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Schlosser J, Ihmels H. Photocontrolled Binding of Styrylnaphthyridine Ligands to Abasic Site-Containing DNA by Reversible [2+2] Cycloaddition and Cycloreversion. Chemistry 2024; 30:e202400423. [PMID: 38545937 DOI: 10.1002/chem.202400423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Indexed: 04/25/2024]
Abstract
Five novel styrylnaphthyridine derivatives were synthesized and shown to operate as photoswitchable, selective ligands for abasic site-containing DNA (AP-DNA), which is an important therapeutic and diagnostic target. These compounds associate with AP-DNA with binding constants of 0.5-8.4×104 M-1 as shown by photometric and fluorimetric titrations. Specifically, these ligands bind preferentially to AP-DNA relative to regularly paired duplex DNA. As a special feature, the association of these ligands with DNA can be controlled by means of a reversible [2+2] photocycloaddition. Upon irradiation at 420 nm the photodimer is formed, which does not bind to AP-DNA. In turn, the naphthyridine is regained with excitation at 315 nm. Most notably, this photoinduced deactivation and release of the DNA ligand can be performed in situ in the presence of AP-DNA, thus providing a tool for on-demand delivery of a DNA binder. Overall, these results provide a promising starting point for the development of functional AP-DNA ligands whose bioactivity can be modulated by light with local and temporal control.
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Affiliation(s)
- Julika Schlosser
- Department of Chemistry and Biology, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), University of Siegen, Adolf-Reichwein Str. 2, 57068, Siegen, Germany
| | - Heiko Ihmels
- Department of Chemistry and Biology, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), University of Siegen, Adolf-Reichwein Str. 2, 57068, Siegen, Germany
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2
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Wickramasinghe NI, Corbin B, Kanakarathna DY, Pang Y, Abeywickrama CS, Wijesinghe KJ. Bright NIR-Emitting Styryl Pyridinium Dyes with Large Stokes' Shift for Sensing Applications. BIOSENSORS 2023; 13:799. [PMID: 37622885 PMCID: PMC10452306 DOI: 10.3390/bios13080799] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 08/02/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023]
Abstract
Two NIR-emitting donor-π-acceptor (D-π-A) type regioisomeric styryl pyridinium dyes (1a-1b) were synthesized and studied for their photophysical performance and environment sensitivity. The two regioisomers, 1a and 1b, exhibited interesting photophysical properties including, longer wavelength excitation (λex ≈ 530-560 nm), bright near-infrared emission (λem ≈ 690-720 nm), high-fluorescence quantum yields (ϕfl ≈ 0.24-0.72) large Stokes' shift (∆λ ≈ 150-240 nm) and high-environmental sensitivity. Probe's photophysical properties were studied in different environmental conditions such as polarity, viscosity, temperature, and concentration. Probes (1a-1b) exhibited noticeable changes in absorbance, emission and Stokes' shift while responding to the changes in physical environment. Probe 1b exhibited a significant bathochromic shift in optical spectra (∆λ ≈ 20-40 nm) compared to its isomer 1a, due to the regio-effect. Probes (1a-1b) exhibited an excellent ability to visualize bacteria (Bacillus megaterium, Escherichia coli), and yeast (Saccharomyces cerevisiae) via fluorescence microscopy.
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Affiliation(s)
| | - Brian Corbin
- Department of Chemistry, The University of Akron, Akron, OH 44325, USA
| | - Devni Y. Kanakarathna
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo 00300, Sri Lanka
| | - Yi Pang
- Department of Chemistry, The University of Akron, Akron, OH 44325, USA
| | | | - Kaveesha J. Wijesinghe
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo 00300, Sri Lanka
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3
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Schlosser J, Ihmels H. Ligands for Abasic Site-containing DNA and their Use as Fluorescent Probes. Curr Org Synth 2023; 20:96-113. [PMID: 35170411 DOI: 10.2174/1570179419666220216091422] [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: 08/14/2021] [Revised: 12/16/2021] [Accepted: 12/16/2021] [Indexed: 12/16/2022]
Abstract
Apurinic and apyrimidinic sites, also referred to as abasic or AP sites, are residues of duplex DNA in which one DNA base is removed from a Watson-Crick base pair. They are formed during the enzymatic repair of DNA and offer binding sites for a variety of guest molecules. Specifically, the AP site may bind an appropriate ligand as a substitute for the missing nucleic base, thus stabilizing the abasic site-containing DNA (AP-DNA). Notably, ligands that bind selectively to abasic sites may be employed for analytical and therapeutical purposes. As a result, there is a search for structural features that establish a strong and selective association of a given ligand with the abasic position in DNA. Against this background, this review provides an overview of the different classes of ligands for abasic site-containing DNA (AP-DNA). This review covers covalently binding substrates, namely amine and oxyamine derivatives, as well as ligands that bind to AP-DNA by noncovalent association, as represented by small heterocyclic aromatic compounds, metal-organic complexes, macrocyclic cyclophanes, and intercalator-nucleobase conjugates. As the systematic development of fluorescent probes for AP-DNA has been somewhat neglected so far, this review article contains a survey of the available reports on the fluorimetric response of the ligand upon binding to the AP-DNA. Based on these data, this compilation shall present a perspective for future developments of fluorescent probes for AP-DNA.
