1
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Rabiei P, Mohabatkar H, Behbahani M. A label-free G-quadruplex aptamer/gold nanoparticle-based colorimetric biosensor for rapid detection of bovine viral diarrhea virus genotype 1. PLoS One 2024; 19:e0293561. [PMID: 39078832 PMCID: PMC11288453 DOI: 10.1371/journal.pone.0293561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/16/2023] [Indexed: 08/02/2024] Open
Abstract
Bovine viral diarrhea virus (BVDV) is the cause of bovine viral diarrhea disease, one of the most economically important livestock diseases worldwide. The majority of BVD disease control programs rely on the detection and then elimination of persistent infection (PI) cattle, as the continuing source of disease. The main purpose of this study was to design and develop an accurate G-quadruplex-based aptasensor for rapid and simple detection of BVDV-1. In this work, we utilized in silico techniques to design a G-quadruplex aptamer specific for the detection of BVDV-1. Also, the rationally designed aptamer was validated experimentally and was used for developing a colorimetric biosensor based on an aptamer-gold nanoparticle system. Firstly, a pool of G-quadruplex forming ssDNA sequences was constructed. Then, based on the stability score in secondary and tertiary structures and molecular docking score, an aptamer (Apt31) was selected. In the experimental part, gold nanoparticles (AuNPs) with an average particle size of 31.7 nm were synthesized and electrostatically linked with the Apt31. The colorimetric test showed that salt-induced color change of AuNPs from red to purple-blue occurs only in the presence of BVDV-Apt31 complex, after 20 min. These results approved the specificity of Apt31 for BVDV. Furthermore, our biosensor could detect the virus at as low as 0.27 copies/ml, which is an acceptable value in comparison to the qPCR method. The specificity of the aptasensor was confirmed through cross-reactivity testing, while its selectivity was confirmed through plasma testing. The sample analysis showed 90% precision and 94% accuracy. It was concluded that the biosensor was adequately sensitive and specific for the detection of BVDV in plasma samples and could be used as a simple and rapid method on the farm.
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Affiliation(s)
- Parisa Rabiei
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Hassan Mohabatkar
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Mandana Behbahani
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
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2
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Luo Y, Granzhan A, Marquevielle J, Cucchiarini A, Lacroix L, Amrane S, Verga D, Mergny JL. Guidelines for G-quadruplexes: I. In vitro characterization. Biochimie 2023; 214:5-23. [PMID: 36596406 DOI: 10.1016/j.biochi.2022.12.019] [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: 10/29/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 01/02/2023]
Abstract
Besides the well-known DNA double-helix, non-canonical nucleic acid structures regulate crucial biological activities. Among these oddities, guanine-rich DNA sequences can form unusual four-stranded secondary structures called G-quadruplexes (G4s). G4-prone sequences have been found in the genomes of most species, and G4s play important roles in essential processes such as transcription, replication, genome integrity and epigenetic regulation. Here, we present a short overview of G-quadruplexes followed by a detailed description of the biophysical and biochemical methods used to characterize G4s in vitro. The principles, experimental details and possible shortcomings of each method are discussed to provide a comprehensive view of the techniques used to study these structures. We aim to provide a set of guidelines for standardizing research on G-quadruplexes; these guidelines are not meant to be a dogmatic set of rules, but should rather provide useful information on the methods currently used to study these fascinating motifs.
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Affiliation(s)
- Yu Luo
- Laboratoire D'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France; CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France; CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France
| | - Julien Marquevielle
- Université de Bordeaux, ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, 33076, Bordeaux, France
| | - Anne Cucchiarini
- Laboratoire D'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Laurent Lacroix
- Institut de Biologie de L'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Samir Amrane
- Université de Bordeaux, ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, 33076, Bordeaux, France
| | - Daniela Verga
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France; CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France.
| | - Jean-Louis Mergny
- Laboratoire D'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France; Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
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3
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Li Y, Chen P, Gao G, Qin L, Yang H, Zhang X. A smart microhydrogel membrane sensor realized by pipette tip. Biosens Bioelectron 2022; 211:114341. [PMID: 35594625 DOI: 10.1016/j.bios.2022.114341] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 11/17/2022]
Abstract
In this paper, we describe a simple and practical way to prepare hydrogel membranes in a conical channel (pipette tip). We used a pipette to create a gas pressure difference on both sides of the gel precursor, which drove the gel precursor to move in the pipette tip. During movement, the shape of the hydrogel precursor gradually becomes thinner as the radius of the tapered channel becomes larger. We use this principle to realize the highly controllable preparation of the hydrogel membrane structure (130 μm at its thinnest). Moreover, we fabricated a hydrogel membrane sensor in one step by implanting smart molecules in the hydrogel, which achieved rapid and sensitive detection of 0.5 μM-500 mM potassium ions. This method of preparing the hydrogel membrane sensor does not rely on professional membrane production equipment and complex molecular design processes, has high gel utilization and simple and controllable membrane thickness, and has a wide range of application value in the field of intelligent hydrogel-based analysis technology.
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Affiliation(s)
- Yansheng Li
- Beijing Key Laboratory for Sensors, Beijing Information Science & Technology University, Beijing, 100192, PR China; Key Laboratory of Modern Measurement and Control Technology, Ministry of Education, Beijing Information Science and Technology University, Beijing, 100192, PR China
| | - Peng Chen
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Robot Intelligent Laboratory of Traditional Chinese Medicine, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, 100700, PR China
| | - Guowei Gao
- Beijing Key Laboratory for Sensors, Beijing Information Science & Technology University, Beijing, 100192, PR China; Key Laboratory of Modern Measurement and Control Technology, Ministry of Education, Beijing Information Science and Technology University, Beijing, 100192, PR China.
| | - Lei Qin
- Beijing Key Laboratory for Sensors, Beijing Information Science & Technology University, Beijing, 100192, PR China
| | - Hongjun Yang
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Robot Intelligent Laboratory of Traditional Chinese Medicine, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, 100700, PR China
| | - Xueji Zhang
- School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, Guangdong, 518060, PR China.
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4
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Bruni L, Manghi M, De Sanctis P, Zucchini C, Croci S. Validation of circular dichroic spectroscopy of synthetic oligonucleotide PS2.M for K + concentration measurements. EUROPEAN PHYSICAL JOURNAL PLUS 2022; 137:433. [PMID: 35411290 PMCID: PMC8988120 DOI: 10.1140/epjp/s13360-022-02581-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
The single-stranded synthetic oligonucleotide PS2.M is known to provide a basis for developing sensors since it tends to fold into structures called G-quadruplexes (G4) having characteristic topology and orientation with probabilities that depend on the chemical environment. The presence and concentration of cation species are among the key factors that determine the outcome of such a process. PS2.M and other aptamers have been used in several applications in conjunction with various probes, such as hemin, at the cost of increased technical complexity and applicability limitations. We instead validated the application limits of Circular Dichroic spectroscopy (CD) as only measurement method to assay PS2.M asK + sensor in a variety of solutions having different chemical complexity. The tested solutions range from simple NaCl and KCl solutions to chemically complex solutions like DMEM-Dulbecco's Modified Eagle Medium-which is widely used in a biological laboratory. PS2.M was also evaluated in solutions of KHCO 3 and D-ribose (K:D-rib), an antioxidant potassium compound, to compare its response to the simple KCl solution case. Our findings show that, within specific concentration applicability ranges, CD spectra can estimate theK + concentration in the examined water solutions even at high Na + concentrations with respect toK + and in the presence of antioxidant molecules. Supplementary Information The online version supplementary material available at 10.1140/epjp/s13360-022-02581-2.
