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Alshubramy MA, Alotaibi FS, Alkahtani HM, Alamry KA, Hussein MA. C3-Symmetric ligands in drug design: An overview of the challenges and opportunities ahead. Bioorg Med Chem Lett 2024; 103:129702. [PMID: 38490620 DOI: 10.1016/j.bmcl.2024.129702] [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: 01/02/2024] [Revised: 02/10/2024] [Accepted: 03/12/2024] [Indexed: 03/17/2024]
Abstract
C3-symmetry is a type of star-shaped molecule consisting of a central core and three symmetrically attached chains. These molecules are used in drug discovery due to their unique three-fold rotational symmetry, which allows for specific binding interactions and improved molecular recognition. In this text, we provide an overview of synthetic approaches with C3-symmetry as a pharmaceutical tool: progress, challenges, and opportunities. C3-symmetric ligands offer both challenges and opportunities in drug design. Their unique symmetry can enhance binding interactions, but careful consideration of rigidity, synthetic complexity, and target compatibility is crucial. Further research and advancements in synthetic methods and modeling tools will likely drive their exploration in drug discovery, leading to the discovery of potent C3-symmetric ligands.
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Affiliation(s)
- Maha A Alshubramy
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
| | - Faez S Alotaibi
- Department of Chemistry, College of Science, Qassim University Buraidah 51452, Saudi Arabia
| | - Hamad M Alkahtani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Khalid A Alamry
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mahmoud A Hussein
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Chemistry Department, Faculty of Science, Assiut University, Assiut 71516, Egypt.
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2
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Palma E, Santos JF, Fernandes C, Paulo A. DNA-Targeted Complexes of Tc and Re for Biomedical Applications. Chemistry 2024; 30:e202303591. [PMID: 38038361 DOI: 10.1002/chem.202303591] [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: 10/30/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/02/2023]
Abstract
Due to their favorable chemical features, Re and Tc complexes have been widely used for the development of new therapeutic agents and imaging probes to solve problems of biomedical relevance. This review provides an update of the most relevant research efforts towards the development of novel cancer theranostic agents using Re and Tc-based compounds interacting with specific DNA structures. This includes a variety of homometallic complexes, namely those containing M(CO)3 (M=Re, Tc) moieties, that exhibit different modes of interaction with DNA, such as covalent binding, intercalation, groove binding or G-quadruplex DNA binding. Additionally, heterometallic complexes, designed to potentiate synergistic effects of different metal centers to improve DNA-targeting, cytotoxicity and fluorescence properties, are also reviewed. Particular attention is also given to 99m Tc- and 188 Re-labeled oligonucleotides that have been widely explored to develop imaging and therapeutic radiopharmaceuticals through the in vivo hybridization with a specific complementary DNA or RNA target sequence to provide useful molecular tools in precision medicine for cancer diagnosis and treatment. Finally, the need for further improvement of DNA-targeted Re and Tc-based compounds as potential therapeutic and diagnostic agents is highlighted, and future directions are discussed.
