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Yu KK, Li K, Wang HY, Li XL, Wu SX, Xu WM, Liu YH, Wu CF, Yu XQ, Bao JK. Construction of Near-Infrared Probes with Remarkable Large Stokes Shift Based on a Novel Purine Platform for the Visualization of mtG4 Upregulation during Mitochondrial Disorder in Somatic Cells and Human Sperms. Anal Chem 2024; 96:11915-11922. [PMID: 39007441 DOI: 10.1021/acs.analchem.4c01638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
G-quadruplex structures within the nuclear genome (nG4) is an important regulatory factor, while the function of G4 in the mitochondrial genome (mtG4) still needs to be explored, especially in human sperms. To gain a better understanding of the relationship between mtG4 and mitochondrial function, it is crucial to develop excellent probes that can selectively visualize and track mtG4 in both somatic cells and sperms. Herein, based on our previous research on purine frameworks, we attempted for the first time to extend the conjugated structure from the C-8 site of purine skeleton and discovered that the purine derivative modified by the C-8 aldehyde group is an ideal platform for constructing near-infrared probes with extremely large Stokes shift (>220 nm). Compared with the compound substituted with methylpyridine (PAP), the molecule substituted with methylthiazole orange (PATO) showed better G4 recognition ability, including longer emission (∼720 nm), more significant fluorescent enhancement (∼67-fold), lower background, and excellent photostability. PATO exhibited a sensitive response to mtG4 variation in both somatic cells and human sperms. Most importantly, PATO helped us to discover that mtG4 was significantly increased in cells with mitochondrial respiratory chain damage caused by complex I inhibitors (6-OHDA and rotenone), as well as in human sperms that suffer from oxidative stress. Altogether, our study not only provides a novel ideal molecular platform for constructing high-performance probes but also develops an effective tool for studying the relationship between mtG4 and mitochondrial function in both somatic cells and human sperms.
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Affiliation(s)
- Kang-Kang Yu
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Kun Li
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Hao-Yuan Wang
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Xiao-Liang Li
- Joint Laboratory of Reproductive Medicine, Key Laboratory of Obstetric, Gynaecologic and Paediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Med-Centre for Manufacturing, Sichuan University, Chengdu 610064, China
| | - Si-Xian Wu
- Joint Laboratory of Reproductive Medicine, Key Laboratory of Obstetric, Gynaecologic and Paediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Med-Centre for Manufacturing, Sichuan University, Chengdu 610064, China
| | - Wen-Ming Xu
- Joint Laboratory of Reproductive Medicine, Key Laboratory of Obstetric, Gynaecologic and Paediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Med-Centre for Manufacturing, Sichuan University, Chengdu 610064, China
| | - Yan-Hong Liu
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Chuan-Fang Wu
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Xiao-Qi Yu
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Jin-Ku Bao
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
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Zucolotto Cocca LH, Pelosi AG, Piguel S, Mendonça CR, Boni LD. Enhancement of optical properties of new purine nucleobases containing electron-donating and -withdrawing peripheral groups. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 234:112524. [PMID: 35843082 DOI: 10.1016/j.jphotobiol.2022.112524] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 07/04/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
Nowadays, a great deal of attention has been focused on synthesizing highly fluorescent unnatural base analogs. This has been motivated by the need to overcome the lack of fluorescence of nucleic acids' natural bases. Fluorescent unnatural base analogs, such as purines, may be used in several applications, such as DNA or RNA optical spectroscopy studies. Moreover, for purines base analogs, the optical properties, for example, emission, can be tunable through molecular engineering, improving their applications as fluorescent probes. Looking in this direction, the synthesis and optical spectroscopic studies of a new set of purines base analogs are of foremost relevance. Here, an increase in the fluorescence quantum yield was observed in molecules with NH-π-CN arrangement. The two-photon absorption (2PA) cross-sections also increased for the lower energy 2PA state. The enhancement of both properties results in a two-photon brightness of 5 and 10 times higher than in compounds lacking the NH-π-CN arrangement. For the higher energy 2PA state, an excited state absorption contribution to the 2PA cross-section values was observed, that was verified through ultrafast transient absorption measurements. The higher 2PA brightness makes the purines base analogs promising candidates as fluorescent probes in RNA and DNA spectroscopic studies.
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Affiliation(s)
- Leandro H Zucolotto Cocca
- Instituto de Física de São Carlos, Universidade de São Paulo, CP 369, 13560-970 São Carlos, SP, Brazil.
| | - André G Pelosi
- Instituto de Física de São Carlos, Universidade de São Paulo, CP 369, 13560-970 São Carlos, SP, Brazil
| | - Sandrine Piguel
- Université Paris-Saclay, Faculté de Pharmacie, CNRS UMR 8076, 92296 Châtenay-Malabry, France
| | - Cleber Renato Mendonça
- Instituto de Física de São Carlos, Universidade de São Paulo, CP 369, 13560-970 São Carlos, SP, Brazil
| | - Leonardo De Boni
- Instituto de Física de São Carlos, Universidade de São Paulo, CP 369, 13560-970 São Carlos, SP, Brazil.
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Biver T. Discriminating between Parallel, Anti-Parallel and Hybrid G-Quadruplexes: Mechanistic Details on Their Binding to Small Molecules. Molecules 2022; 27:molecules27134165. [PMID: 35807410 PMCID: PMC9268745 DOI: 10.3390/molecules27134165] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 12/04/2022] Open
Abstract
G-quadruplexes (G4) are now extensively recognised as a peculiar non-canonical DNA geometry that plays a prime importance role in processes of biological relevance whose number is increasing continuously. The same is true for the less-studied RNA G4 counterpart. G4s are stable structures; however, their geometrical parameters may be finely tuned not only by the presence of particular sequences of nucleotides but also by the salt content of the medium or by a small molecule that may act as a peculiar topology inducer. As far as the interest in G4s increases and our knowledge of these species deepens, researchers do not only verify the G4s binding by small molecules and the subsequent G4 stabilisation. The most innovative studies now aim to elucidate the mechanistic details of the interaction and the ability of a target species (drug) to bind only to a peculiar G4 geometry. In this focused review, we survey the advances in the studies of the binding of small molecules of medical interest to G4s, with particular attention to the ability of these species to bind differently (intercalation, lateral binding or sitting atop) to different G4 topologies (parallel, anti-parallel or hybrid structures). Some species, given the very high affinity with some peculiar G4 topology, can first bind to a less favourable geometry and then induce its conversion. This aspect is also considered.
