1
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Zhang L, Liu J, Gao M, Han L, Liu X, Xing X. Fluorescent Determination of Mercury(II) and Glutathione with Binding to Thymine–Guanine Base Pairs. ANAL LETT 2022. [DOI: 10.1080/00032719.2022.2109044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Liyuan Zhang
- College of Chemistry and Pharmaceutical Engineering, Nanyang Normal University, Nanyang, China
| | - Jinxiao Liu
- College of Materials Science and Engineering, Zhengzhou University, Zhengzhou, China
| | - Mengying Gao
- College of Chemistry and Pharmaceutical Engineering, Nanyang Normal University, Nanyang, China
| | - Li Han
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Department of Biology and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
| | - Xueguo Liu
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Department of Biology and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
| | - Xiaojing Xing
- College of Chemistry and Pharmaceutical Engineering, Nanyang Normal University, Nanyang, China
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2
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Li T, Hu Z, Yu S, Liu Z, Zhou X, Liu R, Liu S, Deng Y, Li S, Chen H, Chen Z. DNA Templated Silver Nanoclusters for Bioanalytical Applications: A Review. J Biomed Nanotechnol 2022. [DOI: 10.1166/jbn.2022.3344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Due to their unique programmability, biocompatibility, photostability and high fluorescent quantum yield, DNA templated silver nanoclusters (DNA Ag NCs) have attracted increasing attention for bioanalytical application. This review summarizes the recent developments in fluorescence
properties of DNA templated Ag NCs, as well as their applications in bioanalysis. Finally, we herein discuss some current challenges in bioanalytical applications, to promote developments of DNA Ag NCs in biochemical analysis.
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Affiliation(s)
- Taotao Li
- Hunan Provincial Key Lab of Dark Tea and Jin-Hua, School of Materials and Chemical Engineering, Hunan City University, Yiyang 413000, China
| | - Zhiyuan Hu
- Hunan Provincial Key Lab of Dark Tea and Jin-Hua, School of Materials and Chemical Engineering, Hunan City University, Yiyang 413000, China
| | - Songlin Yu
- Hunan Provincial Key Lab of Dark Tea and Jin-Hua, School of Materials and Chemical Engineering, Hunan City University, Yiyang 413000, China
| | - Zhanjun Liu
- Hunan Provincial Key Lab of Dark Tea and Jin-Hua, School of Materials and Chemical Engineering, Hunan City University, Yiyang 413000, China
| | - Xiaohong Zhou
- Hunan Provincial Key Lab of Dark Tea and Jin-Hua, School of Materials and Chemical Engineering, Hunan City University, Yiyang 413000, China
| | - Rong Liu
- Hunan Provincial Key Lab of Dark Tea and Jin-Hua, School of Materials and Chemical Engineering, Hunan City University, Yiyang 413000, China
| | - Shiquan Liu
- Hunan Provincial Key Lab of Dark Tea and Jin-Hua, School of Materials and Chemical Engineering, Hunan City University, Yiyang 413000, China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Hui Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
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3
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Lee HJ, Kim BH. Pyrene-Modified Guanine Cluster Probes Forming DNA/RNA Hybrid Three-Way Junctions for Imaging of Intracellular MicroRNAs. ACS APPLIED BIO MATERIALS 2021; 4:1668-1676. [PMID: 35014514 DOI: 10.1021/acsabm.0c01476] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) regulate gene expression in cells; high levels of expression are associated with various cancers. In this paper, we describe PyA-modified nucleic acid probes that can detect intracellular miRNAs by forming DNA/RNA hybrid three-way junction structures containing a fluorescent scaffold-a so-called G-cluster. This G-cluster featured two mismatched strands, four guanine residues, and one fluorescent adenine residue having a pyrene moiety covalently connected at the 8-position through an acetylene linker. The scaffold underwent a dramatic shift in its emission wavelength when two mismatched strands formed a duplex, similar to the behavior of an adenine pentad system (A-cluster). We applied the G-cluster scaffold in a three-way junction system to probe for miRNAs; its red-shifted fluorescence intensity and stability were greater than those reported previously for A-cluster three-way junction probes. Furthermore, confocal microscopy of cancer cell lines revealed bright fluorescence emissions in response to the miRNAs in the cells. Thus, this system can be applied intracellularly as a potential fluorescent probe for the detection of various biologically important nucleic acids.
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Affiliation(s)
- Ha Jung Lee
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
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4
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Wang D, Geng F, Wang Y, Ma Y, Li G, Qu P, Shao C, Xu M. Design of a Fluorescence Turn-on and Label-free Aptasensor Using the Intrinsic Quenching Power of G-Quadruplex to AMT. ANAL SCI 2020; 36:965-970. [PMID: 32062632 DOI: 10.2116/analsci.19p455] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A novel fluorescent aptasensor based on the G-quadruplex induced fluorescent quenching of psoralen and the competitive interactions between 4'-aminomethyl-4,5',8-trimethylpsoralen (AMT), adenosine triphosphate (ATP) and G-rich DNA functionalized split ATP aptamer was proposed. The binding of ATP to the G-rich DNA functionalized split aptamer induced a significant enhancement in fluorescence emission intensity while undergoing excitation at 340 nm. Under the optimal conditions, the developed aptasensor showed high selectivity and good accuracy for detecting ATP. The practicality of the proposed aptasensor has been confirmed by successfully analyzing ATP in spiked human blood serum samples with satisfactory results. As far as we know, this is the first time that the intrinsic quenching ability of G-quadruplex was applied to simply construct a fluorescence turn-on and label-free aptasensor. On account of the superiority of the simplicity of the design strategy, more work is expected in the future to develop a variety of novel sensors for other important analytes using the quenching capability of G-quadruplex through reasonable designs.
