1
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Xu Y, Komiyama M. G-Quadruplexes in Human Telomere: Structures, Properties, and Applications. Molecules 2023; 29:174. [PMID: 38202757 PMCID: PMC10780218 DOI: 10.3390/molecules29010174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
G-quadruplexes, intricate four-stranded structures composed of G-tetrads formed by four guanine bases, are prevalent in both DNA and RNA. Notably, these structures play pivotal roles in human telomeres, contributing to essential cellular functions. Additionally, the existence of DNA:RNA hybrid G-quadruplexes adds a layer of complexity to their structural diversity. This review provides a comprehensive overview of recent advancements in unraveling the intricacies of DNA and RNA G-quadruplexes within human telomeres. Detailed insights into their structural features are presented, encompassing the latest developments in chemical approaches designed to probe these G-quadruplex structures. Furthermore, this review explores the applications of G-quadruplex structures in targeting human telomeres. Finally, the manuscript outlines the imminent challenges in this evolving field, setting the stage for future investigations.
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Affiliation(s)
- Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Makoto Komiyama
- Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
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2
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Saleh LY, Ora M, Lönnberg T. Organomercury oligonucleotide conjugates as artificial ribonucleases. J Inorg Biochem 2023; 247:112331. [PMID: 37480764 DOI: 10.1016/j.jinorgbio.2023.112331] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/03/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023]
Abstract
Two oligonucleotide conjugates sharing the same sequence but incorporating a different 5'-terminal organometallic moiety were synthesized, by either direct mercuration in solution or oximation with an organomercury aldehyde on solid support. The potential of these conjugates to serve as new type of artificial ribonucleases was tested with a complementary 2´-O-methyl-RNA target sequence featuring a single cleavable RNA phosphodiester linkage. Both organomercury oligonucleotides greatly outperformed their metal-free counterparts as well as the previously reported small molecule organomercury RNA cleaving agent in catalytic activity, providing an important proof-of-concept. Compared to state-of-the-art metal-dependent artificial ribonucleases, however, the observed activity was modest.
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Affiliation(s)
- Lange Yakubu Saleh
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland
| | - Mikko Ora
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
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3
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Chatain J, Hatem G, Delagoutte E, Riou JF, Alberti P, Saintomé C. Multiple hPOT1-TPP1 cooperatively unfold contiguous telomeric G-quadruplexes proceeding from 3' toward 5', a feature due to a 3'-end binding preference and to structuring of telomeric DNA. Nucleic Acids Res 2021; 49:10735-10746. [PMID: 34534331 PMCID: PMC8501996 DOI: 10.1093/nar/gkab768] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 08/04/2021] [Accepted: 09/15/2021] [Indexed: 02/07/2023] Open
Abstract
Telomeres are DNA repeated sequences that associate with shelterin proteins and protect the ends of eukaryotic chromosomes. Human telomeres are composed of 5'TTAGGG repeats and ends with a 3' single-stranded tail, called G-overhang, that can be specifically bound by the shelterin protein hPOT1 (human Protection of Telomeres 1). In vitro studies have shown that the telomeric G-strand can fold into stable contiguous G-quadruplexes (G4). In the present study we investigated how hPOT1, in complex with its shelterin partner TPP1, binds to telomeric sequences structured into contiguous G4 in potassium solutions. We observed that binding of multiple hPOT1-TPP1 preferentially proceeds from 3' toward 5'. We explain this directionality in terms of two factors: (i) the preference of hPOT1-TPP1 for the binding site situated at the 3' end of a telomeric sequence and (ii) the cooperative binding displayed by hPOT1-TPP1 in potassium. By comparing binding in K+ and in Li+, we demonstrate that this cooperative behaviour does not stem from protein-protein interactions, but from structuring of the telomeric DNA substrate into contiguous G4 in potassium. Our study suggests that POT1-TPP1, in physiological conditions, might preferentially cover the telomeric G-overhang starting from the 3'-end and proceeding toward 5'.
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Affiliation(s)
- Jean Chatain
- Structure et Instabilité des Génomes, Muséum national d'Histoire naturelle, CNRS, INSERM, 43 rue Cuvier, F-75005 Paris, France
| | - Georges Hatem
- Structure et Instabilité des Génomes, Muséum national d'Histoire naturelle, CNRS, INSERM, 43 rue Cuvier, F-75005 Paris, France
| | - Emmanuelle Delagoutte
- Structure et Instabilité des Génomes, Muséum national d'Histoire naturelle, CNRS, INSERM, 43 rue Cuvier, F-75005 Paris, France
| | - Jean-François Riou
- Structure et Instabilité des Génomes, Muséum national d'Histoire naturelle, CNRS, INSERM, 43 rue Cuvier, F-75005 Paris, France
| | - Patrizia Alberti
- Structure et Instabilité des Génomes, Muséum national d'Histoire naturelle, CNRS, INSERM, 43 rue Cuvier, F-75005 Paris, France
| | - Carole Saintomé
- Structure et Instabilité des Génomes, Muséum national d'Histoire naturelle, CNRS, INSERM, 43 rue Cuvier, F-75005 Paris, France.,Sorbonne Université, UFR927, F-75005 Paris, France
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4
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Cadoni E, De Paepe L, Manicardi A, Madder A. Beyond small molecules: targeting G-quadruplex structures with oligonucleotides and their analogues. Nucleic Acids Res 2021; 49:6638-6659. [PMID: 33978760 PMCID: PMC8266634 DOI: 10.1093/nar/gkab334] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/15/2021] [Accepted: 04/29/2021] [Indexed: 12/20/2022] Open
Abstract
G-Quadruplexes (G4s) are widely studied secondary DNA/RNA structures, naturally occurring when G-rich sequences are present. The strategic localization of G4s in genome areas of crucial importance, such as proto-oncogenes and telomeres, entails fundamental implications in terms of gene expression regulation and other important biological processes. Although thousands of small molecules capable to induce G4 stabilization have been reported over the past 20 years, approaches based on the hybridization of a synthetic probe, allowing sequence-specific G4-recognition and targeting are still rather limited. In this review, after introducing important general notions about G4s, we aim to list, explain and critically analyse in more detail the principal approaches available to target G4s by using oligonucleotides and synthetic analogues such as Locked Nucleic Acids (LNAs) and Peptide Nucleic Acids (PNAs), reporting on the most relevant examples described in literature to date.