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Affiliation(s)
- Luca Bruni
- National Institute for Biostructures and Biosystems, Rome, Italy
| | - Massimo Manghi
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Paola De Sanctis
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, Università di Bologna, Bologna, Italy
| | - Cinzia Zucchini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, Università di Bologna, Bologna, Italy
| | - Simonetta Croci
- National Institute for Biostructures and Biosystems, Rome, Italy
- Department of Medicine and Surgery, University of Parma, Parma, Italy
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5
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Fluorescent AgNCs Formed on Bifunctional DNA Template for Potassium Ion Detection. CHEMOSENSORS 2021. [DOI: 10.3390/chemosensors9120349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In this study, we examined properties of silver nanoclusters, which are AgNCs stabilized by DNA oligonucleotide scaffold containing G-quadruplex-forming sequences: human telomeric (Tel22) or thrombin-binding aptamer (TBA). Thus, we obtained two fluorescent probes abbreviated as Tel22C12-AgNCs and TBAC12-AgNCs, which were characterized using absorption, circular dichroism and fluorescence spectroscopy. Both probes emit green and red fluorescence. The presence of silver nanoclusters did not destabilize the formed G-quadruplexes. The structural changes of probes upon binding K+ or Na+ ions cause quenching in their red emission. Green emission was slightly quenched only in the case of Tel22C12-AgNCs; on the contrary, for TBAC12-AgNC’s green emission, we observed an increasing fluorescence signal. Moreover, the Tel22C12-AgNCs system shows not only a higher binding preference for K+ over Na+, but it was able to monitor small changes in K+ concentrations in the buffer mimicking extracellular conditions (high content of Na+ ions). These results suggest that Tel22C12-AgNCs exhibit the potential to monitor transmembrane potassium transport.
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6
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Fluorescent probes for the stabilization and detection of G-quadruplexes and their prospective applications. J INDIAN CHEM SOC 2021. [DOI: 10.1016/j.jics.2021.100078] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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7
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Xi H, Juhas M, Zhang Y. G-quadruplex based biosensor: A potential tool for SARS-CoV-2 detection. Biosens Bioelectron 2020; 167:112494. [PMID: 32791468 PMCID: PMC7403137 DOI: 10.1016/j.bios.2020.112494] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/26/2020] [Accepted: 07/31/2020] [Indexed: 12/29/2022]
Abstract
G-quadruplex is a non-canonical nucleic acid structure formed by the folding of guanine rich DNA or RNA. The conformation and function of G-quadruplex are determined by a number of factors, including the number and polarity of nucleotide strands, the type of cations and the binding targets. Recent studies led to the discovery of additional advantageous attributes of G-quadruplex with the potential to be used in novel biosensors, such as improved ligand binding and unique folding properties. G-quadruplex based biosensor can detect various substances, such as metal ions, organic macromolecules, proteins and nucleic acids with improved affinity and specificity compared to standard biosensors. The recently developed G-quadruplex based biosensors include electrochemical and optical biosensors. A novel G-quadruplex based biosensors also show better performance and broader applications in the detection of a wide spectrum of pathogens, including SARS-CoV-2, the causative agent of COVID-19 disease. This review highlights the latest developments in the field of G-quadruplex based biosensors, with particular focus on the G-quadruplex sequences and recent applications and the potential of G-quadruplex based biosensors in SARS-CoV-2 detection.
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Affiliation(s)
- Hui Xi
- College of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, 518055, China
| | - Mario Juhas
- Medical and Molecular Microbiology Unit, Department of Medicine, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Yang Zhang
- College of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, 518055, China.
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8
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Kong RM, Ma L, Han X, Ma C, Qu F, Xia L. Hg 2+-mediated stabilization of G-triplex based molecular beacon for label-free fluorescence detection of Hg 2+, reduced glutathione, and glutathione reductase activity. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 228:117855. [PMID: 31784222 DOI: 10.1016/j.saa.2019.117855] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 11/21/2019] [Accepted: 11/23/2019] [Indexed: 06/10/2023]
Abstract
G-triplexes have been reported recently with the similar function to G-quadruplex that can combine with thioflavin T (ThT) and emit strong fluorescence but easier to be controlled and excited. In this work, we report an Hg2+-mediated stabilization of G-triplex based functional molecular beacon (G3TMB) sensing system for the label-free detection of Hg2+, reduced glutathione (GSH), and glutathione reductase (GR) activity. In the presence of Hg2+, the extended G-triplex sequence containing the "T" bases can form a stable hairpin structure due to the strong interactions of "T-Hg2+-T", resulting in the locking of G-tracts in the stem of the G3TMB effectively. However, the hairpin structure of the G3TMB can be opened by the introduction of GSH through the stronger "GSH-Hg2+" interaction. Therefore, by employing the fact that GR can catalyze the reduction of oxidized glutathione (GSSG) into GSH, this concept can be applied to fluorescence "off-on" detection of GR activity, with a linear range of 0.02-30 mU/mL and detection limit of 0.01 mU/mL. This work may expand a new perspective of G-triplex based functional molecular beacon as the label-free fluorescent probes in the detection of small biomolecule and enzyme activity.
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Affiliation(s)
- Rong-Mei Kong
- College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong 273165, PR China.
| | - Lin Ma
- College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong 273165, PR China
| | - Xue Han
- College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong 273165, PR China
| | - Chunran Ma
- College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong 273165, PR China
| | - Fengli Qu
- College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong 273165, PR China
| | - Lian Xia
- College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong 273165, PR China
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9
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Label-free Pb2+ detection on the layer-by-layer platform using real-time dual polarization interferometry. Talanta 2019; 202:336-341. [DOI: 10.1016/j.talanta.2019.05.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/20/2019] [Accepted: 05/02/2019] [Indexed: 11/17/2022]
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10
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Umar MI, Ji D, Chan CY, Kwok CK. G-Quadruplex-Based Fluorescent Turn-On Ligands and Aptamers: From Development to Applications. Molecules 2019; 24:E2416. [PMID: 31262059 PMCID: PMC6650947 DOI: 10.3390/molecules24132416] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 06/17/2019] [Accepted: 06/24/2019] [Indexed: 02/08/2023] Open
Abstract
Guanine (G)-quadruplexes (G4s) are unique nucleic acid structures that are formed by stacked G-tetrads in G-rich DNA or RNA sequences. G4s have been reported to play significant roles in various cellular events in both macro- and micro-organisms. The identification and characterization of G4s can help to understand their different biological roles and potential applications in diagnosis and therapy. In addition to biophysical and biochemical methods to interrogate G4 formation, G4 fluorescent turn-on ligands can be used to target and visualize G4 formation both in vitro and in cells. Here, we review several representative classes of G4 fluorescent turn-on ligands in terms of their interaction mechanism and application perspectives. Interestingly, G4 structures are commonly identified in DNA and RNA aptamers against targets that include proteins and small molecules, which can be utilized as G4 tools for diverse applications. We therefore also summarize the recent development of G4-containing aptamers and highlight their applications in biosensing, bioimaging, and therapy. Moreover, we discuss the current challenges and future perspectives of G4 fluorescent turn-on ligands and G4-containing aptamers.