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Affiliation(s)
- Julika Schlosser
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Heiko Ihmels
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
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4
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Jiang C, Huang H, Kang X, Yang L, Xi Z, Sun H, Pluth MD, Yi L. NBD-based synthetic probes for sensing small molecules and proteins: design, sensing mechanisms and biological applications. Chem Soc Rev 2021; 50:7436-7495. [PMID: 34075930 PMCID: PMC8763210 DOI: 10.1039/d0cs01096k] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Compounds with a nitrobenzoxadiazole (NBD) skeleton exhibit prominent useful properties including environmental sensitivity, high reactivity toward amines and biothiols (including H2S) accompanied by distinct colorimetric and fluorescent changes, fluorescence-quenching ability, and small size, all of which facilitate biomolecular sensing and self-assembly. Amines are important biological nucleophiles, and the unique activity of NBD ethers with amines has allowed for site-specific protein labelling and for the detection of enzyme activities. Both H2S and biothiols are involved in a wide range of physiological processes in mammals, and misregulation of these small molecules is associated with numerous diseases including cancers. In this review, we focus on NBD-based synthetic probes as advanced chemical tools for biomolecular sensing. Specifically, we discuss the sensing mechanisms and selectivity of the probes, the design strategies for multi-reactable multi-quenching probes, and the associated biological applications of these important constructs. We also highlight self-assembled NBD-based probes and outline future directions for NBD-based chemosensors. We hope that this comprehensive review will facilitate the development of future probes for investigating and understanding different biological processes and aid the development of potential theranostic agents.
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Affiliation(s)
- Chenyang Jiang
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology (BUCT), Beijing 100029, China.
| | - Haojie Huang
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology (BUCT), Beijing 100029, China.
| | - Xueying Kang
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology (BUCT), Beijing 100029, China.
| | - Liu Yang
- Department of Chemistry and Center of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China.
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, National Pesticide Engineering Research Center, Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China.
| | - Hongyan Sun
- Department of Chemistry and Center of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China. and Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
| | - Michael D Pluth
- Department of Chemistry and Biochemistry, Materials Science Institute, Knight Campus for Accelerating Scientific Impact, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.
| | - Long Yi
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology (BUCT), Beijing 100029, China.
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5
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Chloro-Substituted Naphthyridine Derivative and Its Conjugate with Thiazole Orange for Highly Selective Fluorescence Sensing of an Orphan Cytosine in the AP Site-Containing Duplexes. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10124133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Fluorescent probes with the binding selectivity to specific structures in DNAs or RNAs have gained much attention as useful tools for the study of nucleic acid functions. Here, chloro-substituted 2-amino-5,7-dimethyl-1,8-naphthyridine (ClNaph) was developed as a strong and highly selective binder for target orphan cytosine opposite an abasic (AP) site in the DNA duplexes. ClNaph was then conjugated with thiazole orange (TO) via an alkyl spacer (ClNaph–TO) to design a light-up probe for the detection of cytosine-related mutations in target DNA. In addition, we found the useful binding and fluorescence signaling of the ClNaph–TO conjugate to target C in AP site-containing DNA/RNA hybrid duplexes with a view toward sequence analysis of microRNAs.