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Affiliation(s)
- Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Lessandro De Paepe
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Alex Manicardi
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
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5
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Punt PM, Langenberg MD, Altan O, Clever GH. Modular Design of G-Quadruplex MetalloDNAzymes for Catalytic C-C Bond Formations with Switchable Enantioselectivity. J Am Chem Soc 2021; 143:3555-3561. [PMID: 33630569 DOI: 10.1021/jacs.0c13251] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metal-binding DNA structures with catalytic function are receiving increasing interest. Although a number of metalloDNAzymes have been reported to be highly efficient, the exact coordination/position of their catalytic metal center is often unknown. Here, we present a new approach to rationally develop metalloDNAzymes for Lewis acid-catalyzed reactions such as enantioselective Michael additions. Our strategy relies on the predictable folding patterns of unimolecular DNA G-quadruplexes, combined with the concept of metal-mediated base-pairing. Transition-metal coordination environments were created in G-quadruplex loop regions, accessible by substrates. Therefore, protein-inspired imidazole ligandoside L was covalently incorporated into a series of G-rich DNA strands by solid-phase synthesis. Iterative rounds of DNA sequence design and catalytic assays allowed us to select tailored metalloDNAzymes giving high conversions and excellent enantioselectivities (≥99%). Based on their primary sequence, folding pattern, and metal coordination mode, valuable information on structure-activity relationships could be extracted. Variation of the number and position of ligand L within the sequence allowed us to control the formation of (S) and (R) enantiomeric reaction products, respectively.
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Affiliation(s)
- Philip M Punt
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Marie D Langenberg
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Okan Altan
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Guido H Clever
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
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6
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Ortiz de Luzuriaga I, Lopez X, Gil A. Learning to Model G-Quadruplexes: Current Methods and Perspectives. Annu Rev Biophys 2021; 50:209-243. [PMID: 33561349 DOI: 10.1146/annurev-biophys-060320-091827] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
G-quadruplexes have raised considerable interest during the past years for the development of therapies against cancer. These noncanonical structures of DNA may be found in telomeres and/or oncogene promoters, and it has been observed that the stabilization of such G-quadruplexes may disturb tumor cell growth. Nevertheless, the mechanisms leading to folding and stabilization of these G-quadruplexes are still not well established, and they are the focus of much current work in this field. In seminal works, stabilization was observed to be produced by cations. However, subsequent studies showed that different kinds of small molecules, from planar and nonplanar organic molecules to square-planar and octahedral metal complexes, may also lead to the stabilization of G-quadruplexes. Thus, the comprehension and rationalization of the interaction of these small molecules with G-quadruplexes are also important topics of current interest in medical applications. To shed light on the questions arising from the literature on the formation of G-quadruplexes, their stabilization, and their interaction with small molecules, synergies between experimental studies and computational works are needed. In this review, we mainly focus on in silico approaches and provide a broad compilation of different leading studies carried out to date by different computational methods. We divide these methods into twomain categories: (a) classical methods, which allow for long-timescale molecular dynamics simulations and the corresponding analysis of dynamical information, and (b) quantum methods (semiempirical, quantum mechanics/molecular mechanics, and density functional theory methods), which allow for the explicit simulation of the electronic structure of the system but, in general, are not capable of being used in long-timescale molecular dynamics simulations and, therefore, give a more static picture of the relevant processes.
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Affiliation(s)
- Iker Ortiz de Luzuriaga
- CIC nanoGUNE BRTA, 20018 Donostia, Euskadi, Spain; .,Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Uniberstitatea, UPV/EHU, 20080 Donostia, Euskadi, Spain
| | - Xabier Lopez
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Uniberstitatea, UPV/EHU, 20080 Donostia, Euskadi, Spain.,Donostia International Physics Center, 20018 Donostia, Spain
| | - Adrià Gil
- CIC nanoGUNE BRTA, 20018 Donostia, Euskadi, Spain; .,BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal;
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7
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Sun Y, Zhao C, Cui T, Qin H, Niu J, Ren J, Qu X. Near-infrared-traceable DNA nano-hydrolase: specific eradication of telomeric G-overhang in vivo. Nucleic Acids Res 2020; 48:9986-9994. [PMID: 32853337 PMCID: PMC7515709 DOI: 10.1093/nar/gkaa693] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 08/05/2020] [Accepted: 08/25/2020] [Indexed: 01/16/2023] Open
Abstract
Telomeric DNA, whose length homeostasis is closely correlated with immortality of cancer cells, is regarded as a molecular clock for cellular lifespan. Regarding the capacity in forming G-quadruplex, G-rich 3′-overhang (G-overhang) has been considered as an attractive anticancer target. However, it is still challenging to precisely target telomeric G-overhang with current ligands because of the polymorphism of G-quadruplexes in cells. Herein, we construct a telomeric G-overhang-specific near-infrared-traceable DNA nano-hydrolase, which is composed of four parts: (i) dexamethasone for targeting cell nuclei; (ii) complementary DNA for hybridizing with G-overhang; (iii) multinuclear Ce(IV) complexes for hydrolyzing G-overhang; and (iv) upconversion nanoparticles for real-time tracking. The multivalent targeted DNA nano-hydrolase can be traced to precisely digest telomeric G-overhang, which contributes to telomeric DNA shortening and thereby causes cell aging and apoptosis. The anticancer treatment is further proved by in vivo studies. In this way, this design provides a telomeric G-overhang-specific eradication strategy based on a non-G-quadruplex targeting manner.