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Affiliation(s)
- Tarita Biver
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
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4
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Hu MH, Lin JH, Huang Q. Discovery of a fluorescent, long chain-bridged bispurine that selectively targets the c-MYC G-quadruplex. Bioorg Chem 2022; 122:105750. [PMID: 35325695 DOI: 10.1016/j.bioorg.2022.105750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/14/2022] [Accepted: 03/17/2022] [Indexed: 11/30/2022]
Abstract
G-quadruplexes (G4s) are special nucleic acid structures which are involved in the regulation of some key biological events like transcription and translation, which are now treated as promising therapeutic targets for cancers. Stabilizing the promoter G4 by small-molecule ligands can suppress the c-MYC oncogene transcription, thus inhibiting cancer cell proliferation. So far, targeting the very structure, a number of ligands have been reported. However, most of them showed unsatisfactory specificity to the c-MYC G4 over other G4s, resulting in uncertain side effects. In this contribution, we discovered a new class of bispurines bridged with flexible hydrocarbon chains, which presented somewhat selectivity to the c-MYC G4 possibly by adaptive binding, which then showed clear inhibition on the c-MYC expression rather than other G4-driven oncogenes. Moreover, these novel molecules had the potential to fluorescently label G4s. We believed that this study may shed light on the discovery of new functional small molecules targeting a specific G4 structure.
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Affiliation(s)
- Ming-Hao Hu
- Nation-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen 518060, China; Shenzhen Key Laboratory for Nano-Biosensing Technology (ZDSYS20210112161400001), Shenzhen University Health Science Center, Shenzhen 518060, China.
| | - Jia-Hong Lin
- Nation-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen 518060, China
| | - Qiong Huang
- Nation-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen 518060, China
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5
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Zucolotto Cocca LH, Pelosi A, Sciuti LF, M. G. Abegão L, Kamada K, Piguel S, Renato Mendonça C, De Boni L. Two-photon brightness of highly fluorescent imidazopyridine derivatives: Two-photon and ultrafast transient absorption studies. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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6
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Gong YP, Yang J, Fang JW, Li Q, Yu ZY, Guan A, Gong HY. A DNA small molecular probe with increasing K + concentration promoted selectivity. RSC Adv 2021; 11:15030-15035. [PMID: 35424063 PMCID: PMC8697834 DOI: 10.1039/d0ra06274j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 03/28/2021] [Indexed: 11/21/2022] Open
Abstract
DNA small molecular probe study was considered as a promising approach to achieve DNA related disease diagnosis. Most related reports were performed under specific salinity. Herein, 4-imino-3-(pyridin-2-yl)-4H-quinolizine-1-carbonitrile (IPQC) was generated via a facile procedure with high yield (85%). It is found that IPQC could act as a universal probe for most tested ssDNA, dsDNA and G4 DNA in low [K+] concentration (less than 20 mM). However, IPQC showed highly selective G4 DNA binding via UV-vis and fluorescence response in increasing [K+] (e.g., 150 mM) conditions. The ion atmosphere effects are instructive for DNA probe exploration. This provides guidance for the design, selection and optimization of the probes for target DNA sensing. DNA small molecular probe study was considered as a promising approach to achieve DNA related disease diagnosis.![]()
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Affiliation(s)
- Ya-Ping Gong
- Department of Chemistry
- Renmin University of China
- Beijing
- P. R. China
- Institute of Chemistry
| | - Jian Yang
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- P. R. China
| | - Ji-Wang Fang
- Department of Chemistry
- Renmin University of China
- Beijing
- P. R. China
- College of Chemistry
| | - Qian Li
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- P. R. China
| | - Zhi-Yong Yu
- Department of Chemistry
- Renmin University of China
- Beijing
- P. R. China
| | - Aijiao Guan
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- P. R. China
| | - Han-Yuan Gong
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- P. R. China
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7
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Zhao J, Yang Z, Zhai Q, Wei D. Specific recognition of telomeric multimeric G-quadruplexes by a simple-structure quinoline derivative. Anal Chim Acta 2020; 1132:93-100. [PMID: 32980115 DOI: 10.1016/j.aca.2020.07.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 07/02/2020] [Accepted: 07/07/2020] [Indexed: 11/17/2022]
Abstract
The development of highly sensitive fluorescence probes for telomeric multimeric G-quadruplexes has attracted extensive attention. However, few probes reported have exhibited selectivity for telomeric multimeric G-quadruplexes. Thus, it is challenging to design fluorescence probes with high specificity and selectivity for telomeric multimeric G-quadruplexes. This study employed a commercially available quinoline derivative BEPQ-1 as an effective switch-on sensor for telomeric multimeric G-quadruplexes. The fluorescence intensity enhanced more than 20 folds upon the addition of telomeric multimeric G-quadruplexes. This probe exhibited good selectivity and sensitivity for telomeric multimeric G-quadruplexes. And the detection limit of BEPQ-1 for the telomeric multimeric G-quadruplex TTA45 was calculated to be 0.11 μM. The distinctive feature of BEPQ-1 is the simple structure and small size. In the light of binding mode, BEPQ-1 could even simultaneously bind to the end two G-quartets of the two adjacent G-quadruplex units in telomeric multimeric G-quadruplex by π-π stacking. To our knowledge, this is the first simple-structure fluorescence probe for telomeric multimeric G-quadruplex. This finding might provide a strategy to design specific probes for telomeric multimeric G-quadruplexes and contribute to understand the structures and functions of G-quadruplexes in the telomere region.
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Affiliation(s)
- Jingfang Zhao
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Ziyan Yang
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Qianqian Zhai
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan, 430070, PR China.
| | - Dengguo Wei
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.