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Affiliation(s)
- Mubarak I Umar
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Danyang Ji
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Chun-Yin Chan
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Chun Kit Kwok
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.
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11
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Ma G, Yu Z, Zhou W, Li Y, Fan L, Li X. Investigation of Na+ and K+ Competitively Binding with a G-Quadruplex and Discovery of a Stable K+–Na+-Quadruplex. J Phys Chem B 2019; 123:5405-5411. [DOI: 10.1021/acs.jpcb.9b02823] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ge Ma
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ze Yu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wei Zhou
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Yunchao Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Louzhen Fan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xiaohong Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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12
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Wang S, Zhao J, Lu S, Sun J, Yang X. A duplex connection can further illuminate G-quadruplex/crystal violet complex. Chem Commun (Camb) 2019; 55:1911-1914. [PMID: 30675884 DOI: 10.1039/c8cc09940e] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Duplex-connected G-quadruplex (dsG4) has a more evident promotion of the fluorescent emission of crystal violet than pure G-quadruplex (G4), which is firstly found and investigated systematically using fluorescence spectra, circular dichroism, and density functional theory. This new phenomenon also shows potential in application for target nucleic acid detection.
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Affiliation(s)
- Shuang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China.
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13
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Sai-Anand G, Sivanesan A, Benzigar MR, Singh G, Gopalan AI, Baskar AV, Ilbeygi H, Ramadass K, Kambala V, Vinu A. Recent Progress on the Sensing of Pathogenic Bacteria Using Advanced Nanostructures. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20180280] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Gopalan Sai-Anand
- Global Innovative Center for Advanced Nanomaterials, Faculty of Built Environment and Engineering, The University of Newcastle, Callaghan 2308, New South Wales, Australia
- Future Industries Institute, Division of Information Technology, Engineering and Environment, University of South Australia, Mawson Lakes, South Australia 5095, Australia
| | - Arumugam Sivanesan
- Future Industries Institute, Division of Information Technology, Engineering and Environment, University of South Australia, Mawson Lakes, South Australia 5095, Australia
- Metrohm Australia, 56 Buffalo Road, Gladesville, NSW 2111, Australia
| | - Mercy R Benzigar
- Future Industries Institute, Division of Information Technology, Engineering and Environment, University of South Australia, Mawson Lakes, South Australia 5095, Australia
| | - Gurwinder Singh
- Global Innovative Center for Advanced Nanomaterials, Faculty of Built Environment and Engineering, The University of Newcastle, Callaghan 2308, New South Wales, Australia
- Future Industries Institute, Division of Information Technology, Engineering and Environment, University of South Australia, Mawson Lakes, South Australia 5095, Australia
| | - Anantha-Iyengar Gopalan
- Research Institute of Advanced Energy Technology, Kyungpook National University, Daegu 41566, Korea
| | - Arun Vijay Baskar
- Global Innovative Center for Advanced Nanomaterials, Faculty of Built Environment and Engineering, The University of Newcastle, Callaghan 2308, New South Wales, Australia
- Future Industries Institute, Division of Information Technology, Engineering and Environment, University of South Australia, Mawson Lakes, South Australia 5095, Australia
| | - Hamid Ilbeygi
- Future Industries Institute, Division of Information Technology, Engineering and Environment, University of South Australia, Mawson Lakes, South Australia 5095, Australia
| | - Kavitha Ramadass
- Global Innovative Center for Advanced Nanomaterials, Faculty of Built Environment and Engineering, The University of Newcastle, Callaghan 2308, New South Wales, Australia
- Future Industries Institute, Division of Information Technology, Engineering and Environment, University of South Australia, Mawson Lakes, South Australia 5095, Australia
| | - Venkata Kambala
- Hudson Marketing Pty Ltd, Level 2/131 Macquarie St, Sydney NSW 2000, Australia
| | - Ajayan Vinu
- Global Innovative Center for Advanced Nanomaterials, Faculty of Built Environment and Engineering, The University of Newcastle, Callaghan 2308, New South Wales, Australia
- Future Industries Institute, Division of Information Technology, Engineering and Environment, University of South Australia, Mawson Lakes, South Australia 5095, Australia
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14
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Świtalska A, Dembska A, Fedoruk-Wyszomirska A, Juskowiak B. Cholesterol-Bearing Fluorescent G-Quadruplex Potassium Probes for Anchoring at the Langmuir Monolayer and Cell Membrane. SENSORS (BASEL, SWITZERLAND) 2018; 18:E2201. [PMID: 29987195 PMCID: PMC6069133 DOI: 10.3390/s18072201] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 06/29/2018] [Accepted: 07/02/2018] [Indexed: 12/31/2022]
Abstract
The purpose of the present work was to design, synthesize and spectrally characterize cholesterol-anchored fluorescent oligonucleotide probes (Ch(F-TBA-T), Ch(py-TBA-py)), based on G-quadruplexes, which were able to incorporate into a lipid structure (Langmuir monolayer, living cell membrane). The probes, based on the thrombin-binding aptamer (TBA) sequence, were labeled with fluorescent dyes which enabled simultaneous monitoring of the formation of G-quadruplex structures and visualization of probe incorporation into the cellular membrane. The combinations of fluorophores used included fluorescence resonance energy transfer (FRET) and excimer emission approaches. The structural changes of the probes upon binding with K⁺ or Na⁺ ions were monitored with fluorescence techniques. These systems showed a very high binding preference for K⁺ over Na⁺ ions. The use of confocal fluorescence microscopy indicated successful anchoring of the cholesterol-bearing fluorescent probes to the living cell membrane. These structurally simple cholesterol-based fluorescent probes have good potential for opening up new and exciting opportunities in the field of biosensors; e.g., in vivo detection of K⁺ ions.
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Affiliation(s)
- Angelika Świtalska
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
| | - Anna Dembska
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
| | | | - Bernard Juskowiak
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
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15
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Benito S, Ferrer A, Benabou S, Aviñó A, Eritja R, Gargallo R. Evaluation of the effect of polymorphism on G-quadruplex-ligand interaction by means of spectroscopic and chromatographic techniques. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 196:185-195. [PMID: 29448171 DOI: 10.1016/j.saa.2018.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/16/2018] [Accepted: 02/04/2018] [Indexed: 06/08/2023]
Abstract
Guanine-rich sequences may fold into highly ordered structures known as G-quadruplexes. Apart from the monomeric G-quadruplex, these sequences may form multimeric structures that are not usually considered when studying interaction with ligands. This work studies the interaction of a ligand, crystal violet, with three guanine-rich DNA sequences with the capacity to form multimeric structures. These sequences correspond to short stretches found near the promoter regions of c-kit and SMARCA4 genes. Instrumental techniques (circular dichroism, molecular fluorescence, size-exclusion chromatography and electrospray ionization mass spectrometry) and multivariate data analysis were used for this purpose. The polymorphism of G-quadruplexes was characterized prior to the interaction studies. The ligand was shown to interact preferentially with the monomeric G-quadruplex; the binding stoichiometry was 1:1 and the binding constant was in the order of 105M-1 for all three sequences. The results highlight the importance of DNA treatment prior to interaction studies.