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Affiliation(s)
- Yuhuan Sun
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.,School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Chuanqi Zhao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Tingting Cui
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.,School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Hongshuang Qin
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Jingsheng Niu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.,School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.,School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.,School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
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8
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Yu Y, Zhang Q, Gao H, Yan C, Zheng X, Yang T, Zhou X, Shao Y. Metalloenzyme-mimic innate G-quadruplex DNAzymes using directly coordinated metal ions as active centers. Dalton Trans 2020; 49:13160-13166. [PMID: 32936164 DOI: 10.1039/d0dt02871a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
G-quadruplex DNAs (G4s) have been reported to exhibit the DNAzyme activities by binding with some metal complexes and functional organic ligands. However, there is a challenge to develop metalloenzyme-mimic G4-based innate DNAzymes using the complexed metal ions directly serving as the active centers. This will diversify DNAzymes for developing novel devices since G4 structures are more polymorphic than the other DNA foldings. In this work, we found that the lanthanide trivalent cerium ion of Ce3+ can bind to the human telomere G4 (htG4) according to a 1 : 2 binding mode favorable for creating metalloenzymes-mimic G4 DNAzymes. This Ce3+-G4 entity exhibits a peroxidase activity towards the oxidation of the substrate of 3,3,5,5-tetramethylbenzidine (TMB) by hydrogen peroxide. The 5' G4 tetrads with the orderly arranged carbonyl oxygen atoms are believed to be the coordination sites for Ce3+ and favor the conversion between Ce3+ and Ce4+. Our work provides an alternative feasibility in developing the G4-based innate DNAzymes for variant applications.
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Affiliation(s)
- Yali Yu
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
| | - Qingqing Zhang
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
| | - Heng Gao
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
| | - Chenxiao Yan
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
| | - Xiong Zheng
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
| | - Tong Yang
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
| | - Xiaoshun Zhou
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
| | - Yong Shao
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
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9
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Punt PM, Stratmann LM, Sevim S, Knauer L, Strohmann C, Clever GH. Heteroleptic Coordination Environments in Metal-Mediated DNA G-Quadruplexes. Front Chem 2020; 8:26. [PMID: 32064249 PMCID: PMC7000376 DOI: 10.3389/fchem.2020.00026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/09/2020] [Indexed: 12/28/2022] Open
Abstract
The presence of metal centers with often highly conserved coordination environments is crucial for roughly half of all proteins, having structural, regulatory, or enzymatic function. To understand and mimic the function of metallo-enzymes, bioinorganic chemists pursue the challenge of synthesizing model compounds with well-defined, often heteroleptic metal sites. Recently, we reported the design of tailored homoleptic coordination environments for various transition metal cations based on unimolecular DNA G-quadruplex structures, templating the regioselective positioning of imidazole ligandosides LI. Here, we expand this modular system to more complex, heteroleptic coordination environments by combining LI with a new benzoate ligandoside LB within the same oligonucleotide. The modifications still allow the correct folding of parallel tetramolecular and antiparallel unimolecular G-quadruplexes. Interestingly, the incorporation of LB results in strong destabilization expressed in lower thermal denaturation temperatures Tm. While no transition metal cations could be bound by G-quadruplexes containing only LB, heteroleptic derivatives containing both LI and LB were found to complex CuII, NiII, and ZnII. Especially in case of CuII we found strong stabilizations of up to ΔTm = +34°C. The here shown system represents an important step toward the design of more complex coordination environments inside DNA scaffolds, promising to culminate in the preparation of functional metallo-DNAzymes.
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Affiliation(s)
- Philip M Punt
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Lukas M Stratmann
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Sinem Sevim
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Lena Knauer
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Carsten Strohmann
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Guido H Clever
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
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10
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Punt PM, Clever GH. Tailored Transition-Metal Coordination Environments in Imidazole-Modified DNA G-Quadruplexes. Chemistry 2019; 25:13987-13993. [PMID: 31468606 PMCID: PMC6899475 DOI: 10.1002/chem.201903445] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/28/2019] [Indexed: 12/18/2022]
Abstract
Two types of imidazole ligands were introduced both at the end of tetramolecular and into the loop region of unimolecular DNA G‐quadruplexes. The modified oligonucleotides were shown to complex a range of different transition‐metal cations including NiII, CuII, ZnII and CoII, as indicated by UV/Vis absorption spectroscopy and ion mobility mass spectrometry. Molecular dynamics simulations were performed to obtain structural insight into the investigated systems. Variation of ligand number and position in the loop region of unimolecular sequences derived from the human telomer region (htel) allows for a controlled design of distinct coordination environments with fine‐tuned metal affinities. It is shown that CuII, which is typically square‐planar coordinated, has a higher affinity for systems offering four ligands, whereas NiII prefers G‐quadruplexes with six ligands. Likewise, the positioning of ligands in a square‐planar versus tetrahedral fashion affects binding affinities of CuII and ZnII cations, respectively. Gaining control over ligand arrangement patterns will spur the rational development of transition‐metal‐modified DNAzymes. Furthermore, this method is suited to combine different types of ligands, for example, those typically found in metalloenzymes, inside a single DNA architecture.
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Affiliation(s)
- Philip M Punt
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
| | - Guido H Clever
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
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11
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Ishizuka T, Bao HL, Xu Y. 19F NMR Spectroscopy for the Analysis of DNA G-Quadruplex Structures Using 19F-Labeled Nucleobase. Methods Mol Biol 2019; 2035:407-433. [PMID: 31444766 DOI: 10.1007/978-1-4939-9666-7_26] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
G-quadruplex structures have been suggested to be biologically important in processes such as transcription and translation, gene expression and regulation in human cancer cells, and regulation of telomere length. Investigation of G-quadruplex structures associated with biological events is therefore essential to understanding the functions of these molecules. We developed the 19F-labeled nucleobases and introduced them into DNA sequences for the 19F NMR spectroscopy analysis. We present the 19F NMR methodology used in our research group for the study of G-quadruplex structures in vitro and in living cells.