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6
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Label-free sensing of abasic DNA using pyrenylamido triazolyl aromatic amino acid scaffold as AIE probe. J Photochem Photobiol A Chem 2020. [DOI: 10.1016/j.jphotochem.2019.112186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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7
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RNA imaging by chemical probes. Adv Drug Deliv Rev 2019; 147:44-58. [PMID: 31398387 DOI: 10.1016/j.addr.2019.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 07/02/2019] [Accepted: 08/02/2019] [Indexed: 12/29/2022]
Abstract
Sequence-specific detection of intracellular RNA is one of the most important approaches to understand life phenomena. However, it is difficult to detect RNA in living cells because of its variety and scarcity. In the last three decades, several chemical probes have been developed for RNA detection in living cells. These probes are composed of DNA or artificial nucleic acid and hybridize with the target RNA in a sequence-specific manner. This hybridization triggers a change of fluorescence or a chemical reaction. In this review, we classify the probes according to the associated fluorogenic mechanism, that is, interaction between fluorophore and quencher, environmental change of fluorophore, and template reaction with/without ligation. In addition, we introduce examples of RNA imaging in living cells.
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Ren Z, Zhu X, Lv H, Liu H, He H, Zhang X, Wang S. A fluorescent method based on magnetic nanoparticles for detection of CGG trinucleotide repeat genes. NEW J CHEM 2019. [DOI: 10.1039/c8nj04686g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A novel fluorescent sensor based on magnetic nanoparticles as the separator and short report DNA was designed and prepared for the detection of d(CGG)ntrinucleotide repeats. The method exhibited high selectivity and sensitivity, and excellent linear correlation from 100 pM to 150 nM, which is useful for the early diagnosis of neurodegenerative diseases.
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Affiliation(s)
- Ziqi Ren
- Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules
- College of Chemistry and Chemical Engineering
- Hubei University
- Youyi Road 368
- Wuchang
| | - Xiaoqian Zhu
- Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules
- College of Chemistry and Chemical Engineering
- Hubei University
- Youyi Road 368
- Wuchang
| | - Hehong Lv
- Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules
- College of Chemistry and Chemical Engineering
- Hubei University
- Youyi Road 368
- Wuchang
| | - Heng Liu
- Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules
- College of Chemistry and Chemical Engineering
- Hubei University
- Youyi Road 368
- Wuchang
| | - Hanping He
- Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules
- College of Chemistry and Chemical Engineering
- Hubei University
- Youyi Road 368
- Wuchang
| | - Xiuhua Zhang
- Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules
- College of Chemistry and Chemical Engineering
- Hubei University
- Youyi Road 368
- Wuchang
| | - Shengfu Wang
- Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules
- College of Chemistry and Chemical Engineering
- Hubei University
- Youyi Road 368
- Wuchang
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9
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Fluorescent Trimethylated Naphthyridine Derivative with an Aminoalkyl Side Chain as the Tightest Non-aminoglycoside Ligand for the Bacterial A-site RNA. Chemistry 2018; 24:13862-13870. [DOI: 10.1002/chem.201802320] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/29/2018] [Indexed: 12/31/2022]
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10
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Zhao X, Lv G, Peng Y, Liu Q, Li X, Wang S, Li K, Qiu L, Lin J. Targeted Delivery of an Activatable Fluorescent Probe for the Detection of Furin Activity in Living Cells. Chembiochem 2018; 19:1060-1065. [DOI: 10.1002/cbic.201800015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Xueyu Zhao
- School of Chemical and Material Engineering; Jiangnan University; Wuxi 214122 China
- Key Laboratory of Nuclear Medicine, Ministry of Health; Jiangsu Key Laboratory of Molecular Nuclear Medicine; Jiangsu Institute of Nuclear Medicine; Wuxi 214063 China
| | - Gaochao Lv
- Key Laboratory of Nuclear Medicine, Ministry of Health; Jiangsu Key Laboratory of Molecular Nuclear Medicine; Jiangsu Institute of Nuclear Medicine; Wuxi 214063 China
| | - Ying Peng
- Key Laboratory of Nuclear Medicine, Ministry of Health; Jiangsu Key Laboratory of Molecular Nuclear Medicine; Jiangsu Institute of Nuclear Medicine; Wuxi 214063 China
| | - Qingzhu Liu
- Key Laboratory of Nuclear Medicine, Ministry of Health; Jiangsu Key Laboratory of Molecular Nuclear Medicine; Jiangsu Institute of Nuclear Medicine; Wuxi 214063 China
| | - Xi Li
- School of Chemical and Material Engineering; Jiangnan University; Wuxi 214122 China