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Affiliation(s)
- Dandan Wang
- College of Chemistry and Chemical Engineering, Xinjiang Normal University
| | - Fenghua Geng
- Henan Key Laboratory of Biomolecular Recognition and Sensing, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, School of Chemistry and Chemical Engineering, Shangqiu Normal University
| | - Yongxiang Wang
- Henan Key Laboratory of Biomolecular Recognition and Sensing, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, School of Chemistry and Chemical Engineering, Shangqiu Normal University.,College of Chemistry and Material Science, Huaibei Normal University
| | - Yu Ma
- Henan Key Laboratory of Biomolecular Recognition and Sensing, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, School of Chemistry and Chemical Engineering, Shangqiu Normal University
| | - Guixin Li
- College of Chemistry and Chemical Engineering, Xinjiang Normal University
| | - Peng Qu
- Henan Key Laboratory of Biomolecular Recognition and Sensing, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, School of Chemistry and Chemical Engineering, Shangqiu Normal University
| | - Congying Shao
- College of Chemistry and Material Science, Huaibei Normal University
| | - Maotian Xu
- Henan Key Laboratory of Biomolecular Recognition and Sensing, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, School of Chemistry and Chemical Engineering, Shangqiu Normal University
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5
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Jose J, Anas A, Jose B, Puthirath AB, Athiyanathil S, Jasmin C, Anantharaman MR, Nair S, Subrahmanyam C, Biju V. Extinction of Antimicrobial Resistant Pathogens Using Silver Embedded Silica Nanoparticles and an Efflux Pump Blocker. ACS APPLIED BIO MATERIALS 2019; 2:4681-4686. [DOI: 10.1021/acsabm.9b00614] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jiya Jose
- Council of Scientific and Industrial Research (CSIR)- National Institute of Oceanography (NIO), Regional Centre Cochin, Kerala, India
| | - Abdulaziz Anas
- Council of Scientific and Industrial Research (CSIR)- National Institute of Oceanography (NIO), Regional Centre Cochin, Kerala, India
| | - Bina Jose
- Council of Scientific and Industrial Research (CSIR)- National Institute of Oceanography (NIO), Regional Centre Cochin, Kerala, India
| | - Anand B. Puthirath
- Department of Physics, Cochin University of Science and Technology, Cochin, Kerala, India
| | - Sujith Athiyanathil
- Department of Chemistry, National Institute of Technology Calicut, Calicut, Kerala, India
| | - Chekidhenkuzhiyil Jasmin
- Council of Scientific and Industrial Research (CSIR)- National Institute of Oceanography (NIO), Regional Centre Cochin, Kerala, India
| | - M. R. Anantharaman
- Department of Physics, Cochin University of Science and Technology, Cochin, Kerala, India
| | - Shanta Nair
- Council of Scientific and Industrial Research (CSIR)- National Institute of Oceanography (NIO), Regional Centre Cochin, Kerala, India
| | - Challapalli Subrahmanyam
- Deparment of Chemistry, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana, India
| | - Vasudevanpillai Biju
- Research Institute for Electronic Science, Hokkaido University, Sapporo 001-0020, Japan
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6
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Chen P, Sawyer E, Sun K, Zhang X, Chen C, Ying B, Wei X, Wu Z, Geng J. A general strategy for label-free homogeneous bioassays based on selective recognition and silver ion-mediated conformational switch. Talanta 2019; 201:9-15. [DOI: 10.1016/j.talanta.2019.03.088] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 03/11/2019] [Accepted: 03/24/2019] [Indexed: 12/26/2022]
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7
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Lu S, Wang S, Zhao J, Sun J, Yang X. Classical Triplex Molecular Beacons for MicroRNA-21 and Vascular Endothelial Growth Factor Detection. ACS Sens 2018; 3:2438-2445. [PMID: 30350592 DOI: 10.1021/acssensors.8b00996] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Triplex molecular beacons (tMBs) possess great potential in biological sensing because of the pH responsiveness and controllability of binding strength. Here, we systematically investigate and rationally design a classical tMB for convenient detection of microRNA-21, a well-known biomarker of cardio-cerebrovascular diseases. In the tMB, we employ the complementary sequence of miR-21 as the loop and the sequences of protonated cytosine-guanine-cytosine (C-G•C+) and thymine-adenine-thymine (T-A•T) as the triplex stem, in which both the Watson-Crick and Hoogsteen base-pairing control the binding strength in cooperation. It is demonstrated for the first time that the presence of miR-21 would only break the Hoogsteen base-pairing in the stem and hybridize with the tMB to form the rigid heterozygous hybrid duplex structure. These would hinder the fluorescence resonance energy transfer (FRET) between the fluorophore (FAM) and quencher (BHQ1) labeled at the ends of the oligonucleotide, and the fluorescence recovery degree of FAM can be used as the standard to quantitate the miR-21. More significantly, the excellent adjustability and sensitivity of our tMBs have been confirmed by constructing the corresponding duplex molecular beacon (dMB) for comparison. The fluorophore FAM in the tMB could be replaced by the fluorescent DNA/silver nanoclusters, which exhibits the universal applicability of energy donor and receptor selection for tMB. Furthermore, our proposed tMB could also be developed as an aptasensor for the detection of vascular endothelial growth factor (VEGF) by only introducing the complementary sequence of its aptamer into the tMB. This work is of great significance for the systematic study of tMBs for the detection of biomarkers such as nucleic acids and proteins.