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Affiliation(s)
- Takumi Ishizuka
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Hong-Liang Bao
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
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12
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Ishizuka T, Zhao PY, Bao HL, Xu Y. A multi-functional guanine derivative for studying the DNA G-quadruplex structure. Analyst 2018; 142:4083-4088. [PMID: 28932835 DOI: 10.1039/c7an00941k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In the present study, we developed a multi-functional guanine derivative, 8FG, as a G-quadruplex stabilizer, a fluorescent probe for the detection of G-quadruplex formation, and a 19F sensor for the observation of the G-quadruplex. We demonstrate that the functional nucleoside bearing a 3,5-bis(trifluoromethyl)benzene group at the 8-position of guanine stabilizes the DNA G-quadruplex structure and fluoresces following the G-quadruplex formation. Furthermore, we show that the functional sensor can be used to directly observe DNA G-quadruplexes by 19F-NMR in living cells. To our knowledge, this is the first study showing that the nucleoside derivative simultaneously allows for three kinds of functions at a single G-quadruplex DNA. Our results suggest that the multi-functional nucleoside derivative can be broadly used for studying the G-quadruplex structure and serves as a powerful tool for examining the molecular basis of G-quadruplex formation in vitro and in living cells.
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Affiliation(s)
- Takumi Ishizuka
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan.
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13
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Molphy Z, Montagner D, Bhat SS, Slator C, Long C, Erxleben A, Kellett A. A phosphate-targeted dinuclear Cu(II) complex combining major groove binding and oxidative DNA cleavage. Nucleic Acids Res 2018; 46:9918-9931. [PMID: 30239938 PMCID: PMC6212767 DOI: 10.1093/nar/gky806] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 08/05/2018] [Accepted: 09/05/2018] [Indexed: 12/18/2022] Open
Abstract
Free radical generation is an inevitable consequence of aerobic existence and is implicated in a wide variety of pathological conditions including cancer, cardiovascular disease, ageing and neurodegenerative disorder. Free radicals can, however, be used to our advantage since their production is catalysed by synthetic inorganic molecules-termed artificial metallonucleases-that cut DNA strands by oxidative cleavage reactions. Here, we report the rational design and DNA binding interactions of a novel di-Cu2+ artificial metallonuclease [Cu2(tetra-(2-pyridyl)-NMe-naphthalene)Cl4] (Cu2TPNap). Cu2TPNap is a high-affinity binder of duplex DNA with an apparent binding constant (Kapp) of 107 M(bp)-1. The agent binds non-intercalatively in the major groove causing condensation and G-C specific destabilization. Artificial metallonuclease activity occurs in the absence of exogenous reductant, is dependent on superoxide and hydrogen peroxide, and gives rise to single strand DNA breaks. Pre-associative molecular docking studies with the 8-mer d(GGGGCCCC)2, a model for poly[d(G-C)2], identified selective major groove incorporation of the complex with ancillary Cu2+-phosphate backbone binding. Molecular mechanics methods then showed the d(GGGGCCCC)2 adduct to relax about the complex and this interaction is supported by UV melting experiments where poly[d(G-C)2] is selectively destabilized.
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Affiliation(s)
- Zara Molphy
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Diego Montagner
- Department of Chemistry, Maynooth University, Maynooth, Kildare, Ireland
| | - Satish S Bhat
- School of Chemistry, National University of Ireland Galway, Galway, Ireland
| | - Creina Slator
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Conor Long
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Andrea Erxleben
- School of Chemistry, National University of Ireland Galway, Galway, Ireland
- Synthesis and Solid-State Pharmaceutical Centre, School of Chemistry, National University of Ireland Galway, Galway, Ireland
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
- Synthesis and Solid-State Pharmaceutical Centre, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
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14
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Engelhard DM, Stratmann LM, Clever GH. Structure-Property Relationships in Cu II -Binding Tetramolecular G-Quadruplex DNA. Chemistry 2017; 24:2117-2125. [PMID: 29139578 DOI: 10.1002/chem.201703409] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Indexed: 12/29/2022]
Abstract
A series of artificial metal-base tetrads composed of a CuII cation coordinating to four pyridines, covalently attached to the ends of tetramolecular G-quadruplex DNA strands [LA-D d(G4 )]4 (LA-D =ligand derivatives), was systematically studied. Structurally, the square-planar [Cu(pyridine)4 ] complex behaves analogously to the canonical guanine quartet. Copper coordination to all studied ligand derivatives was found to increase G-quadruplex thermodynamic stability, tolerating a great variety of ligand linker lengths (1-5 atoms) and thus demonstrating the robustness of the chosen ligand design. Only at long linker lengths, the stabilizing effect of copper binding is compensated by the loss of conformational freedom. A previously reported ligand LE with chiral backbone enables incorporation at any oligonucleotide position. We show that ligand chirality distinctly steers CuII -induced G-quadruplex stabilization. 5'-End formation of two metal-base tetrads by tetramolecular G-quadruplex [LE2 d(G)4 ]4 shows that stabilization in the presence of CuII is not additive. All results are based on UV/Vis thermal denaturation, thermal difference, circular dichroism experiments and molecular dynamics simulations.
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Affiliation(s)
- David M Engelhard
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
| | - Lukas M Stratmann
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
| | - Guido H Clever
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
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15
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Sagi J. In What Ways Do Synthetic Nucleotides and Natural Base Lesions Alter the Structural Stability of G-Quadruplex Nucleic Acids? J Nucleic Acids 2017; 2017:1641845. [PMID: 29181193 PMCID: PMC5664352 DOI: 10.1155/2017/1641845] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/15/2017] [Indexed: 01/03/2023] Open
Abstract
Synthetic analogs of natural nucleotides have long been utilized for structural studies of canonical and noncanonical nucleic acids, including the extensively investigated polymorphic G-quadruplexes (GQs). Dependence on the sequence and nucleotide modifications of the folding landscape of GQs has been reviewed by several recent studies. Here, an overview is compiled on the thermodynamic stability of the modified GQ folds and on how the stereochemical preferences of more than 70 synthetic and natural derivatives of nucleotides substituting for natural ones determine the stability as well as the conformation. Groups of nucleotide analogs only stabilize or only destabilize the GQ, while the majority of analogs alter the GQ stability in both ways. This depends on the preferred syn or anti N-glycosidic linkage of the modified building blocks, the position of substitution, and the folding architecture of the native GQ. Natural base lesions and epigenetic modifications of GQs explored so far also stabilize or destabilize the GQ assemblies. Learning the effect of synthetic nucleotide analogs on the stability of GQs can assist in engineering a required stable GQ topology, and exploring the in vitro action of the single and clustered natural base damage on GQ architectures may provide indications for the cellular events.