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Affiliation(s)
- Elisa Palma
- C2TN - Centro de Ciências e Tecnologias, Nucleares Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - Joana F Santos
- C2TN - Centro de Ciências e Tecnologias, Nucleares Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - Célia Fernandes
- C2TN - Centro de Ciências e Tecnologias, Nucleares Instituto Superior Técnico, Universidade de Lisboa, Portugal
- DECN - Departamento de Engenharia e Ciências Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - António Paulo
- C2TN - Centro de Ciências e Tecnologias, Nucleares Instituto Superior Técnico, Universidade de Lisboa, Portugal
- DECN - Departamento de Engenharia e Ciências Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Portugal
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3
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Luo C, Xie Y, He M, Xia Y, Li Y, He L, Li J, Wang L, Han X, Zhang L, Yuan X, Wang Z, Liu Y, Tan W. Artificial Nucleobase-Directed Programmable Synthesis and Assembly of Amphiphilic Nucleic Acids as an All-in-One Platform for Cation-Free siRNA Delivery. ACS APPLIED MATERIALS & INTERFACES 2022; 14:44019-44028. [PMID: 36149091 DOI: 10.1021/acsami.2c09406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Efficient transport of nucleic acid therapeutics into targeted cells is the key step of genetic modulation in disease treatment. Nowadays, delivery systems strongly rely on cationic materials, but how to balance the trade-off between effectiveness and toxicity of these exogenous materials remains incredibly challenging. Here, we take inspiration from nucleic acid chemistry and introduce a new concept of amphiphilic nucleic acids (ANAs), as an all-in-one platform for cation-free nucleic acid delivery, by programmatically conjugating two different artifical nucleobases with sequence-independent activities. Specifically, the hydrophilic artificial nucleobases in ANAs act as both delivery vectors and therapeutic cargos for integrated benefits, while the hydrophobic nucleobases enable molecular self-assembly for improved stability and endosomal membrane oxidation for enhanced endosomal escape. By virtue of these merits, this platform is successfully used for short interference RNA (siRNA) delivery, which demonstrates a high siRNA loading capacity, rapid cellular uptake, and efficient endosomal escape, eliciting remarkable gene silencing and synergistic inhibitory effects on cancer cell proliferation and migration. This work is a case study in exploiting the basis of nucleic acid chemistry to afford new paradigms for advanced cancer theranostics.
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Affiliation(s)
- Can Luo
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hu-nan University, Changsha 410082, Hunan, China
| | - Yuqi Xie
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hu-nan University, Changsha 410082, Hunan, China
| | - Minze He
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hu-nan University, Changsha 410082, Hunan, China
| | - Yinghao Xia
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hu-nan University, Changsha 410082, Hunan, China
| | - Yazhou Li
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hu-nan University, Changsha 410082, Hunan, China
| | - Lei He
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
| | - Jili Li
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hu-nan University, Changsha 410082, Hunan, China
| | - Linlin Wang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hu-nan University, Changsha 410082, Hunan, China
| | - Xiaoyan Han
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hu-nan University, Changsha 410082, Hunan, China
| | - Lili Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hu-nan University, Changsha 410082, Hunan, China
| | - Xi Yuan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hu-nan University, Changsha 410082, Hunan, China
| | - Zhiqiang Wang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hu-nan University, Changsha 410082, Hunan, China
| | - Yanlan Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hu-nan University, Changsha 410082, Hunan, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hu-nan University, Changsha 410082, Hunan, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
- Institute of Molecular Medicine, Renji Hospital, Shanghai JiaoTong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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McStay N, Slator C, Singh V, Gibney A, Westerlund F, Kellett A. Click and Cut: a click chemistry approach to developing oxidative DNA damaging agents. Nucleic Acids Res 2021; 49:10289-10308. [PMID: 34570227 PMCID: PMC8501983 DOI: 10.1093/nar/gkab817] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 09/01/2021] [Accepted: 09/07/2021] [Indexed: 01/04/2023] Open
Abstract
Metallodrugs provide important first-line treatment against various forms of human cancer. To overcome chemotherapeutic resistance and widen treatment possibilities, new agents with improved or alternative modes of action are highly sought after. Here, we present a click chemistry strategy for developing DNA damaging metallodrugs. The approach involves the development of a series of polyamine ligands where three primary, secondary or tertiary alkyne-amines were selected and ‘clicked’ using the copper-catalysed azide-alkyne cycloaddition reaction to a 1,3,5-azide mesitylene core to produce a family of compounds we call the ‘Tri-Click’ (TC) series. From the isolated library, one dominant ligand (TC1) emerged as a high-affinity copper(II) binding agent with potent DNA recognition and damaging properties. Using a range of in vitro biophysical and molecular techniques—including free radical scavengers, spin trapping antioxidants and base excision repair (BER) enzymes—the oxidative DNA damaging mechanism of copper-bound TC1 was elucidated. This activity was then compared to intracellular results obtained from peripheral blood mononuclear cells exposed to Cu(II)–TC1 where use of BER enzymes and fluorescently modified dNTPs enabled the characterisation and quantification of genomic DNA lesions produced by the complex. The approach can serve as a new avenue for the design of DNA damaging agents with unique activity profiles.