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Affiliation(s)
- S Benito
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Martí i Franquès, 1-11, E-08028 Barcelona, Spain
| | - A Ferrer
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Martí i Franquès, 1-11, E-08028 Barcelona, Spain
| | - S Benabou
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Martí i Franquès, 1-11, E-08028 Barcelona, Spain
| | - A Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN, Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - R Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN, Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - R Gargallo
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Martí i Franquès, 1-11, E-08028 Barcelona, Spain.
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16
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Uda RM, Matsui T, Takei M. Binding of malachite green promotes stability and shows preference for a human telomere DNA G-quadruplex. Supramol Chem 2017. [DOI: 10.1080/10610278.2017.1297447] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ryoko M. Uda
- Department of Chemical Engineering, National Institute of Technology, Nara College, Yamato-koriyama, Japan
| | - Takashi Matsui
- Department of Chemical Engineering, National Institute of Technology, Nara College, Yamato-koriyama, Japan
| | - Michiko Takei
- Department of Chemical Engineering, National Institute of Technology, Nara College, Yamato-koriyama, Japan
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17
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Panich S, Haj Sleiman M, Steer I, Ladame S, Edel JB. Real-Time Monitoring of Ligand Binding to G-Quadruplex and Duplex DNA by Whispering Gallery Mode Sensing. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00301] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sirirat Panich
- Department of Chemistry and ‡Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom
| | - Mazen Haj Sleiman
- Department of Chemistry and ‡Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom
| | - Isobel Steer
- Department of Chemistry and ‡Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom
| | - Sylvain Ladame
- Department of Chemistry and ‡Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom
| | - Joshua B. Edel
- Department of Chemistry and ‡Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom
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18
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Wang M, Mao Z, Kang TS, Wong CY, Mergny JL, Leung CH, Ma DL. Conjugating a groove-binding motif to an Ir(iii) complex for the enhancement of G-quadruplex probe behavior. Chem Sci 2016; 7:2516-2523. [PMID: 28660021 PMCID: PMC5477052 DOI: 10.1039/c6sc00001k] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Accepted: 01/28/2016] [Indexed: 12/15/2022] Open
Abstract
G-quadruplex groove binder benzo[d,e]isoquinoline was linked to a Ir(iii) complex to generate a highly selective DNA probe.
In this study, the reported G-quadruplex groove binder benzo[d,e]isoquinoline was linked to a cyclometallated Ir(iii) complex to generate a highly selective DNA probe 1 that retains the favorable photophysical properties of the parent complex. The linked complex 1 showed advantages of both parent complex 2 and groove binder 3. Similar to 3, the conjugated complex 1 exhibits a superior affinity and selectivity for G-quadruplex DNA over other conformations of DNA or proteins, with the fold enhancement ratio obviously improved compared with parent complex 2. The molecular modelling revealed a groove-binding mode between complex 1 and G-quadruplex. Meanwhile 1 also possesses the prominent advantages of transition metal complex probes such as a large Stokes shift and long lifetime phosphorescence, which could be recognized in strong fluorescence media through time-resolved emission spectroscopy (TRES). We then employed 1 to develop a detection assay for AGR2, a potential cancer biomarker, as a “proof-of-principle” demonstration of the application of a linked complex for DNA-based detection in diluted fetal bovine serum. We anticipate that this conjugation method may be further employed in the development of DNA probes and have applications in label-free DNA-based diagnostic platforms.
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Affiliation(s)
- Modi Wang
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
| | - Zhifeng Mao
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
| | - Tian-Shu Kang
- State Key Laboratory of Quality Research in Chinese Medicine , Institute of Chinese Medical Sciences , University of Macau , Macao , China .
| | - Chun-Yuen Wong
- Department of Biology and Chemistry , City University of Hong Kong , Kowloon Tong , Hong Kong , China
| | - Jean-Louis Mergny
- University of Bordeaux , ARNA Laboratory , Bordeaux , France . .,INSERM , U869 , IECB , Pessac , France
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine , Institute of Chinese Medical Sciences , University of Macau , Macao , China .
| | - Dik-Lung Ma
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
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19
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Zhang S, Zhang R, Ma B, Qiu J, Li J, Sang Y, Liu W, Liu H. Specific detection of potassium ion in serum by a modified G-quadruplex method. RSC Adv 2016. [DOI: 10.1039/c6ra04046b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A modified dual-labelled G-quadruplex method is successfully designed to rapidly detect K+ in complex matrix of real serum.
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Affiliation(s)
- Shan Zhang
- State Key Laboratory of Crystal Materials
- Shandong University
- Jinan
- China
| | - Ruibin Zhang
- Blood Purification Center
- Jinan Central Hospital
- Jinan
- China
| | - Baojin Ma
- State Key Laboratory of Crystal Materials
- Shandong University
- Jinan
- China
| | - Jichuan Qiu
- State Key Laboratory of Crystal Materials
- Shandong University
- Jinan
- China
| | - Jianhua Li
- State Key Laboratory of Crystal Materials
- Shandong University
- Jinan
- China
| | - Yuanhua Sang
- State Key Laboratory of Crystal Materials
- Shandong University
- Jinan
- China
| | - Wei Liu
- State Key Laboratory of Crystal Materials
- Shandong University
- Jinan
- China
| | - Hong Liu
- State Key Laboratory of Crystal Materials
- Shandong University
- Jinan
- China
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20
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Wu T, Zhang C, Wang Z, Ren H, Kang Y, Du Y. Tuning the sensing range of potassium ions by changing the loop size of G-quadruplex sensors. NEW J CHEM 2016. [DOI: 10.1039/c6nj02136k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluorescence spectroscopy and thermodynamics were combined for the study of the loop size effect of G-quadruplex sensors in the K+ sensing range.