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Affiliation(s)
- Janos Sagi
- Rimstone Laboratory, RLI, Carlsbad, CA 92010, USA
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16
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Engelhard DM, Nowack J, Clever GH. Kupfer-vermittelte Topologieänderung und Thrombin-Inhibierung mit telomerischen DNA-G-Quadruplexen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201705724] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- David M. Engelhard
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 6 44227 Dortmund Deutschland
| | - Julia Nowack
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 6 44227 Dortmund Deutschland
| | - Guido H. Clever
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 6 44227 Dortmund Deutschland
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17
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Engelhard DM, Nowack J, Clever GH. Copper-Induced Topology Switching and Thrombin Inhibition with Telomeric DNA G-Quadruplexes. Angew Chem Int Ed Engl 2017; 56:11640-11644. [DOI: 10.1002/anie.201705724] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Indexed: 11/10/2022]
Affiliation(s)
- David M. Engelhard
- Department of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Julia Nowack
- Department of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Guido H. Clever
- Department of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
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18
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Synthesis and photophysical characterization of luminescent lanthanide complexes of nucleotide-functionalized cyclen- and dipicolinate-based ligands. Inorganica Chim Acta 2017. [DOI: 10.1016/j.ica.2016.07.047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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19
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Cao Q, Li Y, Freisinger E, Qin PZ, Sigel RKO, Mao ZW. G-quadruplex DNA targeted metal complexes acting as potential anticancer drugs. Inorg Chem Front 2017. [DOI: 10.1039/c6qi00300a] [Citation(s) in RCA: 174] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This review summarizes the recent development of G4 DNA targeted metal complexes and discusses their potential as anticancer drugs.
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Affiliation(s)
- Qian Cao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou 510275
- China
| | - Yi Li
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou 510275
- China
| | - Eva Freisinger
- University of Zurich
- Department of Chemistry
- CH-8057 Zurich
- Switzerland
| | - Peter Z. Qin
- Department of Chemistry
- University of Southern California
- Los Angeles
- USA
| | | | - Zong-Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou 510275
- China
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20
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Zhao C, Sun Y, Ren J, Qu X. Recent progress in lanthanide complexes for DNA sensing and targeting specific DNA structures. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.04.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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21
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Chen Z, Ji H, Liu C, Bing W, Wang Z, Qu X. A Multinuclear Metal Complex Based DNase-Mimetic Artificial Enzyme: Matrix Cleavage for Combating Bacterial Biofilms. Angew Chem Int Ed Engl 2016; 55:10732-6. [PMID: 27484616 DOI: 10.1002/anie.201605296] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/04/2016] [Indexed: 12/18/2022]
Abstract
Extracellular DNA (eDNA) is an essential structural component during biofilm formation, including initial bacterial adhesion, subsequent development, and final maturation. Herein, the construction of a DNase-mimetic artificial enzyme (DMAE) for anti-biofilm applications is described. By confining passivated gold nanoparticles with multiple cerium(IV) complexes on the surface of colloidal magnetic Fe3 O4 /SiO2 core/shell particles, a robust and recoverable artificial enzyme with DNase-like activity was obtained, which exhibited high cleavage ability towards both model substrates and eDNA. Compared to the high environmental sensitivity of natural DNase in anti-biofilm applications, DMAE exhibited a much better operational stability and easier recoverability. When DMAE was coated on substratum surfaces, biofilm formation was inhibited for prolonged periods of time, and the DMAE excelled in the dispersion of established biofilms of various ages. Finally, the presence of DMAE remarkably potentiated the efficiency of traditional antibiotics to kill biofilm-encased bacteria and eradiate biofilms.
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Affiliation(s)
- Zhaowei Chen
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.,University of Chinese Academy of Sciences, Beijing, 100039, China.,Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Raleigh, NC, 27695, USA
| | - Haiwei Ji
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Chaoqun Liu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Wei Bing
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Zhenzhen Wang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.
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22
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Chen Z, Ji H, Liu C, Bing W, Wang Z, Qu X. A Multinuclear Metal Complex Based DNase-Mimetic Artificial Enzyme: Matrix Cleavage for Combating Bacterial Biofilms. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605296] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Zhaowei Chen
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 China
- University of Chinese Academy of Sciences; Beijing 100039 China
- Joint Department of Biomedical Engineering; University of North Carolina at Chapel Hill and North Carolina State University; Raleigh NC 27695 USA
| | - Haiwei Ji
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 China
- University of Chinese Academy of Sciences; Beijing 100039 China
| | - Chaoqun Liu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 China
- University of Chinese Academy of Sciences; Beijing 100039 China
| | - Wei Bing
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 China
- University of Chinese Academy of Sciences; Beijing 100039 China
| | - Zhenzhen Wang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 China
- University of Chinese Academy of Sciences; Beijing 100039 China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 China
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23
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Ida S, Iwamaru K, Fujita M, Okamoto Y, Kudo Y, Kurosaki H, Otsuka M. l-Histidyl-glycyl-glycyl-l-histidine. Amino-acid structuring of the bleomycin-type pentadentate metal-binding environment capable of efficient double-strand cleavage of plasmid DNA. Bioorg Chem 2015; 62:8-14. [DOI: 10.1016/j.bioorg.2015.06.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Revised: 06/09/2015] [Accepted: 06/29/2015] [Indexed: 11/28/2022]
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24
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Chen Z, Zhang J, Zhang S. Oxidative DNA cleavage promoted by two phenolate-bridged binuclear copper(ii) complexes. NEW J CHEM 2015. [DOI: 10.1039/c4nj01623h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Both the binuclear copper complexes 1 and 2 could efficiently cleave the supercoiled pUC19 plasmid DNA into its nicked and linear forms in the presence of excessive ascorbic acid (Vc) under nearly physiological conditions. The DNA binding ability and the DNA cleavage efficacy of 1 are superior to 2.