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8
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Liao TC, Ma TZ, Chen SB, Cilibrizzi A, Zhang MJ, Li JH, Zhou CQ. Human telomere double G-quadruplex recognition by berberine-bisquinolinium imaging conjugates in vitro and cells. Int J Biol Macromol 2020; 158:S0141-8130(20)33034-8. [PMID: 32339571 DOI: 10.1016/j.ijbiomac.2020.04.171] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/21/2020] [Accepted: 04/21/2020] [Indexed: 10/24/2022]
Abstract
Molecular tools of double or multimeric G-quadruplexes have been given higher requirements on detection sensitivity, thermal stabilization and cell imaging to establish functions of these G-quadruplex aggregates and biological mechanisms as anticancer reagents. Here, two smart berberine-bisquinolinium conjugates (Ber-360A and Ber-PDS) by linking the berberine fluorophore ligand and an established G-quadruplex binder (i.e. bisquinolinium scaffold), have been designed and evaluated their activities and mechanisms for G-quadruplex aggregation. Two conjugates, especially Ber-PDS, are two highly selective, sensitive and fluorescent sensors which can distinguish human telomere double G-quadruplexes from other type G-quadruplexes and ds DNA. These two ligands could be the first example to stack two adjacent G-quadruplex units and fluorescently recognize human telomere double G-quadruplexes. Furthermore, conjugate Ber-PDS could enter the nucleoli and target G-quadruplex DNA through microscopy experiments, and also display strong telomerase inhibition and antitumor activities.
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Affiliation(s)
- Ting-Cong Liao
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Tian-Zhu Ma
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Suo-Bin Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 51006, PR China
| | - Agostino Cilibrizzi
- Institute of Pharmaceutical Science, King's College London, London SE1 9NH, United Kingdom
| | - Meng-Jia Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Jun-Hui Li
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Chun-Qiong Zhou
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China.
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9
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Wei YF, Wang Y, Wei XR, Sun R, Xu YJ, Ge JF. Adenine-based small molecule fluorescent probe for imaging mitochondrial nucleic acid. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 229:117865. [PMID: 31813730 DOI: 10.1016/j.saa.2019.117865] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 11/26/2019] [Accepted: 11/26/2019] [Indexed: 06/10/2023]
Abstract
A small molecule fluorescent probe (probe 1) based on adenine-coumarin derivative was designed and synthesized in this paper. Probe 1 exhibited a significant fluorescence-enhancing response to nucleic acids at 495 nm (for DNA) and 487 nm (for RNA). The fluorescence enhancement of probe 1 for DNA and RNA was 5.68 and 9.73 times respectively, the fluorescence quantum yield was changed from 2.5% to 11.7% and 22.5% accordingly. Meanwhile, an excellent linear relationship of fluorescence intensity at 495 nm or 487 nm versus the nucleic acid concentration (1 μM for probe 1, 0-350 μg/mL for DNA and 0-300 μg/mL for RNA) was obtained. Co-staining and nucleic acid digestion experiments showed that probe 1 could selectively image nucleic acids in mitochondria and nucleoli in HeLa cells.
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Affiliation(s)
- Yu-Fang Wei
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, 199 Ren'Ai Road, Suzhou 215123, China
| | - Yue Wang
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, 199 Ren'Ai Road, Suzhou 215123, China
| | - Xue-Rui Wei
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Ru Sun
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, 199 Ren'Ai Road, Suzhou 215123, China.
| | - Yu-Jie Xu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Jian-Feng Ge
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, 199 Ren'Ai Road, Suzhou 215123, China; Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China.
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10
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Dhamodharan V, Pradeepkumar PI. Specific Recognition of Promoter G-Quadruplex DNAs by Small Molecule Ligands and Light-up Probes. ACS Chem Biol 2019; 14:2102-2114. [PMID: 31532996 DOI: 10.1021/acschembio.9b00475] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
G-Quadruplexes (G4s) are four-stranded nucleic acid structures whose underlying G-rich sequences are present across the chromosome and transcriptome. These highly structured elements are known to regulate many key biological functions such as replication, transcription, translation, and genomic stability, thereby providing an additional layer of gene regulation. G4s are structurally dynamic and diverse, and they can fold into numerous topologies. They are potential targets for small molecules, which can modulate their functions. To this end, myriad classes of small molecules have been developed and studied for their ability to bind and stabilize these unique structures. Though many of them can selectively target G4s over duplex DNA, only a few of them can distinguish one G4 topology from others. Design and development of G4-specific ligands are challenging owing to the subtle structural variations among G4 structures. However, screening assays and computational methods have identified a few classes of ligands that preferentially or specifically target the G4 topology of interest over others. This review focuses on the small molecules and fluorescent probes that specifically target human promoter G4s associated with oncogenes. Targeting promoter G4s could circumvent the issues such as undruggability and development of drug resistance associated with the protein targets. The ligands discussed here highlight that development of G4-specific ligands is an achievable goal in spite of the limited structural data available. The future goal is to pursue the development of G4-specific ligands endowed with drug-like properties for G4-based therapeutics and diagnostics.
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Affiliation(s)
- V. Dhamodharan
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
- Okinawa Institute of Science and Technology Graduate University, Okinawa 9040495, Japan
| | - P. I. Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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11
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Jin M, Liu X, Zhang X, Wang L, Bing T, Zhang N, Zhang Y, Shangguan D. Thiazole Orange-Modified Carbon Dots for Ratiometric Fluorescence Detection of G-Quadruplex and Double-Stranded DNA. ACS APPLIED MATERIALS & INTERFACES 2018; 10:25166-25173. [PMID: 29979027 DOI: 10.1021/acsami.8b07869] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
A new carbon dot (CD)-based nanoprobe for the ratiometric fluorescence detection of DNA was constructed in this work. Thiazole orange (TO), a specific organic small molecular probe toward DNA, is covalently linked to the surface of CDs, acting as the recognition element and the fluorescence response unit. In the absence of DNA, the nanoprobe only emitted the blue fluorescence of CDs, whereas TO was almost nonfluorescent. Upon addition of DNA, a turn-on emission at 530 nm appeared and gradually enhanced along with the increasing of the target DNA, whereas the fluorescence of CDs was unchanged, which realized the ratiometric detection of the target DNA. The CD-TO nanoprobe showed good selectivity to parallel G-quadruplex (G4) and double-stranded (ds) DNA over antiparallel G4 and single-stranded DNA. Moreover, the ratiometric fluorescence nanoprobe exhibited high sensitivity for ssab (a dsDNA) and c-myc (a parallel G4) with a low detection limit of 0.90 and 3.31 nM, respectively. Additionally, the G4/hemin peroxidase activity inhibition experiment demonstrated that CD-TO bound to the G4s through the end-stacking mode.