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Affiliation(s)
- Ting Wu
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Chuanjing Zhang
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Zhenping Wang
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Hongxin Ren
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Yan Kang
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Yiping Du
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
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21
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Wang M, Wang W, Kang TS, Leung CH, Ma DL. Development of an Iridium(III) Complex as a G-Quadruplex Probe and Its Application for the G-Quadruplex-Based Luminescent Detection of Picomolar Insulin. Anal Chem 2015; 88:981-7. [DOI: 10.1021/acs.analchem.5b04064] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Modi Wang
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Wanhe Wang
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Tian-Shu Kang
- State
Key Laboratory of Quality Research in Chinese Medicine, Institute
of Chinese Medical Sciences, University of Macau, Macao, China
| | - Chung-Hang Leung
- State
Key Laboratory of Quality Research in Chinese Medicine, Institute
of Chinese Medical Sciences, University of Macau, Macao, China
| | - Dik-Lung Ma
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
- Partner
State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China
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22
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Luboch E, Szarmach M, Buczkowska A, Wagner-Wysiecka E, Kania M, Danikiewicz W. Synthesis of thiol derivatives of azobenzocrown ethers. The preliminary studies on recognition of alkali metal ions by gold nanoparticles functionalized with azobenzocrown and lipoic acid. J INCL PHENOM MACRO 2015; 83:321-334. [PMID: 26549980 PMCID: PMC4630251 DOI: 10.1007/s10847-015-0567-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 09/18/2015] [Indexed: 01/23/2023]
Abstract
The article presents the synthesis of novel 13- and 16-membered azobenzocrown derivatives with peripheral thiol moieties and preliminary studies assessing their possible application in plasmonic sensors based on gold nanoparticles. The effect of the length of the chain connecting the macrocycle with the thiol group and the effect of the presence of the additional functional compound, i.e. lipoic acid, on the sensor response was analyzed. Colloidal gold nanoparticles modified with a 16-membered crown with a thiol group on oxyethylene (compound 12) or oxybutylene (compound 13) linker was found to have good properties, allowing for detection of potassium ions in aqueous solutions at concentrations 8-20 mM for bifunctionalized nanogold and 4-26 mM for less stable, colloidal gold modified only with thiol derivatives of azobenzocrowns. The response towards potassium cations of bifunctionalized nanogold modified with compound 13 was more stable in time than for the system incorporating compound 12. Compound 13, obtained with the highest yield among all presented thiol derivatives of azobenzocrowns, was selected for further, more detailed, studies.
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Affiliation(s)
- Elżbieta Luboch
- Department of Chemistry and Technology of Functional Materials, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland
| | - Mirosław Szarmach
- Department of Chemistry and Technology of Functional Materials, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland
| | - Anna Buczkowska
- Department of Chemistry and Technology of Functional Materials, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland
| | - Ewa Wagner-Wysiecka
- Department of Chemistry and Technology of Functional Materials, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland
| | - Magdalena Kania
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Witold Danikiewicz
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
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23
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König SLB, Evans AC, Huppert JL. Seven essential questions on G-quadruplexes. Biomol Concepts 2015; 1:197-213. [PMID: 25961997 DOI: 10.1515/bmc.2010.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The helical duplex architecture of DNA was discovered by Francis Crick and James Watson in 1951 and is well known and understood. However, nucleic acids can also adopt alternative structural conformations that are less familiar, although no less biologically relevant, such as the G-quadruplex. G-quadruplexes continue to be the subject of a rapidly expanding area of research, owing to their significant potential as therapeutic targets and their unique biophysical properties. This review begins by focusing on G-quadruplex structure, elucidating the intermolecular and intramolecular interactions underlying its formation and highlighting several substructural variants. A variety of methods used to characterize these structures are also outlined. The current state of G-quadruplex research is then addressed by proffering seven pertinent questions for discussion. This review concludes with an overview of possible directions for future research trajectories in this exciting and relevant field.
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24
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Leung KH, He HZ, He B, Zhong HJ, Lin S, Wang YT, Ma DL, Leung CH. Label-free luminescence switch-on detection of hepatitis C virus NS3 helicase activity using a G-quadruplex-selective probe. Chem Sci 2015; 6:2166-2171. [PMID: 28808523 PMCID: PMC5539802 DOI: 10.1039/c4sc03319a] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 11/16/2014] [Indexed: 12/16/2022] Open
Abstract
A series of luminescent Ir(iii) complexes were synthesised and evaluated for their ability to act as luminescent G-quadruplex-selective probes. The Ir(iii) complex 9, [Ir(phq)2(phen)]PF6 (where phq = 2-phenylquinoline; phen = 1,10-phenanthroline), exhibited high luminescence in the presence of G-quadruplex DNA compared to dsDNA and ssDNA, and was employed to construct a label-free G-quadruplex-based assay for hepatitis C virus NS3 helicase activity in aqueous solution. Moreover, the application of the assay for screening potential helicase inhibitors was demonstrated. To our knowledge, this is the first G-quadruplex-based assay for helicase activity.
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Affiliation(s)
- Ka-Ho Leung
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
| | - Hong-Zhang He
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
| | - Bingyong He
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
| | - Hai-Jing Zhong
- State Key Laboratory of Quality Research in Chinese Medicine , Institute of Chinese Medical Sciences , University of Macau , Macao , China .
| | - Sheng Lin
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
| | - Yi-Tao Wang
- State Key Laboratory of Quality Research in Chinese Medicine , Institute of Chinese Medical Sciences , University of Macau , Macao , China .
| | - Dik-Lung Ma
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine , Institute of Chinese Medical Sciences , University of Macau , Macao , China .
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25
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Ren J, Wang T, Wang E, Wang J. Versatile G-quadruplex-mediated strategies in label-free biosensors and logic systems. Analyst 2015; 140:2556-72. [DOI: 10.1039/c4an02282c] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This review addresses how G-quadruplex (G4)-mediated biosensors convert the events of target recognition into a measurable physical signal. The application of label-free G4-strategies in the construction of logic systems is also discussed.
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Affiliation(s)
- Jiangtao Ren
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Tianshu Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
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26
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Lin JH, Tseng WL. Ultrasensitive detection of target analyte-induced aggregation of gold nanoparticles using laser-induced nanoparticle Rayleigh scattering. Talanta 2015; 132:44-51. [DOI: 10.1016/j.talanta.2014.08.055] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 08/19/2014] [Accepted: 08/20/2014] [Indexed: 01/09/2023]
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27
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Bhasikuttan AC, Mohanty J. Targeting G-quadruplex structures with extrinsic fluorogenic dyes: promising fluorescence sensors. Chem Commun (Camb) 2015; 51:7581-97. [DOI: 10.1039/c4cc10030a] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This article provides a brief account of the recent reports on the fluorescence properties of some of the fluorogenic dyes towards G-quadruplex DNAs, which have been turned into promising bio-analytical methods.
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Affiliation(s)
| | - Jyotirmayee Mohanty
- Radiation & Photochemistry Division
- Bhabha Atomic Research Centre
- Mumbai 400 085
- India
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28
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Guo Y, Zhou L, Xu L, Zhou X, Hu J, Pei R. Multiple types of logic gates based on a single G-quadruplex DNA strand. Sci Rep 2014; 4:7315. [PMID: 25472865 PMCID: PMC4255190 DOI: 10.1038/srep07315] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 11/17/2014] [Indexed: 11/23/2022] Open
Abstract
In this work, we demonstrate the use of a single DNA strand and G-quadruplex-specific dye NMM as a label-free switch for the construction of series of basic logic gates (YES, NOT, OR, INHIBIT, NOR, AND). The simple GT-rich sequence could be used to interact with several molecules (K+, thrombin, Hg2+, and Pb2+) to form different structures that can be distinguished by the label-free dye NMM. Our study showed that a single G-qudruplex DNA strand can function as multiple types of one-input and two-input logic gates with different combinations of input molecules.