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Affiliation(s)
- Zhanfen Chen
- Hubei Collaborative Innovation Center for Rare Metal Chemistry
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology
- College of Chemistry & Chemical Engineering
- Hubei Normal University
- Huangshi 435002
| | - Jian Zhang
- Hubei Collaborative Innovation Center for Rare Metal Chemistry
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology
- College of Chemistry & Chemical Engineering
- Hubei Normal University
- Huangshi 435002
| | - Shuping Zhang
- Hubei Collaborative Innovation Center for Rare Metal Chemistry
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology
- College of Chemistry & Chemical Engineering
- Hubei Normal University
- Huangshi 435002
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25
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Komiyama M. Chemical modifications of artificial restriction DNA cutter (ARCUT) to promote its in vivo and in vitro applications. ARTIFICIAL DNA, PNA & XNA 2014; 5:e1112457. [PMID: 26744220 PMCID: PMC5329899 DOI: 10.1080/1949095x.2015.1112457] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/14/2015] [Accepted: 10/15/2015] [Indexed: 05/10/2023]
Abstract
Recently, completely chemistry-based tools for site-selective scission of DNA (ARCUT) have been prepared by combining 2 strands of pseudo-complementary PNA (pcPNA: site-selective activator) and a Ce(IV)-EDTA complex (molecular scissors). Its site-specificity is sufficient to cut the whole human genome at one predetermined site. In this first-generation ARCUT, however, there still remain several problems to be solved for wider applications. This review presents recent approaches to solve these problems. They are divided into (i) covalent modification of pcPNA with other functional groups and (ii) new strategies using conventional PNA, in place of pcPNA, as site-selective activator. Among various chemical modifications, conjugation with positively-charged nuclear localization signal peptide is especially effective. Furthermore, unimolecular activators, a single strand of which successfully activates the target site in DNA for site-selective scission, have been also developed. As the result of these modifications, the site-selective scission by Ce(IV)-EDTA was achieved promptly even under high salt conditions which are otherwise unfavourable for double-duplex invasion. Furthermore, it has been shown that "molecular crowding effect," which characterizes the inside of living cells, enormously promotes the invasion, and thus the invasion seems to proceed effectively and spontaneously in the cells. Strong potential of pcPNA for further applications in vivo and in vitro has been confirmed.
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Affiliation(s)
- Makoto Komiyama
- Life Science Center of Tsukuba Advanced Research Alliance; University of Tsukuba; Tsukuba, Ibaraki, Japan
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26
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Yu Z, Han M, Cowan JA. Toward the Design of a Catalytic Metallodrug: Selective Cleavage of G-Quadruplex Telomeric DNA by an Anticancer Copper-Acridine-ATCUN Complex. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201410434] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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27
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Yu Z, Han M, Cowan JA. Toward the design of a catalytic metallodrug: selective cleavage of G-quadruplex telomeric DNA by an anticancer copper-acridine-ATCUN complex. Angew Chem Int Ed Engl 2014; 54:1901-5. [PMID: 25504651 DOI: 10.1002/anie.201410434] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Indexed: 11/11/2022]
Abstract
Telomeric DNA represents a novel target for the development of anticancer drugs. By application of a catalytic metallodrug strategy, a copper-acridine-ATCUN complex (CuGGHK-Acr) has been designed that targets G-quadruplex telomeric DNA. Both fluorescence solution assays and gel sequencing demonstrate the CuGGHK-Acr catalyst to selectively bind and cleave the G-quadruplex telomere sequence. The cleavage pathway has been mapped by matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) experiments. CuGGHK-Acr promotes significant inhibition of cancer cell proliferation and shortening of telomere length. Both senescence and apoptosis are induced in the breast cancer cell line MCF7.
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Affiliation(s)
- Zhen Yu
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210 (USA)
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28
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Yang JW, Lin YL, Dong C, Zhou CQ, Chen JX, Wang B, Zhou ZZ, Sun B, Chen WH. Synthesis, hydrolytic DNA-cleaving activities and cytotoxicities of EDTA analogue-tethered pyrrole-polyamide dimer-based Ce(IV) complexes. Eur J Med Chem 2014; 87:168-74. [PMID: 25247773 DOI: 10.1016/j.ejmech.2014.09.057] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 09/16/2014] [Accepted: 09/17/2014] [Indexed: 12/31/2022]
Abstract
Two EDTA analogue-tethered C2-symmetrical dimeric monopyrrole-polyamide 5 and dipyrrole-polyamide 6, and their corresponding Ce(IV) complexes Ce-5 and Ce-6 were synthesized and fully characterized. Agarose gel electrophoresis studies on pBR322 DNA cleavage indicate that complexes Ce-5 and Ce-6 exhibited potent DNA-cleaving activities under physiological conditions. The maximal first-order rate constants (kmax's) were (0.42 ± 0.02) h(-1) for Ce-5 and (0.52 ± 0.02) h(-1) for Ce-6, respectively, suggesting that both complexes catalyzed the cleavage of supercoiled DNA by up to approximately 10(8)-fold. Complex Ce-6 exhibited ca 10-fold higher overall catalytic activity (kmax/KM) than Ce-5, which may be ascribed to its higher DNA-binding affinity. Inhibition experiments and a model study convincingly suggest that both complexes Ce-5 and Ce-6 functioned as hydrolytic DNA-cleavers. In addition, both complexes were found to display moderate inhibitory activity toward A549 and HepG-2 cells.
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Affiliation(s)
- Jian-Wei Yang
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Yan-Ling Lin
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Cheng Dong
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Chun-Qiong Zhou
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China.
| | - Jin-Xiang Chen
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Bo Wang
- School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Zhong-Zhen Zhou
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Bin Sun
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Wen-Hua Chen
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China.