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Affiliation(s)
- Ming Jin
- College of Chemistry and Chemical Engineering , Lanzhou University , Lanzhou 730000 , China
| | - Xiangjun Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Xin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Linlin Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Tao Bing
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Nan Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China
| | - Yun Zhang
- College of Chemistry and Chemical Engineering , Lanzhou University , Lanzhou 730000 , China
| | - Dihua Shangguan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
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12
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Accurate high-throughput identification of parallel G-quadruplex topology by a new tetraaryl-substituted imidazole. Biosens Bioelectron 2016; 83:77-84. [DOI: 10.1016/j.bios.2016.04.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 03/15/2016] [Accepted: 04/11/2016] [Indexed: 11/21/2022]
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13
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Chauhan A, Paul R, Debnath M, Bessi I, Mandal S, Schwalbe H, Dash J. Synthesis of Fluorescent Binaphthyl Amines That Bind c-MYC G-Quadruplex DNA and Repress c-MYC Expression. J Med Chem 2016; 59:7275-81. [PMID: 27442915 DOI: 10.1021/acs.jmedchem.6b00328] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Two novel binaphthyl amines have been designed and synthesized using Buchwald amination and oxidative homocoupling as key steps. The binaphthyl amine containing two triazole rings shows higher affinity for c-MYC G-quadruplex, exhibits fluorescence "turn-on" response with c-MYC, and stains the nucleus in cells. The triazolyl binaphthyl amine shows cytotoxicity for cancer cells by inducing G2/M phase cell cycle arrest and apoptosis. Moreover, both ligands can downregulate c-MYC expression at transcriptional and translational levels.
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Affiliation(s)
- Ajay Chauhan
- Department of Chemical Sciences, Indian Institute of Science Education and Research , Mohanpur, West Bengal 741252, India
| | - Rakesh Paul
- Department of Organic Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032, India
| | - Manish Debnath
- Department of Organic Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032, India
| | - Irene Bessi
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt , Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
| | - Samir Mandal
- Department of Organic Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032, India
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt , Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
| | - Jyotirmayee Dash
- Department of Chemical Sciences, Indian Institute of Science Education and Research , Mohanpur, West Bengal 741252, India.,Department of Organic Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032, India
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14
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Sabale PM, Srivatsan SG. Responsive Fluorescent PNA Analogue as a Tool for Detecting G-quadruplex Motifs of Oncogenes and Activity of Toxic Ribosome-Inactivating Proteins. Chembiochem 2016; 17:1665-73. [PMID: 27271025 DOI: 10.1002/cbic.201600192] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Indexed: 12/13/2022]
Abstract
Fluorescent oligomers that are resistant to enzymatic degradation and report their binding to target oligonucleotides (ONs) by changes in fluorescence properties are highly useful in developing nucleic-acid-based diagnostic tools and therapeutic strategies. Here, we describe the synthesis and photophysical characterization of fluorescent peptide nucleic acid (PNA) building blocks made of microenvironment-sensitive 5-(benzofuran-2-yl)- and 5-(benzothiophen-2-yl)-uracil cores. The emissive monomers, when incorporated into PNA oligomers and hybridized to complementary ONs, are minimally perturbing and are highly sensitive to their neighboring base environment. In particular, benzothiophene-modified PNA reports the hybridization process with significant enhancement in fluorescence intensity, even when placed in the vicinity of guanine residues, which often quench fluorescence. This feature was used in the turn-on detection of G-quadruplex-forming promoter DNA sequences of human proto-oncogenes (c-myc and c-kit). Furthermore, the ability of benzothiophene-modified PNA oligomer to report the presence of an abasic site in RNA enabled us to develop a simple fluorescence hybridization assay to detect and estimate the depurination activity of ribosome-inactivating protein toxins. Our results demonstrate that this approach with responsive PNA probes will provide new opportunities to develop robust tools to study nucleic acids.
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Affiliation(s)
- Pramod M Sabale
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India.
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15
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Wu S, Wang L, Zhang N, Liu Y, Zheng W, Chang A, Wang F, Li S, Shangguan D. A Bis(methylpiperazinylstyryl)phenanthroline as a Fluorescent Ligand for G-Quadruplexes. Chemistry 2016; 22:6037-47. [PMID: 26990217 DOI: 10.1002/chem.201505170] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Indexed: 11/08/2022]
Abstract
G-quadruplex (G4)-forming sequences are prevalent in the genome and are considered to play important roles in gene regulation, and hence have been viewed as potential therapeutic targets in oncology. However, the structures and functions of most G4s in the genome are poorly understood. Therefore, the development of fluorescent probes and ligands for G4s is important for G4 research and drug discovery. Herein, we report a new G4 ligand, 2,9-bis[4-(4-methylpiperazin-1-yl)styryl]-1,10-phenanthroline (BMSP), which was synthesized by a simple process. BMSP exhibits almost no fluorescence in aqueous buffer. The interaction of BMSP with G4s greatly enhances its fluorescence with a large Stokes' shift of 160 nm. Antiparallel human telomeric G4s exhibit the strongest binding affinity (Kd ≈0.13 μm) to BMSP and induce a fluorescence enhancement of up to 150-fold. BMSP binds to G4s through π-π stacking on the terminal G-quartets. BMSP can enter live cells, and it strongly inhibits the growth of cancer cells rather than causing cell death. Our results suggest that BMSP has the potential to serve both as a fluorescent probe for some G4s and as a chemotherapeutic agent for cancer treatment.
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Affiliation(s)
- Shangrong Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China), Fax: (+86) 10-62528509.,College of Chemistry, Xiangtan University, Xiangtan, 411100, China
| | - Linlin Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China), Fax: (+86) 10-62528509
| | - Nan Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China), Fax: (+86) 10-62528509
| | - Ying Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China), Fax: (+86) 10-62528509
| | - Wei Zheng
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China), Fax: (+86) 10-62528509
| | - Ang Chang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China), Fax: (+86) 10-62528509.,College of Chemistry, Xiangtan University, Xiangtan, 411100, China
| | - Fuyi Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China), Fax: (+86) 10-62528509
| | - Songqin Li
- College of Chemistry, Xiangtan University, Xiangtan, 411100, China
| | - Dihua Shangguan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China), Fax: (+86) 10-62528509.