- Key Laboratory of Nuclear Medicine, Ministry of Health; Jiangsu Key Laboratory of Molecular Nuclear Medicine; Jiangsu Institute of Nuclear Medicine; Wuxi 214063 China
| | - Shanshan Wang
- School of Chemical and Material Engineering; Jiangnan University; Wuxi 214122 China
- Key Laboratory of Nuclear Medicine, Ministry of Health; Jiangsu Key Laboratory of Molecular Nuclear Medicine; Jiangsu Institute of Nuclear Medicine; Wuxi 214063 China
| | - Ke Li
- Key Laboratory of Nuclear Medicine, Ministry of Health; Jiangsu Key Laboratory of Molecular Nuclear Medicine; Jiangsu Institute of Nuclear Medicine; Wuxi 214063 China
| | - Ling Qiu
- School of Chemical and Material Engineering; Jiangnan University; Wuxi 214122 China
- Key Laboratory of Nuclear Medicine, Ministry of Health; Jiangsu Key Laboratory of Molecular Nuclear Medicine; Jiangsu Institute of Nuclear Medicine; Wuxi 214063 China
| | - Jianguo Lin
- Key Laboratory of Nuclear Medicine, Ministry of Health; Jiangsu Key Laboratory of Molecular Nuclear Medicine; Jiangsu Institute of Nuclear Medicine; Wuxi 214063 China
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11
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Fang GM, Seitz O. Bivalent Display of Dicysteine on Peptide Nucleic Acids for Homogenous DNA/RNA Detection through in Situ Fluorescence Labelling. Chembiochem 2016; 18:189-194. [PMID: 27883258 DOI: 10.1002/cbic.201600623] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Indexed: 01/06/2023]
Abstract
Fluorogenic probes that signal the presence of specific DNA or RNA sequences are key enabling tools for molecular disease diagnosis and imaging studies. Usually, at least one fluorophore is attached through covalent bonding to an oligonucleotide probe. However, the additional conjugation step increases costs. Here we introduce a method that avoids the requirement for the preparation of fluorescence-labelled oligonucleotides and provides the opportunity to alter the fluorogenic reporter dye without resynthesis. The method is based on adjacent hybridization of two dicysteine-containing peptide nucleic acid (PNA) probes to form a bipartite tetracysteine motif that binds profluorescent bisarsenical dyes such as FIAsH, ReAsH or CrAsH. Binding is accompanied by strong increases in fluorescence emission (with response factors of up to 80-fold and high brightness up to 50 mL mol-1 cm-1 ). The detection system provides sub-nanomolar limits of detection and allows discrimination of single nucleotide variations through more than 20-fold changes in fluorescence intensity. To demonstrate its usefulness, the FIAsH-based readout of the bivalent CysCys-PNA display was interfaced with a rolling-circle amplification (RCA) assay used to detect disease-associated microRNA let-7a.
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Affiliation(s)
- Ge-Min Fang
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489, Berlin, Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489, Berlin, Germany
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12
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GOU GAOZHANG, ZHOU BO, YAN HEPING, HONG YONG, LIU WEI, CHI SHAOMING, MANG CHAOYONG. Synthesis, Spectroscopic Properties and DFT Calculation of Novel Pyrrolo[1′,5′-a]-1,8-naphthyridine Derivatives through a Facile One-pot Process. J CHEM SCI 2016. [DOI: 10.1007/s12039-016-1163-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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13
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Dong YP, Gao TT, Zhou Y, Jiang LP, Zhu JJ. Anodic Electrogenerated Chemiluminescence of Ru(bpy)3(2+) with CdSe Quantum Dots as Coreactant and Its Application in Quantitative Detection of DNA. Sci Rep 2015; 5:15392. [PMID: 26472243 PMCID: PMC4607998 DOI: 10.1038/srep15392] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 09/14/2015] [Indexed: 12/27/2022] Open
Abstract
In the present paper, we report that CdSe quantum dots (QDs) can act as the coreactant of Ru(bpy)32+ electrogenerated chemiluminescence (ECL) in neutral condition. Strong anodic ECL signal was observed at ~1.10 V at CdSe QDs modified glassy carbon electrode (CdSe/GCE), which might be mainly attributed to the apparent electrocatalytic effect of QDs on the oxidation of Ru(bpy)32+. Ru(bpy)32+ can be intercalated into the loop of hairpin DNA through the electrostatic interaction to fabricate a probe. When the probe was bound to the CdSe QDs modified on the GCE, the intense ECL signal was obtained. The more Ru(bpy)32+ can be intercalated when DNA loop has larger diameter and the stronger ECL signal can be observed. The loop of hairpin DNA can be opened in the presence of target DNA to release the immobilized Ru(bpy)32+, which can result in the decrease of ECL signal. The decreased ECL signal varied linearly with the concentration of target DNA, which showed the ECL biosensor can be used in the sensitive detection of DNA. The proposed ECL biosensor showed an excellent performance with high specificity, wide linear range and low detection limit.