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29
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Engelhard DM, Pievo R, Clever GH. Reversible Stabilization of Transition-Metal-Binding DNA G-Quadruplexes. Angew Chem Int Ed Engl 2013; 52:12843-7. [DOI: 10.1002/anie.201307594] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Indexed: 12/17/2022]
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30
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Engelhard DM, Pievo R, Clever GH. Reversible Stabilisierung von übergangsmetallbindenden DNA-G-Quadruplexen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201307594] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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31
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Abstract
This review summarizes the results of structural studies carried out with analogs of G-quadruplexes built from natural nucleotides. Several dozens of base-, sugar-, and phosphate derivatives of the biological building blocks have been incorporated into more than 50 potentially quadruplex forming DNA and RNA oligonucleotides and the stability and folding topology of the resultant intramolecular, bimolecular and tetramolecular architectures characterized. The TG4T, TG5T, the 15 nucleotide-long thrombin binding aptamer, and the human telomere repeat AG3(TTAG3)3 sequences were modified in most cases, and four guanine analogs can be noted as being particularly useful in structural studies. These are the fluorescent 2-aminopurine, the 8-bromo-, and 8-methylguanines, and the hypoxanthine. The latter three analogs stabilize a given fold in a mixture of structures making possible accurate structural determinations by circular dichroism and nuclear magnetic resonance measurements.
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Affiliation(s)
- Janos Sagi
- a Rimstone Laboratory , RLI, 29 Lancaster Way, Cheshire , CT , 06410 , USA
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32
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Doluca O, Withers JM, Filichev VV. Molecular engineering of guanine-rich sequences: Z-DNA, DNA triplexes, and G-quadruplexes. Chem Rev 2013; 113:3044-83. [PMID: 23391174 DOI: 10.1021/cr300225q] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Osman Doluca
- Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, New Zealand
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33
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Inui Y, Shiro M, Fukuzumi S, Kojima T. Quartet formation of a guanine derivative with an isopropyl group: crystal structures of “naked” G-quartets and thermodynamics of G-quartet formation. Org Biomol Chem 2013; 11:758-64. [DOI: 10.1039/c2ob26877a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Crisalli P, Hernández AR, Kool ET. Fluorescence quenchers for hydrazone and oxime orthogonal bioconjugation. Bioconjug Chem 2012; 23:1969-80. [PMID: 22913527 PMCID: PMC3447104 DOI: 10.1021/bc300344b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We describe the synthesis and properties of new fluorescence quenchers containing aldehyde, hydrazine, and aminooxy groups, allowing convenient bioconjugation as oximes or hydrazones. Conjugation to oligonucleotides proceeded in high yield with aniline as catalyst. Kinetics studies of conjugation show that, under optimal conditions, a hydrazine or aminooxy quencher can react with aldehyde-modified DNA to form a stable hydrazone or oxime adduct in as little as five minutes. The resulting quencher-containing DNAs were assessed for their ability to quench the emission of fluorescein in labeled complements and compared to the commercially available dabcyl and Black Hole Quencher 2 (BHQ2), which were conjugated as phosphoramidites. Results show that the new quenchers possess slightly different absorbance properties compared to dabcyl and are as efficient as the commercial quenchers in quenching fluorescein emission. Hydrazone-based quenchers were further successfully incorporated into molecular beacons and shown to give high signal to background ratios in single nucleotide polymorphism detection in vitro. Finally, aminooxy and hydrazine quenchers were applied to quenching of an aldehyde-containing fluorophore associated with living cells, demonstrating cellular quenching within one hour.
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Affiliation(s)
- Pete Crisalli
- Department of Chemistry, Stanford University Stanford, California 94305-5080, USA
| | - Armando R. Hernández
- Department of Chemistry, Stanford University Stanford, California 94305-5080, USA
| | - Eric T. Kool
- Department of Chemistry, Stanford University Stanford, California 94305-5080, USA
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Ishizuka T, Yang J, Komiyama M, Xu Y. G-rich sequence-specific recognition and scission of human genome by PNA/DNA hybrid G-quadruplex formation. Angew Chem Int Ed Engl 2012; 51:7198-202. [PMID: 22700182 DOI: 10.1002/anie.201201176] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 04/12/2012] [Indexed: 12/17/2022]
Abstract
Hole in one: A single peptide nucleic acid (PNA) effectively targets the G-rich region in double-stranded DNA through formation of a PNA/DNA hybrid G-quadruplex. Only one target site in the whole human genome was selectively cleaved by the hybrid G-quadruplex. Such site-selective scission of DNA is central to gene manipulation for molecular biology, biotechnology, and therapy.
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Affiliation(s)
- Takumi Ishizuka
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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Ishizuka T, Yang J, Komiyama M, Xu Y. G-Rich Sequence-Specific Recognition and Scission of Human Genome by PNA/DNA Hybrid G-Quadruplex Formation. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201176] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Aiba Y, Honda Y, Han Y, Komiyama M. Introduction of multiphosphonate ligand to peptide nucleic acid for metal ion conjugation. ARTIFICIAL DNA, PNA & XNA 2012; 3:73-9. [PMID: 22772037 PMCID: PMC3429533 DOI: 10.4161/adna.20727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Peptide nucleic acid (PNA) is one of the most widely used synthetic DNA analogs. Conjugation of functional molecules to PNA is very effective to further widen its potential applications. For this purpose, here we report the synthesis of several ligand monomers and introduced them to PNA. These ligand-modified PNAs attract cerium ion and are useful for site-selective DNA hydrolysis. It should be noted that these ligands on PNA are also effective even under the conditions of invasion complex.