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16
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New pyridinium-based fluorescent dyes: A comparison of symmetry and side-group effects on G-Quadruplex DNA binding selectivity and application in live cell imaging. Biosens Bioelectron 2016; 81:373-381. [PMID: 26994364 DOI: 10.1016/j.bios.2016.03.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 03/07/2016] [Accepted: 03/07/2016] [Indexed: 11/22/2022]
Abstract
A series of C1-, C2-and C3-symmetric pyridinium conjugates with different styrene-like side groups were synthesized and were utilized as G-quadruplex selective fluorescent probes. The new compounds were well-characterized. Their selectivity, sensitivity, and stability towards G-quadruplex were studied by fluorescence titration, native PAGE experiments, FRET and circular dichroism (CD) analyses. These new compounds investigated in the fluorescence assays were preferentially bound with G-quadruplex DNA compared with other type of nucleic acids and it is fascinating to realize the effects of molecular symmetry and associated side groups showing unexpectedly great influence on the fluorescent signal enhancement for the discrimination of G-quadruplexes DNA from other nucleic acids. This may correlate with the pocket symmetry and shape of the G-quadruplex DNA inherently. Among the compounds, a C2-symmetric dye (2,6-bis-((E)-2-(1H-indol-3-yl)-vinyl)-1-methylpyridin-1-ium iodide) with indolyl-groups substituted was screened out from the series giving the best selectivity and sensitivity towards G-quadruplexes DNA, particularly telo21, due to its high equilibrium binding constant (K=2.17×10(5)M(-1)). In addition, the limit of detection (LOD) of the dye to determine telo21 DNA in bioassays was found as low as 33nM. The results of the study give insight and certain crucial factors, such as molecular symmetry and the associated side groups, on developing of effective fluorescent dyes for G-quadruplex DNA applications including G-quadruplex structure stabilization, biosensing and clinical applications. The compound was also demonstrated as a very selective G-quadruplex fluorescent agent for living cell staining and imaging.
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17
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Hu MH, Chen SB, Guo RJ, Ou TM, Huang ZS, Tan JH. Development of a highly sensitive fluorescent light-up probe for G-quadruplexes. Analyst 2016; 140:4616-25. [PMID: 26027520 DOI: 10.1039/c5an00761e] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
G-quadruplexes are higher-order nucleic acid structures that have attracted extensive attention because of their biological significance and potential applications in supramolecular chemistry. An ever-increasing interest in G-quadruplexes has promoted the development of selective and sensitive fluorescent probes as research tools for these structures. However, most current studies primarily focus on the improved selectivity of probes for G-quadruplexes. Their detection limits or ways to improve their detection limits are rarely described. In this study, a new set of di-substituted triarylimidazole fluorescent probes were designed and synthesized, with the aim of upgrading the detection limit of a lead triarylimidazole IZCM-1 for G-quadruplexes. Among these compounds, IZCM-7 was the most promising candidate. The limit of detection (LOD) value of IZCM-7 for the G-quadruplex was up to 3 nM in solution and up to 5 ng in a gel matrix. These values were significantly improved in comparison with those of IZCM-1. Further biophysical studies revealed that the fluorescence quantum yield and binding affinity of IZCM-7 for G-quadruplexes were markedly increased, and these two factors might be responsible for the significantly improved detection limit of IZCM-7. In addition, the sensitive and selective fluorescence performance of IZCM-7 for G-quadruplexes remained the same even in the presence of large amounts of non-G-quadruplex competitors, suggesting its promising application prospect.
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Affiliation(s)
- Ming-Hao Hu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
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18
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Pavan Kumar Y, Saha P, Saha D, Bessi I, Schwalbe H, Chowdhury S, Dash J. Fluorescent Dansyl-Guanosine Conjugates that Bindc-MYCPromoter G-Quadruplex and Downregulatec-MYCExpression. Chembiochem 2016; 17:388-93. [DOI: 10.1002/cbic.201500631] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Indexed: 01/15/2023]
Affiliation(s)
- Y. Pavan Kumar
- Department of Organic Chemistry; Indian Association for the Cultivation of Science; Jadavpur University; 2A ∞ B Raja S. C. Mullick Road Jadavpur Kolkata 700032 India
| | - Puja Saha
- Department of Organic Chemistry; Indian Association for the Cultivation of Science; Jadavpur University; 2A ∞ B Raja S. C. Mullick Road Jadavpur Kolkata 700032 India
| | - Dhurjhoti Saha
- CSIR-Institute of Genomics and Integrative Biology; Mathura Road Delhi 110 025 India
| | - Irene Bessi
- Institute of Organic Chemistry and Chemical Biology; Goethe University Frankfurt; and Center for Biomolecular Magnetic Resonance; Max-von-Laue Strasse 7 60438 Frankfurt am Main Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology; Goethe University Frankfurt; and Center for Biomolecular Magnetic Resonance; Max-von-Laue Strasse 7 60438 Frankfurt am Main Germany
| | - Shantanu Chowdhury
- CSIR-Institute of Genomics and Integrative Biology; Mathura Road Delhi 110 025 India
| | - Jyotirmayee Dash
- Department of Organic Chemistry; Indian Association for the Cultivation of Science; Jadavpur University; 2A ∞ B Raja S. C. Mullick Road Jadavpur Kolkata 700032 India
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19
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Zhou CQ, Yang JW, Dong C, Wang YM, Sun B, Chen JX, Xu YS, Chen WH. Highly selective, sensitive and fluorescent sensing of dimeric G-quadruplexes by a dimeric berberine. Org Biomol Chem 2016; 14:191-7. [DOI: 10.1039/c5ob01723h] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
This paper describes the highly selective, sensitive and topology-specific fluorescent sensing of dimeric G-quadruplexes by a polyether-tethered dimeric berberine.
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Affiliation(s)
- Chun-Qiong Zhou
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Jian-Wei Yang
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Cheng Dong
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Yong-Min Wang
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Bin Sun
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Jin-Xiang Chen
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Ya-Shi Xu
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Wen-Hua Chen
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
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20
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Chen X, Wang J, Jiang G, Zu G, Liu M, Zhou L, Pei R. The development of a light-up red-emitting fluorescent probe based on a G-quadruplex specific cyanine dye. RSC Adv 2016. [DOI: 10.1039/c6ra11152a] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Cyanine dye-dimethylindole red containing an anionic propylsulfonate substituent and an extending polymethine chain was found to behave as a highly specific red-emitting G-quadruplex probe, especially for parallel G-quadruplex c-myc.