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Affiliation(s)
- Yahui Guo
- 1] Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Collaborative Innovation Center of Suzhou Nano Science and Technology, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123 (China) [2] Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry &Molecular Sciences, Wuhan University, Wuhan, 430072 (China)
| | - Lu Zhou
- Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Collaborative Innovation Center of Suzhou Nano Science and Technology, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123 (China)
| | - Lijun Xu
- Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Collaborative Innovation Center of Suzhou Nano Science and Technology, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123 (China)
| | - Xiaodong Zhou
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry &Molecular Sciences, Wuhan University, Wuhan, 430072 (China)
| | - Jiming Hu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry &Molecular Sciences, Wuhan University, Wuhan, 430072 (China)
| | - Renjun Pei
- Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Collaborative Innovation Center of Suzhou Nano Science and Technology, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123 (China)
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29
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Chen Z, Zhou T, Zhang C, Ma H, Lin Y, Li K. Aptasensor for label-free square-wave voltammetry detection of potassium ions based on gold nanoparticle amplification. RSC Adv 2014. [DOI: 10.1039/c4ra05058d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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30
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Catherine AT, Shishido SN, Robbins-Welty GA, Diegelman-Parente A. Rational design of a structure-switching DNA aptamer for potassium ions. FEBS Open Bio 2014; 4:788-95. [PMID: 25352996 PMCID: PMC4209343 DOI: 10.1016/j.fob.2014.08.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 08/20/2014] [Accepted: 08/30/2014] [Indexed: 11/18/2022] Open
Abstract
We report the rational design of structure-switching DNA aptamers for potassium. The shift between non-binding and binding-competent states was determined experimentally. The stability of the non-binding state was estimated computationally. A linear free energy relationship between these values was established.
Structure-switching molecules provide a unique means for analyte detection, generating a response to analyte concentration through a binding-specific conformational change between non-binding and binding-competent states. While most ligand-binding molecules are not structure switching by default, many can be engineered to be so through the introduction of an alternative non-binding (and thus non-signalling) conformation. This population-shift mechanism is particularly effective with oligonucleotides and has led to the creation of structure-switching aptamers for many target ligands. Here, we report the rational design of structure-switching DNA aptamers, based on the thrombin binding aptamer (TBA), that bind potassium with affinities that bridge the gap between previously reported weak-binding and strong-binding aptamers. We also demonstrate a correlation between the free energy of the experimentally determined binding affinity for potassium and the computationally estimated free energy of the alternative (non-binding) structure.
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Affiliation(s)
- Andrew T. Catherine
- Department of Chemistry, Penn State Altoona, Altoona, PA 16601, United States
| | | | - Gregg A. Robbins-Welty
- Department of Chemistry and Biochemistry, Mercyhurst University, Erie, PA 16546, United States
| | - Amy Diegelman-Parente
- Department of Chemistry and Biochemistry, Mercyhurst University, Erie, PA 16546, United States
- Corresponding author. Tel./fax: +1 814 824 3876.
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31
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Xu Y, Zhou W, Zhou M, Xiang Y, Yuan R, Chai Y. Toehold strand displacement-driven assembly of G-quadruplex DNA for enzyme-free and non-label sensitive fluorescent detection of thrombin. Biosens Bioelectron 2014; 64:306-10. [PMID: 25240130 DOI: 10.1016/j.bios.2014.09.018] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/03/2014] [Accepted: 09/04/2014] [Indexed: 01/08/2023]
Abstract
Based on a new signal amplification strategy by the toehold strand displacement-driven cyclic assembly of G-quadruplex DNA, the development of an enzyme-free and non-label aptamer sensing approach for sensitive fluorescent detection of thrombin is described. The target thrombin associates with the corresponding aptamer of the partial dsDNA probes and liberates single stranded initiation sequences, which trigger the toehold strand displacement assembly of two G-quadruplex containing hairpin DNAs. This toehold strand displacement reaction leads to the cyclic reuse of the initiation sequences and the production of DNA assemblies with numerous G-quadruplex structures. The fluorescent dye, N-Methyl mesoporphyrin IX, binds to these G-quadruplex structures and generates significantly amplified fluorescent signals to achieve highly sensitive detection of thrombin down to 5 pM. Besides, this method shows high selectivity towards the target thrombin against other control proteins. The developed thrombin sensing method herein avoids the modification of the probes and the involvement of any enzyme or nanomaterial labels for signal amplification. With the successful demonstration for thrombin detection, our approach can be easily adopted to monitor other target molecules in a simple, low-cost, sensitive and selective way by choosing appropriate aptamer/ligand pairs.
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Affiliation(s)
- Yunying Xu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Wenjiao Zhou
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ming Zhou
- (b)Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Yun Xiang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yaqin Chai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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32
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Lu L, Shiu-Hin Chan D, Kwong DWJ, He HZ, Leung CH, Ma DL. Detection of nicking endonuclease activity using a G-quadruplex-selective luminescent switch-on probe. Chem Sci 2014. [DOI: 10.1039/c4sc02032d] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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33
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Zheng B, Cheng S, Dong H, Liang H, Liu J, Lam MHW. Label Free Determination of Potassium Ions Using Crystal Violet and Thrombin-Binding Aptamer. ANAL LETT 2014. [DOI: 10.1080/00032719.2014.883520] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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34
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Liu L, Shao Y, Peng J, Huang C, Liu H, Zhang L. Molecular Rotor-Based Fluorescent Probe for Selective Recognition of Hybrid G-Quadruplex and as a K+ Sensor. Anal Chem 2014; 86:1622-31. [DOI: 10.1021/ac403326m] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Lingling Liu
- Institute of Physical
Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
| | - Yong Shao
- Institute of Physical
Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
| | - Jian Peng
- Institute of Physical
Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
| | - Chaobiao Huang
- Department
of Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People’s Republic of China
| | - Hua Liu
- Institute of Physical
Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
| | - Lihua Zhang
- Institute of Physical
Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
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35
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G-quadruplexes as sensing probes. Molecules 2013; 18:14760-79. [PMID: 24288003 PMCID: PMC6270327 DOI: 10.3390/molecules181214760] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 11/13/2013] [Accepted: 11/13/2013] [Indexed: 01/09/2023] Open
Abstract
Guanine-rich sequences of DNA are able to create tetrastranded structures known as G-quadruplexes; they are formed by the stacking of planar G-quartets composed of four guanines paired by Hoogsteen hydrogen bonding. G-quadruplexes act as ligands for metal ions and aptamers for various molecules. Interestingly, the G-quadruplexes form a complex with anionic porphyrin hemin and exhibit peroxidase-like activity. This review focuses on overview of sensing techniques based on G-quadruplex complexes with anionic porphyrins for detection of various analytes, including metal ions such as K+, Ca2+, Ag+, Hg2+, Cu2+, Pb2+, Sr2+, organic molecules, nucleic acids, and proteins. Principles of G-quadruplex-based detection methods involve DNA conformational change caused by the presence of analyte which leads to a decrease or an increase in peroxidase activity, fluorescence, or electrochemical signal of the used probe. The advantages of various detection techniques are also discussed.