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Affiliation(s)
- Yuichiro Aiba
- Research Center for Advanced Science and Technology; The University of Tokyo, Tokyo, Japan
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39
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Franceschin M, Borbone N, Oliviero G, Casagrande V, Scuotto M, Coppola T, Borioni S, Mayol L, Ortaggi G, Bianco A, Amato J, Varra M. Synthesis of a dibromoperylene phosphoramidite building block and its incorporation at the 5' end of a G-quadruplex forming oligonucleotide: spectroscopic properties and structural studies of the resulting dibromoperylene conjugate. Bioconjug Chem 2011; 22:1309-19. [PMID: 21688831 DOI: 10.1021/bc100526q] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Previous studies indicate that some perylene bisimide derivatives can drive the assembly of DNA G-quadruplexes, thus suggesting the possible advantage in the adoption of perylene-conjugated G-rich oligonucleotides in biological and biotechnological applications. Nevertheless, the typical poor solubility of perylene bisimides strongly limits the number of suitable chemical strategies to prepare perylene-conjugated oligonucleotides. In order to overcome these difficulties, we employed the earlier described core twisted perylene derivatives possessing unique optical and electronic properties, besides good solubility in common solvents. As a first result, the large-scale synthesis of a new dibromoperylene derivative (PEOEBr) phosphoramidite building block is herein reported. Furthermore, the structural behavior of the conjugated PEOEBr-GGGTTAGGG (HTRp2) human telomeric repeat was investigated by using CD, UV, fluorescence, and gel electrophoresis techniques in desalted water and in K(+)- and Na(+)-containing buffers. We observed that the peculiar property of PEOEBr moieties to form dimers instead of extended aggregates drives the HTRp2 strands toward dimerization and mainly promotes the formation of quadruplex species having both the 5'-ends located at the same side of the structures. However, the counterions present in solutions (K(+) or Na(+)) as well as the strand concentration, also contribute to influence the topology and the stoichiometry of formed structures. Furthermore, unlike the unmodified sequence GGGTTAGGG (HTR2), HTRp2 strands quickly associate into G-quadruplexes even in desalted water, as assessed by CD experiments.
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Affiliation(s)
- Marco Franceschin
- Dipartimento di Chimica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Roma, Italy
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40
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Xu Y. Chemistry in human telomere biology: structure, function and targeting of telomere DNA/RNA. Chem Soc Rev 2011; 40:2719-40. [DOI: 10.1039/c0cs00134a] [Citation(s) in RCA: 249] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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41
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Kolevzon N, Yavin E. Site-Specific DNA Photocleavage and Photomodulation by Oligonucleotide Conjugates. Oligonucleotides 2010; 20:263-75. [DOI: 10.1089/oli.2010.0247] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Netanel Kolevzon
- The School of Pharmacy, The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eylon Yavin
- The School of Pharmacy, The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
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42
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Georgiades SN, Abd Karim NH, Suntharalingam K, Vilar R. Interaction of metal complexes with G-quadruplex DNA. Angew Chem Int Ed Engl 2010; 49:4020-34. [PMID: 20503216 DOI: 10.1002/anie.200906363] [Citation(s) in RCA: 380] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Guanine-rich sequences of DNA can assemble into tetrastranded structures known as G-quadruplexes. It has been suggested that these secondary DNA structures could be involved in the regulation of several key biological processes. In the human genome, guanine-rich sequences with the potential to form G-quadruplexes exist in the telomere as well as in promoter regions of certain oncogenes. The identification of these sequences as novel targets for the development of anticancer drugs has sparked great interest in the design of molecules that can interact with quadruplex DNA. While most reported quadruplex DNA binders are based on purely organic templates, numerous metal complexes have more recently been shown to interact effectively with this DNA secondary structure. This Review provides an overview of the important roles that metal complexes can play as quadruplex DNA binding molecules, highlighting the unique properties metals can confer to these molecules.
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Affiliation(s)
- Savvas N Georgiades
- Department of Chemistry, Imperial College London, South Kensington, London SW7 2AZ, UK
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43
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Georgiades S, Abd Karim N, Suntharalingam K, Vilar R. Wechselwirkung von Metallkomplexen mit G-Quadruplex-DNA. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906363] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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44
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Xu Y, Ito K, Suzuki Y, Komiyama M. A 6-mer photocontrolled oligonucleotide as an effective telomerase inhibitor. J Am Chem Soc 2010; 132:631-7. [PMID: 20014834 DOI: 10.1021/ja907417r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Telomerase is a relevant target for cancer therapy. A small 6-mer psoralen-containing oligonucleotide is shown to cause efficient photo-cross-linking to human telomere DNA by G-quadruplex formation. The small, photocontrolled oligonucleotide shows effective telomerase inhibition, both in vitro and in vivo, only when light irradiated. Data suggest that it is a promising agent for the treatment of cancer.
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Affiliation(s)
- Yan Xu
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.
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Dong X, Wang X, Lin M, Sun H, Yang X, Guo Z. Promotive Effect of the Platinum Moiety on the DNA Cleavage Activity of Copper-Based Artificial Nucleases. Inorg Chem 2010; 49:2541-9. [DOI: 10.1021/ic100001x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xindian Dong
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering
| | - Xiaoyong Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, People's Republic of China
| | - Miaoxin Lin
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering
| | - Hui Sun
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering
| | - Xiaoliang Yang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering
| | - Zijian Guo
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering
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Quinone methides tethered to naphthalene diimides as selective G-quadruplex alkylating agents. J Am Chem Soc 2010; 131:13132-41. [PMID: 19694465 DOI: 10.1021/ja904876q] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have developed novel G-quadruplex (G-4) ligand/alkylating hybrid structures, tethering the naphthalene diimide moiety to quaternary ammonium salts of Mannich bases, as quinone-methide precursors, activatable by mild thermal digestion (40 degrees C). The bis-substituted naphthalene diimides were efficiently synthesized, and their reactivity as activatable bis-alkylating agents was investigated in the presence of thiols and amines in aqueous buffered solutions. The electrophilic intermediate, quinone-methide, involved in the alkylation process was trapped, in the presence of ethyl vinyl ether, in a hetero Diels-Alder [4 + 2] cycloaddition reaction, yielding a substituted 2-ethoxychroman. The DNA recognition and alkylation properties of these new derivatives were investigated by gel electrophoresis, circular dichroism, and enzymatic assays. The alkylation process occurred preferentially on the G-4 structure in comparison to other DNA conformations. By dissecting reversible recognition and alkylation events, we found that the reversible process is a prerequisite to DNA alkylation, which in turn reinforces the G-quadruplex structural rearrangement.
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47
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Bonomi R, Scrimin P, Mancin F. Phosphate diesters cleavage mediated by Ce(iv) complexes self-assembled on gold nanoparticles. Org Biomol Chem 2010; 8:2622-6. [DOI: 10.1039/b926916a] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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