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Affiliation(s)
- Xing Chen
- Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
| | - Jine Wang
- Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
| | - Guimei Jiang
- Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
| | - Guangyue Zu
- Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
| | - Min Liu
- Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
| | - Lu Zhou
- Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
| | - Renjun Pei
- Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
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21
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Dang DT, Phan AT. Development of Fluorescent Protein Probes Specific for Parallel DNA and RNA G-Quadruplexes. Chembiochem 2015; 17:42-5. [DOI: 10.1002/cbic.201500503] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Indexed: 12/16/2022]
Affiliation(s)
- Dung Thanh Dang
- School of Physical and Mathematical Sciences; Nanyang Technological University; 21 Nanyang Link Singapore 637371 Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences; Nanyang Technological University; 21 Nanyang Link Singapore 637371 Singapore
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22
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Hu MH, Chen X, Chen SB, Ou TM, Yao M, Gu LQ, Huang ZS, Tan JH. A new application of click chemistry in situ: development of fluorescent probe for specific G-quadruplex topology. Sci Rep 2015; 5:17202. [PMID: 26603780 PMCID: PMC4658637 DOI: 10.1038/srep17202] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/27/2015] [Indexed: 11/28/2022] Open
Abstract
Target-guided synthesis is an approach to drug discovery that allows the target to self-assemble its own binding agents. So far, target-guided synthesis and especially in situ click chemistry have attracted extensive attention and have led to the identification of highly potent inhibitors for proteins. In this study, we expand the application of in situ click chemistry and present a procedure using this approach to identify selective fluorescent probes for a specific topology of G-quadruplex nucleic acids, the parallel G-quadruplexes. On this basis, compound 15 assembled by triarylimidazole scaffold and carboxyl side chain was a positive hit, demonstrating highly potential in the sensitive and selective detection of parallel G-quadruplexes. Such selective fluorescence response can be rationalized in terms of different binding affinities between 15 and G-quadruplexes. Our work accordingly represents a new development towards the application of in situ click chemistry to develop selective fluorescent probes and may also shed light on the search for probes for a specific G-quadruplex topology.
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Affiliation(s)
- Ming-Hao Hu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xiao Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Shuo-Bin Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Tian-Miao Ou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Meicun Yao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Lian-Quan Gu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
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23
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Chen CH, Hu TH, Huang TC, Chen YL, Chen YR, Cheng CC, Chen CT. Delineation of G-Quadruplex Alkylation Sites Mediated by 3,6-Bis(1-methyl-4-vinylpyridinium iodide)carbazole-Aniline Mustard Conjugates. Chemistry 2015; 21:17379-90. [PMID: 26769627 DOI: 10.1002/chem.201502595] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Indexed: 11/12/2022]
Abstract
A new G-quadruplex (G-4)-directing alkylating agent BMVC-C3M was designed and synthesized to integrate 3,6-bis(1-methyl-4-vinylpyridinium iodide)carbazole (BMVC) with aniline mustard. Various telomeric G-4 structures (hybrid-2 type and antiparallel) and an oncogene promoter, c-MYC (parallel), were constructed to react with BMVC-C3M, yielding 35 % alkylation yield toward G-4 DNA over other DNA categories (<6 %) and high specificity under competition conditions. Analysis of the intact alkylation adducts by electrospray ionization mass spectroscopy (ESI-MS) revealed the stepwise DNA alkylation mechanism of aniline mustard for the first time. Furthermore, the monoalkylation sites and intrastrand cross-linking sites were determined and found to be dependent on G-4 topology based on the results of footprinting analysis in combination with mass spectroscopic techniques and in silico modeling. The results indicated that BMVC-C3M preferentially alkylated at A15 (H26), G12 (H24), and G2 (c-MYC), respectively, as monoalkylated adducts and formed A15-C3M-A21 (H26), G12-C3M-G4 (H24), and G2-C3M-G4/G17 (c-MYC), respectively, as cross-linked dialkylated adducts. Collectively, the stability and site-selective cross-linking capacity of BMVC-C3M provides a credible tool for the structural and functional characterization of G-4 DNAs in biological systems.
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Affiliation(s)
- Chien-Han Chen
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan (R.O.C.), Fax: (+886) 2-23636359
| | - Tsung-Hao Hu
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan (R.O.C.), Fax: (+886) 2-23636359
| | - Tzu-Chiao Huang
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan (R.O.C.), Fax: (+886) 2-23636359
| | - Ying-Lan Chen
- Agricultural Biotechnology Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Taipei, 11529 Taiwan (R.O.C.).,Institute of Plant Biology and Department of Life Science, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan (R.O.C.)
| | - Yet-Ran Chen
- Agricultural Biotechnology Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Taipei, 11529 Taiwan (R.O.C.)
| | - Chien-Chung Cheng
- Department of Applied Chemistry, Chia-Yi University, No. 300, Xuefu Road, Chiayi City, 60004 Taiwan (R.O.C.), Fax: (+886) 5-2717901.
| | - Chao-Tsen Chen
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan (R.O.C.), Fax: (+886) 2-23636359.
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24
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Lu YJ, Deng Q, Hu DP, Wang ZY, Huang BH, Du ZY, Fang YX, Wong WL, Zhang K, Chow CF. A molecular fluorescent dye for specific staining and imaging of RNA in live cells: a novel ligand integration from classical thiazole orange and styryl compounds. Chem Commun (Camb) 2015; 51:15241-4. [PMID: 26329127 DOI: 10.1039/c5cc05551b] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A new RNA-selective fluorescent dye integrated with a thiazole orange and a p-(methylthio)styryl moiety shows better nucleolus RNA staining and imaging performance in live cells than the commercial stains. It also exhibits excellent photostability, cell tolerance, and counterstain compatibility with 4',6-diamidino-2-phenylindole for specific RNA-DNA colocalization in bioassays.
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Affiliation(s)
- Yu-Jing Lu
- Institute of Natural Medicine and Green Chemistry, School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou 510006, P. R. China.
