targeted diagnostic and therapeutic applications. Herein, we report on a near-infrared (NIR) two-photon poly(cationic) anthracene-based macromolecule able to selectively target G-quadruplexes (G4s) over genomic double-stranded DNA. In particular, the striking changes in its linear and third-order nonlinear optical properties, combined with the emergence of a strong induced electronic circular dichroism (ECD) signal upon binding to canonical and noncanonical DNA secondary structures allowed for a highly specific detection of several different G4s. Furthermore, through a detailed computational analysis we bring compelling evidence that our probe intercalation within G4s is a thermodynamically favored event, and we fully rationalize the spectroscopic evolution resulting from this complexation event by providing a reasonable explanation regarding the origin of the peculiar ECD effect that accompanies it.
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Affiliation(s)
- Marco Deiana
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology , Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Bastien Mettra
- Université Lyon, ENS de Lyon, CNRS UMR 5182, Université Lyon 1 , Laboratoire de Chimie, F69342, Lyon, France
| | - Lara Martinez-Fernandez
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini , 80134 Naples, Italy
- LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette, France
| | - Leszek M Mazur
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology , Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Krzysztof Pawlik
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences , Rudolfa Weigla 12, 53-114 Wroclaw, Poland
| | - Chantal Andraud
- Université Lyon, ENS de Lyon, CNRS UMR 5182, Université Lyon 1 , Laboratoire de Chimie, F69342, Lyon, France
| | - Marek Samoc
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology , Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini , 80134 Naples, Italy
- LIDYL, CEA, CNRS, Université Paris-Saclay , F-91191 Gif-sur-Yvette, France
| | - Cyrille Monnereau
- Université Lyon, ENS de Lyon, CNRS UMR 5182, Université Lyon 1 , Laboratoire de Chimie, F69342, Lyon, France
| | - Katarzyna Matczyszyn
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology , Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
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15
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Mitrasinovic PM. Structural insights into the binding of small ligand molecules to a G-quadruplex DNA located in the HIV-1 promoter. J Biomol Struct Dyn 2017; 36:2292-2302. [DOI: 10.1080/07391102.2017.1358670] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Petar M. Mitrasinovic
- Center for Biophysical and Chemical Research, Department of Natural Sciences, Belgrade Institute of Science and Technology, Belgrade, Serbia
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16
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Bončina M, Hamon F, Islam B, Teulade-Fichou MP, Vesnaver G, Haider S, Lah J. Dominant Driving Forces in Human Telomere Quadruplex Binding-Induced Structural Alterations. Biophys J 2016; 108:2903-11. [PMID: 26083930 DOI: 10.1016/j.bpj.2015.05.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 04/07/2015] [Accepted: 05/03/2015] [Indexed: 01/23/2023] Open
Abstract
Recently various pathways of human telomere (ht) DNA folding into G-quadruplexes and of ligand binding to these structures have been proposed. However, the key issue as to the nature of forces driving the folding and recognition processes remains unanswered. In this study, structural changes of 22-mer ht-DNA fragment (Tel22), induced by binding of ions (K(+), Na(+)) and specific bisquinolinium ligands, were monitored by calorimetric and spectroscopic methods and by gel electrophoresis. Using the global model analysis of a wide variety of experimental data, we were able to characterize the thermodynamic forces that govern the formation of stable Tel22 G-quadruplexes, folding intermediates, and ligand-quadruplex complexes, and then predict Tel22 behavior in aqueous solutions as a function of temperature, salt concentration, and ligand concentration. On the basis of the above, we believe that our work sets the framework for better understanding the heterogeneity of ht-DNA folding and binding pathways, and its structural polymorphism.
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Affiliation(s)
- Matjaž Bončina
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Florian Hamon
- Institut Curie, Centre National de la Recherche Scientifique UMR-176, Centre Universitaire d'Orsay, Orsay, France
| | - Barira Islam
- Centre for Cancer Research and Cell Biology, Queen's University of Belfast, Belfast, UK
| | - Marie-Paule Teulade-Fichou
- Institut Curie, Centre National de la Recherche Scientifique UMR-176, Centre Universitaire d'Orsay, Orsay, France
| | - Gorazd Vesnaver
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Shozeb Haider
- Centre for Cancer Research and Cell Biology, Queen's University of Belfast, Belfast, UK; University College London School of Pharmacy, Bloomsbury, London, UK
| | - Jurij Lah
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia.