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36
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Ma DL, He HZ, Leung KH, Zhong HJ, Chan DSH, Leung CH. Label-free luminescent oligonucleotide-based probes. Chem Soc Rev 2013; 42:3427-40. [PMID: 23348604 DOI: 10.1039/c2cs35472a] [Citation(s) in RCA: 180] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Breakthrough advances in chemistry and biology over the last two decades have vastly expanded the repertoire of nucleic acid structure and function with potential application in multiple areas of science and technology, including sensing and analytical applications. DNA oligonucleotides represent popular tools for the development of sensing platforms due to their low cost, rich structural polymorphism, and their ability to bind to cognate ligands with sensitivity and specificity rivaling those for protein enzymes and antibodies. In this review, we give an overview of the "label-free" approach that has been a particular focus of our group and others for the construction of luminescent DNA-based sensing platforms. The label-free strategy aims to overcome some of the drawbacks associated with the use of covalently-labeled oligonucleotides prevalent in electrochemical and optical platforms. Label-free DNA-based probes harness the selective interaction between luminescent dyes and functional oligonucleotides that exhibit a "structure-switching" response upon binding to analytes. Based on the numerous examples of label-free luminescent DNA-based probes reported recently, we envisage that this field would continue to thrive and mature in the years to come.
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Affiliation(s)
- Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China.
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37
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He HZ, Wang M, Chan DSH, Leung CH, Qiu JW, Ma DL. A label-free G-quadruplex-based luminescent switch-on assay for the selective detection of histidine. Methods 2013; 64:205-11. [PMID: 23891801 DOI: 10.1016/j.ymeth.2013.07.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/14/2013] [Accepted: 07/15/2013] [Indexed: 12/16/2022] Open
Abstract
A label-free G-quadruplex-based luminescent switch-on assay has been developed for the selective detection of micromolar histidine in aqueous solution. In this study, an iridium(III) complex was employed as a G-quadruplex-specific luminescent probe while a guanine-rich oligonucleotide (Pu27, 5'-TG4AG3TG4AG3TG4A2G2-3')/cupric ion (Cu(2+)) ensemble was employed as a recognition unit for histidine. The initial luminescence of the iridium(III) complex in the presence of G-quadruplex DNA is effectively quenched by Cu(2+) ions due to the Cu(2+)-mediated unfolding of the G-quadruplex motif. The addition of histidine sequesters Cu(2+) ions from the ensemble, thereby restoring the luminescence of the system. The assay could detect down to 1 μM of histidine in aqueous media, and also exhibited good selectivity for histidine over other amino acids with the use of the cysteine, masking agent N-ethylmaleimide. Furthermore, the application of the assay for the detection of histidine in diluted urine samples was demonstrated.
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Affiliation(s)
- Hong-Zhang He
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
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38
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Colorimetric detection of potassium ions using aptamer-functionalized gold nanoparticles. Anal Chim Acta 2013; 787:189-92. [PMID: 23830438 DOI: 10.1016/j.aca.2013.05.020] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 04/27/2013] [Accepted: 05/06/2013] [Indexed: 11/20/2022]
Abstract
Herein, a simple and novel colorimetric method for detection of potassium ions (K(+)) was developed. The colorimetric experiments revealed that upon the addition of K(+), the conformation of anti-K(+) aptamer in solution changed from random coil structure to compact rigid G-quadruplex one. This compact rigid G-quadruplex structure could not protect AuNPs against K(+)-induced aggregation, and thus the visible color change from wine-red to blue-purple could be observed by the naked eye. The linear range of the colorimetric aptasensor covered a large variation of K(+) concentration from 5 nM to 1 μM and the detection limit of 5 nM was obtained. Moreover, this assay was able to detect K(+) with high selectivity and had great potential applications.
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39
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Chen Z, Chen L, Ma H, Zhou T, Li X. Aptamer biosensor for label-free impedance spectroscopy detection of potassium ion based on DNA G-quadruplex conformation. Biosens Bioelectron 2013; 48:108-12. [PMID: 23665159 DOI: 10.1016/j.bios.2013.04.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 03/22/2013] [Accepted: 04/02/2013] [Indexed: 01/06/2023]
Abstract
Herein, a label-free and highly sensitive electrochemical impedance spectroscopy (EIS) aptasensor for the detection of potassium ion (K⁺) was developed based on a conformational change in which a K⁺-stabilized single stranded DNA (ssDNA) with G-rich sequence was used as the recognition element. In the measurement of K⁺ ions, the change in interfacial electron transfer resistance (R(ct)) of the sensor using a redox couple of [Fe(CN)₆]³⁻/⁴⁻ as the probe was monitored. In the presence of K⁺, the G-rich DNA folded into the G-quadruplex structure, and then K⁺ can bind to the G-quadruplex structure, leading to an increase in the R(ct). The Rct increased with K⁺ concentration, and the plot of R(ct) against the logarithm of K⁺ concentration is linear over the range from 0.1 nM to 1 mM with a detection limit of 0.1 nM. Other metal ions, such as Ca²⁺, Mg²⁺, Na⁺, Li⁺, Al³⁺, Zn²⁺, Cu²⁺, and Ni²⁺ caused no notable interference on the detection of K⁺. The scheme reported herein is applicable to the detection of other kinds of G-rich aptamer-binding chemicals and biomolecules.
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Affiliation(s)
- Zhengbo Chen
- Department of Chemistry, Capital Normal University, Beijing 100048, China.
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40
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Sun H, Xiang J, Gai W, Liu Y, Guan A, Yang Q, Li Q, Shang Q, Su H, Tang Y, Xu G. Quantification of the Na+/K+ ratio based on the different response of a newly identified G-quadruplex to Na+ and K+. Chem Commun (Camb) 2013; 49:4510-2. [PMID: 23577345 DOI: 10.1039/c3cc39020a] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A G-quadruplex is identified which can exhibit two different motifs, respectively, corresponding to Na(+) and K(+). The relative amount of each motif is related to the Na(+)/K(+) ratio. Based on selective recognition of the G-quadruplex motifs by a cyanine dye aggregate, a method for both colorimetric and quantitative measurements of Na(+)/K(+) ratios is constructed.
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Affiliation(s)
- Hongxia Sun
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North 1st street 2, Beijing 100190, PR China
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41
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He HZ, Chan DSH, Leung CH, Ma DL. G-quadruplexes for luminescent sensing and logic gates. Nucleic Acids Res 2013; 41:4345-59. [PMID: 23435319 PMCID: PMC3632106 DOI: 10.1093/nar/gkt108] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 02/03/2013] [Accepted: 02/04/2013] [Indexed: 01/06/2023] Open
Abstract
G-quadruplexes represent a versatile sensing platform for the construction of label-free molecular detection assays owing to their diverse structures that can be selectively recognized by G-quadruplex-specific luminescent probes. In this Survey and Summary, we highlight recent examples of the application of the label-free strategy for the development of G-quadruplex-based luminescent detection platforms with a view towards the potential application of tetraplex structures in the design of DNA logic gates.