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Affiliation(s)
- Yong-Ping Dong
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, Nanjing 210093, China.,School of Chemistry and Chemical Engineering, Anhui University of Technology, Maanshan 243002, China
| | - Ting-Ting Gao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, Nanjing 210093, China.,School of Chemistry and Chemical Engineering, Anhui University of Technology, Maanshan 243002, China
| | - Ying Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, Nanjing 210093, China.,School of Chemistry and Chemical Engineering, Anhui University of Technology, Maanshan 243002, China
| | - Li-Ping Jiang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, Nanjing 210093, China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, Nanjing 210093, China
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14
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Leng Y, Sun K, Chen X, Li W. Suspension arrays based on nanoparticle-encoded microspheres for high-throughput multiplexed detection. Chem Soc Rev 2015; 44:5552-95. [PMID: 26021602 PMCID: PMC5223091 DOI: 10.1039/c4cs00382a] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Spectrometrically or optically encoded microsphere based suspension array technology (SAT) is applicable to the high-throughput, simultaneous detection of multiple analytes within a small, single sample volume. Thanks to the rapid development of nanotechnology, tremendous progress has been made in the multiplexed detecting capability, sensitivity, and photostability of suspension arrays. In this review, we first focus on the current stock of nanoparticle-based barcodes as well as the manufacturing technologies required for their production. We then move on to discuss all existing barcode-based bioanalysis patterns, including the various labels used in suspension arrays, label-free platforms, signal amplification methods, and fluorescence resonance energy transfer (FRET)-based platforms. We then introduce automatic platforms for suspension arrays that use superparamagnetic nanoparticle-based microspheres. Finally, we summarize the current challenges and their proposed solutions, which are centered on improving encoding capacities, alternative probe possibilities, nonspecificity suppression, directional immobilization, and "point of care" platforms. Throughout this review, we aim to provide a comprehensive guide for the design of suspension arrays, with the goal of improving their performance in areas such as multiplexing capacity, throughput, sensitivity, and cost effectiveness. We hope that our summary on the state-of-the-art development of these arrays, our commentary on future challenges, and some proposed avenues for further advances will help drive the development of suspension array technology and its related fields.
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Affiliation(s)
- Yuankui Leng
- The State Key Lab of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
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15
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Yuan Y, Zhang J, Cao Q, An L, Liang G. Intracellular Disassembly of Self-Quenched Nanoparticles Turns NIR Fluorescence on for Sensing Furin Activity in Cells and in Tumors. Anal Chem 2015; 87:6180-5. [DOI: 10.1021/acs.analchem.5b01656] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Yue Yuan
- CAS Key Laboratory of Soft
Matter Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jia Zhang
- CAS Key Laboratory of Soft
Matter Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Qinjingwen Cao
- CAS Key Laboratory of Soft
Matter Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Linna An
- CAS Key Laboratory of Soft
Matter Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Gaolin Liang
- CAS Key Laboratory of Soft
Matter Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
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16
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Sato Y, Kudo M, Toriyabe Y, Kuchitsu S, Wang CX, Nishizawa S, Teramae N. Abasic site-binding ligands conjugated with cyanine dyes for “off–on” fluorescence sensing of orphan nucleobases in DNA duplexes and DNA–RNA hybrids. Chem Commun (Camb) 2014; 50:515-7. [DOI: 10.1039/c3cc47717g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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17
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NISHIZAWA S, SATO Y, TERAMAE N. Recent Progress in Abasic Site-binding Small Molecules for Detecting Single-base Mutations in DNA. ANAL SCI 2014; 30:137-42. [DOI: 10.2116/analsci.30.137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Seiichi NISHIZAWA