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Affiliation(s)
- Natasha McStay
- 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
| | - Creina Slator
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Vandana Singh
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Alex Gibney
- 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
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - 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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5
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Fantoni NZ, Brown T, Kellett A. DNA-Targeted Metallodrugs: An Untapped Source of Artificial Gene Editing Technology. Chembiochem 2021; 22:2184-2205. [PMID: 33570813 DOI: 10.1002/cbic.202000838] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 02/09/2021] [Indexed: 12/20/2022]
Abstract
DNA binding metal complexes are synonymous with anticancer drug discovery. Given the array of structural and chemical reactivity properties available through careful design, metal complexes have been directed to bind nucleic acid structures through covalent or noncovalent binding modes. Several recognition modes - including crosslinking, intercalation, and oxidation - are central to the clinical success of broad-spectrum anticancer metallodrugs. However, recent progress in nucleic acid click chemistry coupled with advancement in our understanding of metal complex-nucleic acid interactions has opened up new avenues in genetic engineering and targeted therapies. Several of these applications are enabled by the hybridisation of oligonucleotide or polyamine probes to discrete metal complexes, which facilitate site-specific reactivity at the nucleic acid interface under the guidance of the probe. This Review focuses on recent advancements in hybrid design and, by way of an introduction to this topic, we provide a detailed overview of nucleic acid structures and metal complex-nucleic acid interactions. Our aim is to provide readers with an insight on the rational design of metal complexes with DNA recognition properties and an understanding of how the sequence-specific targeting of these interactions can be achieved for gene engineering applications.
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Affiliation(s)
- Nicolò Zuin Fantoni
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Tom Brown
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for, Cellular Biotechnology and Nano Research Facility, Dublin City University, Glasnevin, Dublin, 9, Ireland
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Pratihar S, Suseela YV, Govindaraju T. Threading Intercalator-Induced Nanocondensates and Role of Endogenous Metal Ions in Decondensation for DNA Delivery. ACS APPLIED BIO MATERIALS 2020; 3:6979-6991. [PMID: 35019357 DOI: 10.1021/acsabm.0c00870] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The interplay of condensation and decondensation of DNA plays a crucial role in chromosome maintenance and gene expression. The molecular architectonics governing the chromatin condensation-decondensation cycle are worth studying, as DNA performs unique and distinct roles in each state and switches between two states without the loss of structural and functional integrity. This phenomenon has been adapted and implemented in transfection studies. Effective gene delivery into the cells to achieve respectable transfection efficiency has remained a challenge and emphasizes the need for understanding the steps involved in DNA delivery and transfection. Especially, recognizing the factors that effectively regulate DNA decondensation can provide logical solutions to the hurdles affecting the transfection efficiency. We designed a set of small molecule-based threading intercalation ligands as model condensing agents to study various factors influencing the DNA condensation and decondensation process. This study revealed condensation of DNA into nanocondensate by the threading intercalator and endogenous stimuli induced effective decondensation. Further, DNA nanocondensates are tracked using the intrinsic fluorescence in the lower pH of endocytic pathway and were evaluated as nonviral vectors for in cellulo delivery of plasmids. The correlation of decondensation of DNA nanocondensate with endogenous metal ions at their physiological concentrations provided valuable insights and implications for intracellular DNA delivery.