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Affiliation(s)
- Hong-Zhang He
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China and State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, China
| | - Daniel Shiu-Hin Chan
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China and State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, China
| | - Chung-Hang Leung
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China and State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, China
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China and State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, China
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42
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He HZ, Leung KH, Yang H, Shiu-Hin Chan D, Leung CH, Zhou J, Bourdoncle A, Mergny JL, Ma DL. Label-free detection of sub-nanomolar lead(II) ions in aqueous solution using a metal-based luminescent switch-on probe. Biosens Bioelectron 2013; 41:871-4. [DOI: 10.1016/j.bios.2012.08.060] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 08/17/2012] [Accepted: 08/30/2012] [Indexed: 12/22/2022]
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43
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G-quadruplex-based ultrasensitive and selective detection of histidine and cysteine. Biosens Bioelectron 2013; 41:563-8. [DOI: 10.1016/j.bios.2012.09.024] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 09/15/2012] [Indexed: 11/20/2022]
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44
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Leung CH, Zhong HJ, Lu L, Chan DSH, Ma DL. Luminescent and colorimetric strategies for the label-free DNA-based detection of enzyme activity. Brief Funct Genomics 2013; 12:525-35. [PMID: 23396725 DOI: 10.1093/bfgp/elt004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Enzymes are critically involved in maintaining normal cellular physiology through the catalysis of highly specific and tightly regulated chemical reactions. The inhibition or undesired activation of particular enzymatic functions has been associated with the pathogenesis of a number of diseases. Consequently, the aberrant activity of certain enzymes can be regarded as biomarkers for the diagnosis or monitoring of particular diseases. With rapid technological advances in the field of DNA nanotechnology, oligonucleotides have recently emerged as attractive recognition units for monitoring the activity of enzymes compared with organic small molecules or protein antibodies. In this review article, we present an overview of advantages and versatility of the 'label-free' approach for the fabrication of DNA-based sensing platforms using colorimetric and luminescent molecules as signal transducing units and highlight recent examples of label-free strategies that have been employed for monitoring enzyme activity.
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Affiliation(s)
- Chung-Hang Leung
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong.
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45
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Zhou Z, Zhu J, Zhang L, Du Y, Dong S, Wang E. G-quadruplex-Based Fluorescent Assay of S1 Nuclease Activity and K+. Anal Chem 2013; 85:2431-5. [DOI: 10.1021/ac303440d] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Zhixue Zhou
- State Key Laboratory of
Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy
of Sciences, Changchun, Jilin 130022, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - Jinbo Zhu
- State Key Laboratory of
Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy
of Sciences, Changchun, Jilin 130022, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - Libing Zhang
- State Key Laboratory of
Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy
of Sciences, Changchun, Jilin 130022, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - Yan Du
- State Key Laboratory of
Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy
of Sciences, Changchun, Jilin 130022, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - Shaojun Dong
- State Key Laboratory of
Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy
of Sciences, Changchun, Jilin 130022, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - Erkang Wang
- State Key Laboratory of
Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy
of Sciences, Changchun, Jilin 130022, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
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46
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Sun H, Li X, Li Y, Fan L, Kraatz HB. A novel colorimetric potassium sensor based on the substitution of lead from G-quadruplex. Analyst 2013; 138:856-62. [DOI: 10.1039/c2an36564b] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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47
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Sun H, Xiang J, Gai W, Shang Q, Li Q, Guan A, Yang Q, Liu Y, Tang Y, Xu G. Visual detection of potassium by a cyanine dye supramolecular aggregate responsive to G-quadruplex motif transition. Analyst 2012; 137:5713-5. [DOI: 10.1039/c2an35944h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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48
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Visualizing the Quadruplex: From Fluorescent Ligands to Light-Up Probes. Top Curr Chem (Cham) 2012; 330:111-77. [DOI: 10.1007/128_2012_346] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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49
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Yuanboonlim W, Siripornnoppakhun W, Niamnont N, Rashatasakhon P, Vilaivan T, Sukwattanasinitt M. Phenylene-ethynylene trication as an efficient fluorescent signal transducer in an aptasensor for potassium ion. Biosens Bioelectron 2011; 33:17-22. [PMID: 22244670 DOI: 10.1016/j.bios.2011.11.049] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 11/25/2011] [Accepted: 11/29/2011] [Indexed: 01/31/2023]
Abstract
A tricationic phenylene-ethynylene (N(3+)) fluorophore is investigated as a fluorescent transducer in homogeneous aptasensing system for potassium ion (K(+)) assay in aqueous media. The enhancement of the fluorescent signal of N(3+) by three K(+) aptamers consisting of 12, 15, and 21 nucleotides are observed and used for the determination of N(3+)-aptamer binding affinities. The binding affinities increase with the length of the aptameric oligonucleotides and are proven to be important to the sensitivity and selectivity of the aptasensors. The enhanced fluorescent signal of each N(3+)-aptamer solution is selectively quenched by K(+) due to the ability of K(+) in stabilizing the G-quadruplex structure of the aptamer. Among three aptamers, the 15-base aptamer provides optimal sensitivity and selectivity over other ions such as Li(+), Na(+), NH(4)(+), Mg(2+), Ca(2+) and Sr(2+). The sensing system shows the detection limit of 1 μM of K(+) in clean buffered solution and 30 μM of K(+) in the solution containing 4800-fold excess of Na(+), with wide linear dynamic ranges of micro- to millimolar concentration. This label-free fluorescence aptasensor is conveniently and effectively applicable for analysis of K(+) in urine samples.
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Affiliation(s)
- Wannapa Yuanboonlim
- Center for Petroleum, Petrochemicals and Advanced Materials, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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50
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Fan X, Li H, Zhao J, Lin F, Zhang L, Zhang Y, Yao S. A novel label-free fluorescent sensor for the detection of potassium ion based on DNAzyme. Talanta 2011; 89:57-62. [PMID: 22284459 DOI: 10.1016/j.talanta.2011.11.056] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2011] [Revised: 11/16/2011] [Accepted: 11/20/2011] [Indexed: 12/13/2022]
Abstract
A novel label-free and sensitive fluorescent aptasensor for the detection of potassium ion (K(+)) was developed based on the horseradish peroxidase-mimicking DNAzyme (HRP-DNAzyme). In this work, we selected a K(+)-stabilized single stranded DNA (ssDNA) with G-rich sequence as the recognition element. In the presence of K(+), the G-rich DNA folded into the G-quadruplex structure, and then hemin can bind to the G-quadruplex structure as a co-factor and form HRP-DNAzyme. 3-(p-Hydroxyphenyl)-propanoic acid (HPPA) can be oxidized by H(2)O(2) into a fluorescent product in the presence of DNAzyme. The fluorescence intensity of the HPPA oxidative product increased with the K(+) concentration. Under the optimal conditions, the fluorescence intensity was linearly related to the logarithm of K(+) concentration in the range of 2.5 μM to 5mM. Other metal ions, such as Na(+), Li(+), NH(4)(+), Mg(2+) and Ca(2+) caused no notable interference on the detection of K(+).
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Affiliation(s)
- Xiaoyu Fan
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, PR China
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