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17
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Jha NS, Mishra S, Mamidi AS, Mishra A, Jha SK, Surolia A. Targeting human telomeric G-quadruplex DNA with curcumin and its synthesized analogues under molecular crowding conditions. RSC Adv 2016. [DOI: 10.1039/c5ra17390f] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The formation of telomeric G-quadruplexes has been shown to inhibit telomerase activity.
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Affiliation(s)
- Niki S. Jha
- Department of Chemistry
- National Institute of Technology
- Patna-800005
- India
| | | | | | - Archita Mishra
- Molecular Biophysics Unit
- Indian Institute of Science
- Bangalore 560012
- India
| | | | - Avadhesha Surolia
- Molecular Biophysics Unit
- Indian Institute of Science
- Bangalore 560012
- India
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18
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Marchand A, Granzhan A, Iida K, Tsushima Y, Ma Y, Nagasawa K, Teulade-Fichou MP, Gabelica V. Ligand-induced conformational changes with cation ejection upon binding to human telomeric DNA G-quadruplexes. J Am Chem Soc 2015; 137:750-6. [PMID: 25525863 DOI: 10.1021/ja5099403] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The rational design of ligands targeting human telomeric DNA G-quadruplexes is a complex problem due to the structural polymorphism that these sequences can adopt in physiological conditions. Moreover, the ability of ligands to switch conformational equilibria between different G-quadruplex structures is often overlooked in docking approaches. Here, we demonstrate that three of the most potent G-quadruplex ligands (360A, Phen-DC3, and pyridostatin) induce conformational changes of telomeric DNA G-quadruplexes to an antiparallel structure (as determined by circular dichroism) containing only one specifically coordinated K(+) (as determined by electrospray mass spectrometry) and, hence, presumably only two consecutive G-quartets. Control ligands TrisQ, known to bind preferentially to hybrid than to antiparallel structures, and L2H2-6M(2)OTD, known not to disrupt the hybrid-1 structure, did not show such K(+) removal. Instead, binding of the cyclic oxazole L2H2-6M(2)OTD was accompanied by the uptake of one additional K(+). Also contrasting with telomeric G-quadruplexes, the parallel-stranded Pu24-myc G-quadruplex, to which Phen-DC3 is known to bind by end-stacking, did not undergo cation removal upon ligand binding. Our study therefore evidences that very affine ligands can induce conformational switching of the human telomeric G-quadruplexes to an antiparallel structure and that this conformational change is accompanied by removal of one interquartet cation.
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Affiliation(s)
- Adrien Marchand
- IECB, ARNA Laboratory, University of Bordeaux , 33600 Pessac, France
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19
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Pu F, Wu L, Ran X, Ren J, Qu X. G-Quartet-Based Nanostructure for Mimicking Light-Harvesting Antenna. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409832] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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20
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Pu F, Wu L, Ran X, Ren J, Qu X. G-quartet-based nanostructure for mimicking light-harvesting antenna. Angew Chem Int Ed Engl 2014; 54:892-6. [PMID: 25423890 DOI: 10.1002/anie.201409832] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Indexed: 12/13/2022]
Abstract
Artificial light-harvesting systems have received great attention for use in photosynthetic and optoelectronic devices. Herein, a system involving G-quartet-based hierarchical nanofibers generated from the self-assembly of guanosine 5'-monophosphate (GMP) and a two-step Förster resonance energy transfer (FRET) is presented that mimics natural light-harvesting antenna. This solid-state property offers advantages for future device fabrication. The generation of photocurrent under visible light shows it has potential for use as a nanoscale photoelectric device. The work will be beneficial for the development of light-harvesting systems by the self-assembly of supramolecular nanostructures.