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25
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Tanpure AA, Srivatsan SG. Conformation-sensitive nucleoside analogues as topology-specific fluorescence turn-on probes for DNA and RNA G-quadruplexes. Nucleic Acids Res 2015. [PMID: 26202965 PMCID: PMC4678839 DOI: 10.1093/nar/gkv743] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Development of probes that can discriminate G-quadruplex (GQ) structures and indentify efficient GQ binders on the basis of topology and nucleic acid type is highly desired to advance GQ-directed therapeutic strategies. In this context, we describe the development of minimally perturbing and environment-sensitive pyrimidine nucleoside analogues, based on a 5-(benzofuran-2-yl)uracil core, as topology-specific fluorescence turn-on probes for human telomeric DNA and RNA GQs. The pyrimidine residues of one of the loop regions (TTA) of telomeric DNA and RNA GQ oligonucleotide (ON) sequences were replaced with 5-benzofuran-modified 2′-deoxyuridine and uridine analogues. Depending on the position of modification the fluorescent nucleoside analogues distinguish antiparallel, mixed parallel-antiparallel and parallel stranded DNA and RNA GQ topologies from corresponding duplexes with significant enhancement in fluorescence intensity and quantum yield. Further, these GQ sensors enabled the development of a simple fluorescence binding assay to quantify topology- and nucleic acid-specific binding of small molecule ligands to GQ structures. Together, our results demonstrate that these nucleoside analogues are useful GQ probes, which are anticipated to provide new opportunities to study and discover efficient G-quadruplex binders of therapeutic potential.
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Affiliation(s)
- Arun A Tanpure
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr Homi Bhabha Road, Pashan, Pune 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr Homi Bhabha Road, Pashan, Pune 411008, India
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26
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Zhang Q, Liu YC, Kong DM, Guo DS. Tetraphenylethene Derivatives with Different Numbers of Positively Charged Side Arms have Different Multimeric G-Quadruplex Recognition Specificity. Chemistry 2015; 21:13253-60. [DOI: 10.1002/chem.201501847] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Indexed: 01/10/2023]
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27
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Ou Z, Feng Z, Liu G, Chen Y, Gao Y, Li Y, Wang X. Synthesis and G-Quadruplex-binding Properties of Cationic Platinum(II) Terpyridine Complexes Containing σ-Alkynyl Auxiliaries. CHEM LETT 2015. [DOI: 10.1246/cl.141045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Zhize Ou
- The Key Laboratory of Space Applied Physics and Chemistry, Ministry of Education, Department of Applied Chemistry, School of Science, Northwestern Polytechnical University
| | - Zhao Feng
- The Key Laboratory of Space Applied Physics and Chemistry, Ministry of Education, Department of Applied Chemistry, School of Science, Northwestern Polytechnical University
| | - Guixia Liu
- The Key Laboratory of Space Applied Physics and Chemistry, Ministry of Education, Department of Applied Chemistry, School of Science, Northwestern Polytechnical University
| | - Yongjie Chen
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, TIPC, CAS
| | - Yunyan Gao
- The Key Laboratory of Space Applied Physics and Chemistry, Ministry of Education, Department of Applied Chemistry, School of Science, Northwestern Polytechnical University
| | - Yi Li
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, TIPC, CAS
| | - Xuesong Wang
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, TIPC, CAS
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28
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Kim KT, Heo W, Joo T, Kim BH. Photophysical and structural investigation of a PyA-modified adenine cluster: its potential use for fluorescent DNA probes exhibiting distinct emission color changes. Org Biomol Chem 2015; 13:8470-8. [DOI: 10.1039/c5ob01159k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A PyA-modified adenine cluster, exhibiting a large Stokes shift based on interstrand stacking interactions of adenines, was investigated and exploited as signaling parts of fluorescent DNA probes.
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Affiliation(s)
- Ki Tae Kim
- Department of Chemistry
- BK School of Molecular Science
- Pohang University of Science and Technology (POSTECH)
- Pohang 790-784
- South Korea
| | - Wooseok Heo
- Department of Chemistry
- BK School of Molecular Science
- Pohang University of Science and Technology (POSTECH)
- Pohang 790-784
- South Korea
| | - Taiha Joo
- Department of Chemistry
- BK School of Molecular Science
- Pohang University of Science and Technology (POSTECH)
- Pohang 790-784
- South Korea
| | - Byeang Hyean Kim
- Department of Chemistry
- BK School of Molecular Science
- Pohang University of Science and Technology (POSTECH)
- Pohang 790-784
- South Korea
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Kataoka Y, Fujita H, Kasahara Y, Yoshihara T, Tobita S, Kuwahara M. Minimal Thioflavin T Modifications Improve Visual Discrimination of Guanine-Quadruplex Topologies and Alter Compound-Induced Topological Structures. Anal Chem 2014; 86:12078-84. [DOI: 10.1021/ac5028325] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yuka Kataoka
- Graduate School of Science and Technology, Gunma University, 1-5-1
Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Hiroto Fujita
- Graduate School of Science and Technology, Gunma University, 1-5-1
Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Yuuya Kasahara
- Graduate School of Science and Technology, Gunma University, 1-5-1
Tenjin-cho, Kiryu, Gunma 376-8515, Japan
- National Institute of Biomedical Innovation (NIBIO), 7-6-8 Asagi, Saito, Ibaraki, Osaka 567-0085, Japan
| | - Toshitada Yoshihara
- Graduate School of Science and Technology, Gunma University, 1-5-1
Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Seiji Tobita
- Graduate School of Science and Technology, Gunma University, 1-5-1
Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Masayasu Kuwahara
- Graduate School of Science and Technology, Gunma University, 1-5-1
Tenjin-cho, Kiryu, Gunma 376-8515, Japan
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Das RN, Debnath M, Gaurav A, Dash J. Environment-Sensitive Probes Containing a 2,6-Diethynylpyridine Motif for Fluorescence Turn-On Detection and Induction of Nanoarchitectures of Human Telomeric Quadruplex. Chemistry 2014; 20:16688-93. [DOI: 10.1002/chem.201404795] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Indexed: 12/24/2022]
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31
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Sabharwal NC, Savikhin V, Turek-Herman JR, Nicoludis JM, Szalai VA, Yatsunyk LA. N-methylmesoporphyrin IX fluorescence as a reporter of strand orientation in guanine quadruplexes. FEBS J 2014; 281:1726-37. [PMID: 24494857 PMCID: PMC4163640 DOI: 10.1111/febs.12734] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 12/24/2013] [Accepted: 01/30/2014] [Indexed: 11/30/2022]
Abstract
Guanine quadruplexes (GQ) are four-stranded DNA structures formed by guanine-rich DNA sequences. The formation of GQs inhibits cancer cell growth, although the detection of GQs in vivo has proven difficult, in part because of their structural diversity. The development of GQ-selective fluorescent reporters would enhance our ability to quantify the number and location of GQs, ultimately advancing biological studies of quadruplex relevance and function. N-methylmesoporphyrin IX (NMM) interacts selectively with parallel-stranded GQs; in addition, its fluorescence is sensitive to the presence of DNA, making this ligand a possible candidate for a quadruplex probe. In the present study, we investigated the effect of DNA secondary structure on NMM fluorescence. We found that NMM fluorescence increases by about 60-fold in the presence of parallel-stranded GQs and by about 40-fold in the presence of hybrid GQs. Antiparallel GQs lead to lower than 10-fold increases in NMM fluorescence. Single-stranded DNA, duplex, or i-motif, induce no change in NMM fluorescence. We conclude that NMM shows promise as a 'turn-on' fluorescent probe for detecting quadruplex structures, as well as for differentiating them on the basis of strand orientation.