- Department of Chemistry, Graduate School of Science, Tohoku University
| | - Yusuke SATO
- Department of Chemistry, Graduate School of Science, Tohoku University
| | - Norio TERAMAE
- Department of Chemistry, Graduate School of Science, Tohoku University
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18
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Futamura A, Uemura A, Imoto T, Kitamura Y, Matsuura H, Wang CX, Ichihashi T, Sato Y, Teramae N, Nishizawa S, Ihara T. Rational design for cooperative recognition of specific nucleobases using β-cyclodextrin-modified DNAs and fluorescent ligands on DNA and RNA scaffolds. Chemistry 2013; 19:10526-35. [PMID: 23821253 DOI: 10.1002/chem.201300985] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Indexed: 01/10/2023]
Abstract
We propose a binary fluorimetric method for DNA and RNA analysis by the combined use of two probes rationally designed to work cooperatively. One probe is an oligonucleotide (ODN) conjugate bearing a β-cyclodextrin (β-CyD). The other probe is a small reporter ligand, which comprises linked molecules of a nucleobase-specific heterocycle and an environment-sensitive fluorophore. The heterocycle of the reporter ligand recognizes a single nucleobase displayed in a gap on the target labeled with the conjugate and, at the same time, the fluorophore moiety forms a luminous inclusion complex with nearby β-CyD. Three reporter ligands, MNDS (naphthyridine-dansyl linked ligand), MNDB (naphthyridine-DBD), and DPDB (pyridine-DBD), were used for DNA and RNA probing with 3'-end or 5'-end modified β-CyD-ODN conjugates. For the DNA target, the β-CyD tethered to the 3'-end of the ODN facing into the gap interacted with the fluorophore sticking out into the major groove of the gap site (MNDS and DPDB). Meanwhile the β-CyD on the 5'-end of the ODN interacted with the fluorophore in the minor groove (MNDB and DPDB). The results obtained by this study could be a guideline for the design of binary DNA/RNA probe systems based on controlling the proximity of functional molecules.
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Affiliation(s)
- Akika Futamura
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University, Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
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19
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Zhuang YD, Chiang PY, Wang CW, Tan KT. Environment-Sensitive Fluorescent Turn-On Probes Targeting Hydrophobic Ligand-Binding Domains for Selective Protein Detection. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302884] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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20
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Zhuang YD, Chiang PY, Wang CW, Tan KT. Environment-sensitive fluorescent turn-on probes targeting hydrophobic ligand-binding domains for selective protein detection. Angew Chem Int Ed Engl 2013; 52:8124-8. [PMID: 23780746 DOI: 10.1002/anie.201302884] [Citation(s) in RCA: 158] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 05/27/2013] [Indexed: 12/15/2022]
Affiliation(s)
- Yu-De Zhuang
- Department of Chemistry, National Tsing Hua University, 101 Sec. 2, Kuang-Fu Rd., Hsinchu 30013, Taiwan, ROC
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21
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Tang X, Zhao D, He J, Li F, Peng J, Zhang M. Quenching of the Electrochemiluminescence of Tris(2,2′-bipyridine)ruthenium(II)/Tri-n-propylamine by Pristine Carbon Nanotube and Its Application to Quantitative Detection of DNA. Anal Chem 2013; 85:1711-8. [DOI: 10.1021/ac303025y] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Xiaofeng Tang
- Department
of Chemistry, Renmin University of China, Beijing 100872, P. R. China
| | - Dan Zhao
- Department
of Chemistry, Renmin University of China, Beijing 100872, P. R. China
| | - Jinchao He
- Department
of Chemistry, Renmin University of China, Beijing 100872, P. R. China
| | - Fengwang Li
- Department
of Chemistry, Renmin University of China, Beijing 100872, P. R. China
| | - Jiaxi Peng
- Department
of Chemistry, Renmin University of China, Beijing 100872, P. R. China
| | - Meining Zhang
- Department
of Chemistry, Renmin University of China, Beijing 100872, P. R. China
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22
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Sato Y, Toriyabe Y, Nishizawa S, Teramae N. 2,4-Diamino-6,7-dimethylpteridine as a fluorescent ligand for binding and sensing an orphan cytosine in RNA duplexes. Chem Commun (Camb) 2013; 49:9983-5. [DOI: 10.1039/c3cc46085a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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