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Affiliation(s)
- Fang Pu
- State Key Laboratory of Rare Earth Resource Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022 (P.R. China)
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21
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Roembke BT, Nakayama S, Sintim HO. Nucleic acid detection using G-quadruplex amplification methodologies. Methods 2013; 64:185-98. [PMID: 24135042 PMCID: PMC7129037 DOI: 10.1016/j.ymeth.2013.10.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 09/19/2013] [Accepted: 10/02/2013] [Indexed: 12/28/2022] Open
Abstract
In the last decade, there has been an explosion in the use of G-quadruplex labels to detect various analytes, including DNA/RNA, proteins, metals and other metabolites. In this review, we focus on strategies for the detection of nucleic acids, using G-quadruplexes as detection labels or as enzyme labels that amplify detection signals. Methods to detect other analytes are briefly mentioned. We highlight various strategies, including split G-quadruplex, hemin-G-quadruplex conjugates, molecular beacon G-quadruplex or inhibited G-quadruplex probes. The tandem use of G-quadruplex labels with various DNA-modifying enzymes, such as polymerases (used for rolling circle amplification), exonucleases and endonucleases, is also discussed. Some of the detection modalities that are discussed in this review include fluorescence, colorimetric, chemiluminescence, and electrochemical methods.
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22
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Sun H, Xiang J, Li Q, Liu Y, Li L, Shang Q, Xu G, Tang Y. Recognize three different human telomeric G-quadruplex conformations by quinacrine. Analyst 2012; 137:862-7. [PMID: 22223064 DOI: 10.1039/c2an15870a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Recognition of different human telomeric G-quadruplex structures has been a very important task for developing anti-cancer drug design. However, it also is a very challenging question since multiple conformational isomers of telomeric G-quadruplexes coexist under some conditions. Here, three different conformations including parallel, antiparallel, and mixed-type telomeric G-quadruplex structures have been well recognized by quinacrine (QNA) through monitoring its absorption, fluorescence, and fluorescence lifetime spectra. The multiple structures of H22 G-quadruplexes under physiological K(+) conditions could also be easily determined to coexist as mixed-type and antiparallel G-quadruplexes. The recognition mechanism based on the different binding affinity and binding sites has been further elucidated by association with the nuclear magnetic resonance (NMR) results.
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Affiliation(s)
- Hongxia Sun
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, PR China
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23
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Zhao C, Geng J, Feng L, Ren J, Qu X. Chiral Metallo-Supramolecular Complexes Selectively Induce Human Telomeric G-Quadruplex Formation under Salt-Deficient Conditions. Chemistry 2011; 17:8209-15. [DOI: 10.1002/chem.201100272] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Indexed: 12/11/2022]
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24
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Sparapani S, Haider SM, Doria F, Gunaratnam M, Neidle S. Rational design of acridine-based ligands with selectivity for human telomeric quadruplexes. J Am Chem Soc 2010; 132:12263-72. [PMID: 20718414 DOI: 10.1021/ja1003944] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Structure-based modeling methods have been used to design a series of disubstituted triazole-linked acridine compounds with selectivity for human telomeric quadruplex DNAs. A focused library of these compounds was prepared using click chemistry and the selectivity concept was validated against two promoter quadruplexes from the c-kit gene with known molecular structures, as well as with duplex DNA using a FRET-based melting method. Lead compounds were found to have reduced effects on the thermal stability of the c-kit quadruplexes and duplex DNA structures. These effects were further explored with a series of competition experiments, which confirmed that binding to duplex DNA is very low even at high duplex:telomeric quadruplex ratios. Selectivity to the c-kit quadruplexes is more complex, with some evidence of their stabilization at increasing excess over human telomeric quadruplex DNA. Selectivity is a result of the dimensions of the triazole-acridine compounds, and in particular the separation of the two alkyl-amino terminal groups. Both lead compounds also have selective inhibitory effects on the proliferation of cancer cell lines compared to a normal cell line, and one has been shown to inhibit the activity of the telomerase enzyme, which is selectively expressed in tumor cells, where it plays a role in maintaining telomere integrity and cellular immortalization.
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Affiliation(s)
- Silvia Sparapani
- CR-UK Biomolecular Structure Group, The School of Pharmacy, University of London, London WC1N 1AX, UK
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25
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Song G, Ren J. Recognition and regulation of unique nucleic acid structures by small molecules. Chem Commun (Camb) 2010; 46:7283-94. [DOI: 10.1039/c0cc01312a] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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