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Affiliation(s)
- Sumon Pratihar
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, P.O., Bengaluru, Karnataka 560064, India
| | - Yelisetty Venkata Suseela
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, P.O., Bengaluru, Karnataka 560064, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, P.O., Bengaluru, Karnataka 560064, India
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7
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de Souza ÍP, Machado BDP, de Carvalho AB, Binatti I, Krambrock K, Molphy Z, Kellett A, Pereira-Maia EC, Silva-Caldeira PP. Exploring the DNA binding, oxidative cleavage, and cytotoxic properties of new ternary copper(II) compounds containing 4-aminoantipyrine and N,N-heterocyclic co-ligands. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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8
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McStay N, Reilly AM, Gathergood N, Kellett A. Efficient DNA Condensation by a C3‐Symmetric Codeine Scaffold. Chempluschem 2018; 84:38-42. [DOI: 10.1002/cplu.201800480] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 11/12/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Natasha McStay
- School of Chemical Sciencesand National Institute for Cellular BiotechnologyDublin City University Glasnevin Dublin 9 Ireland
| | - Anthony M. Reilly
- School of Chemical SciencesDublin City University Glasnevin Dublin 9 Ireland
- Synthesis and Solid-State Pharmaceutical CentreSchool of Chemical SciencesDublin City University Glasnevin Dublin 9 Ireland
| | - Nicholas Gathergood
- Department of Chemistry and BiotechnologyTallinn University of Technology Akadeemia tee 15 12618 Tallinn Estonia
| | - Andrew Kellett
- School of Chemical Sciencesand National Institute for Cellular BiotechnologyDublin City University Glasnevin Dublin 9 Ireland
- Synthesis and Solid-State Pharmaceutical CentreSchool of Chemical SciencesDublin City University Glasnevin Dublin 9 Ireland
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Sun N, Li D, Hou J, Long W, Guo Q, Lu Y, Zhang K, Yuan W, Wong WL. A propeller-like small molecule as a novel G-quadruplex DNA binder: The study of fluorescent sensing property and preferential interactions with human telo21 structure. Chem Biol Drug Des 2018; 93:979-985. [PMID: 30218500 DOI: 10.1111/cbdd.13394] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 08/22/2018] [Accepted: 09/02/2018] [Indexed: 01/15/2023]
Abstract
A new propeller-like small molecule was synthesized with three terminal amino side groups. The molecule was found to be a selective nucleic acid binder towards telo21 G-quadruplex DNA compared with other representative nucleic acids including single-stranded DNA (dA21), duplex DNA (ds26) and RNA. The fluorescent signal of the molecule upon interaction with telo21 G-quadruplex structure shows remarkable enhancement (Fmax /F0 = 17.9) while interaction with other nucleic acids shows the signal enhancement which is less than 2.1. In addition, a good linear relationship of binding signal correlated with the concentration of telo21 DNA was obtained. Molecular docking study was also performed to acquire the binding behaviour and its interaction modes of the molecule with the structure of human telomeric DNA G-quadruplex. The modelling results show that the three conjugated terminal units (dimethylaminobenzyl groups) associated through the ethylene bridges with the central methylated pyridine ring formed a co-planar conformation upon stacking onto the G-quartets via pi-pi stacking interactions. This could be the key reason that the molecule shows excellent fluorescent signal of binding towards telo21 G-quadruplex DNA rather than other types of nucleic acids.
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Affiliation(s)
- Ning Sun
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Dongli Li
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China.,International Healthcare Innovation Institute (Jiangmen), Jiangmen, China
| | - Jinqiang Hou
- Institute of Natural Medicine and Green Chemistry, School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, China
| | - Wei Long
- Institute of Natural Medicine and Green Chemistry, School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, China
| | - Qi Guo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yujing Lu
- Institute of Natural Medicine and Green Chemistry, School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, China
| | - Kun Zhang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China.,International Healthcare Innovation Institute (Jiangmen), Jiangmen, China
| | - Wenchang Yuan
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wing-Leung Wong
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China.,International Healthcare Innovation Institute (Jiangmen), Jiangmen, China
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