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Affiliation(s)
- Navin C Sabharwal
- Department of Chemistry and Biochemistry, Swarthmore College, PA, USA
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32
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Discovery of a structural-element specific G-quadruplex "light-up" probe. Sci Rep 2014; 4:3776. [PMID: 24441075 PMCID: PMC3895904 DOI: 10.1038/srep03776] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 12/23/2013] [Indexed: 01/26/2023] Open
Abstract
The development of a fluorescent probe capable of detecting and distinguishing the wide diversity of G-quadruplex structures is particularly challenging. Herein, we report a novel BODIPY-based fluorescent sensor (GQR) that shows unprecedented selectivity to parallel-stranded G-quadruplexes with exposed ends and four medium grooves. Mechanistic studies suggest that GQR associates with G-quadruplex grooves close to the end of the tetrad core, which may explain the dye's specificity to only a subset of parallel structures. This specific recognition favours the disaggregation of GQR in aqueous solutions thereby recovering the inherent fluorescence of the dye. Due to its unique features, GQR represents a valuable tool for basic biological research and the rapid discovery of novel, specific ligands that target similar structural features of G-quadruplexes.
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33
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Lai H, Xiao Y, Yan S, Tian F, Zhong C, Liu Y, Weng X, Zhou X. Symmetric cyanovinyl-pyridinium triphenylamine: a novel fluorescent switch-on probe for an antiparallel G-quadruplex. Analyst 2014; 139:1834-8. [DOI: 10.1039/c3an02269b] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We describe a probe based on a cyanovinyl pyridinium triphenylamine (CPT) derivative, which showed fluorescent switch-on properties toward an antiparallel G-quadruplex.
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Affiliation(s)
- Hai Lai
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072, P. R. China
| | - Yijie Xiao
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072, P. R. China
| | - Shengyong Yan
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072, P. R. China
| | - Fangfang Tian
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072, P. R. China
| | - Cheng Zhong
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072, P. R. China
| | - Yi Liu
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072, P. R. China
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072, P. R. China
- The State Key Laboratory of Natural and Biomimetic Drugs
- State
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan 430072, P. R. China
- The State Key Laboratory of Natural and Biomimetic Drugs
- State
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34
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Chen SB, Wu WB, Hu MH, Ou TM, Gu LQ, Tan JH, Huang ZS. Discovery of a new fluorescent light-up probe specific to parallel G-quadruplexes. Chem Commun (Camb) 2014; 50:12173-6. [DOI: 10.1039/c4cc05394j] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A sensitive probe was developed for the detection of parallel G-quadruplexes without affecting their topology or thermal stability.
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Affiliation(s)
- Shuo-Bin Chen
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006, China
| | - Wei-Bin Wu
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006, China
| | - Ming-Hao Hu
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006, China
| | - Tian-Miao Ou
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006, China
| | - Lian-Quan Gu
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006, China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006, China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006, China
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35
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Chen Y, Yan S, Yuan L, Zhou Y, Song Y, Xiao H, Weng X, Zhou X. Nonlinear optical dye TSQ1 as an efficiently selective fluorescent probe for G-quadruplex DNA. Org Chem Front 2014. [DOI: 10.1039/c3qo00048f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Gabelica V, Maeda R, Fujimoto T, Yaku H, Murashima T, Sugimoto N, Miyoshi D. Multiple and cooperative binding of fluorescence light-up probe thioflavin T with human telomere DNA G-quadruplex. Biochemistry 2013; 52:5620-8. [PMID: 23909872 DOI: 10.1021/bi4006072] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Thioflavin T (ThT), a typical probe for protein fibrils, also binds human telomeric G-quadruplexes with a fluorescent light-up signal change and high specificity against DNA duplexes. Cell penetration and low cytotoxicity of fibril probes having been widely established, modifying ThT and other fibril probes is an attractive means of generating new G-quadruplex ligands. Thus, elucidating the binding mechanism is important for the design of new drugs and fluorescent probes based on ThT. Here, we investigated the binding mechanism of ThT with several variants of the human telomeric sequence in the presence of monovalent cations. Fluorescence titrations and electrospray ionization mass spectrometry (ESI-MS) analyses demonstrated that each G-quadruplex unit cooperatively binds to several ThT molecules. ThT brightly fluoresces when a single ligand is bound to the G-quadruplex and is quenched as ligand binding stoichiometry increases. Both the light-up signal and the dissociation constants are exquisitely sensitive to the base sequence and to the G-quadruplex structure. These results are crucial for the sensible design and interpretation of G-quadruplex detection assays using fluorescent ligands in general and ThT in particular.
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Affiliation(s)
- Valérie Gabelica
- Physical Chemistry and Mass Spectrometry Laboratory, Department of Chemistry, University of Liège, B-4000 Liège, Belgium.
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37
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Kumar YP, Bhowmik S, Das RN, Bessi I, Paladhi S, Ghosh R, Schwalbe H, Dash J. A Fluorescent Guanosine Dinucleoside as a Selective Switch-On Sensor forc-mycG-Quadruplex DNA with Potent Anticancer Activities. Chemistry 2013; 19:11502-6. [DOI: 10.1002/chem.201302107] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Indexed: 02/01/2023]
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