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Affiliation(s)
- Shasha Lu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Shuang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jiahui Zhao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Sun
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Xiurong Yang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
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8
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Affiliation(s)
- Wenhu Zhou
- Xiangya
School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Runjhun Saran
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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9
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Lai QQ, Liu MD, Gu CC, Nie HG, Xu XJ, Li ZH, Yang Z, Huang SM. A novel label-free fluorescence strategy for methyltransferase activity assay based on dsDNA-templated copper nanoparticles coupled with an endonuclease-assisted signal transduction system. Analyst 2016; 141:1383-9. [DOI: 10.1039/c5an02123e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A novel label-free fluorescence method by coupling dsDNA-templated CuNPs with endonuclease-assisted signal transduction has been developed for methyltransferase activity assay.
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Affiliation(s)
- Q. Q. Lai
- Nanomaterials and Chemistry Key Laboratory
- College of Chemistry and Materials Engineering
- Wenzhou University
- Wenzhou
- P. R. China
| | - M. D. Liu
- Nanomaterials and Chemistry Key Laboratory
- College of Chemistry and Materials Engineering
- Wenzhou University
- Wenzhou
- P. R. China
| | - C. C. Gu
- Nanomaterials and Chemistry Key Laboratory
- College of Chemistry and Materials Engineering
- Wenzhou University
- Wenzhou
- P. R. China
| | - H. G. Nie
- Nanomaterials and Chemistry Key Laboratory
- College of Chemistry and Materials Engineering
- Wenzhou University
- Wenzhou
- P. R. China
| | - X. J. Xu
- Nanomaterials and Chemistry Key Laboratory
- College of Chemistry and Materials Engineering
- Wenzhou University
- Wenzhou
- P. R. China
| | - Z. H. Li
- The Institute of Molecular Medicine
- School of Optometry and Ophthalmology and Eye Hospital
- Wenzhou Medical University
- Wenzhou
- P. R. China
| | - Z. Yang
- Nanomaterials and Chemistry Key Laboratory
- College of Chemistry and Materials Engineering
- Wenzhou University
- Wenzhou
- P. R. China
| | - S. M. Huang
- Nanomaterials and Chemistry Key Laboratory
- College of Chemistry and Materials Engineering
- Wenzhou University
- Wenzhou
- P. R. China
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10
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Park KS, Lee CY, Park HG. Metal ion triggers for reversible switching of DNA polymerase. Chem Commun (Camb) 2016; 52:4868-71. [DOI: 10.1039/c6cc00454g] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A new strategy to modulate DNA polymerase activity in a reversible and switchable manner was devised by using the novel interactions between DNA bases and metal ions.
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Affiliation(s)
- Ki Soo Park
- Department of Chemical and Biomolecular Engineering (BK 21+ program)
- KAIST
- Daejeon 305-338
- Republic of Korea
| | - Chang Yeol Lee
- Department of Chemical and Biomolecular Engineering (BK 21+ program)
- KAIST
- Daejeon 305-338
- Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK 21+ program)
- KAIST
- Daejeon 305-338
- Republic of Korea
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11
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Kondo J, Tada Y, Dairaku T, Saneyoshi H, Okamoto I, Tanaka Y, Ono A. High‐Resolution Crystal Structure of a Silver(I)–RNA Hybrid Duplex Containing Watson–Crick‐like CSilver(I)C Metallo‐Base Pairs. Angew Chem Int Ed Engl 2015; 54:13323-6. [DOI: 10.1002/anie.201507894] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Jiro Kondo
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7‐1 Kioi‐cho, Chiyoda‐ku, Tokyo 102‐8554 (Japan)
- Graduate School of Science and Technology, Sophia University, 7‐1 Kioi‐cho, Chiyoda‐ku, Tokyo 102‐8554 (Japan)
| | - Yoshinari Tada
- Graduate School of Science and Technology, Sophia University, 7‐1 Kioi‐cho, Chiyoda‐ku, Tokyo 102‐8554 (Japan)
| | - Takenori Dairaku
- Laboratory of Molecular Transformation, Graduate School of Pharmaceutical Sciences, Tohoku University, 6‐3 Aza‐Aoba, Aramaki, Aoba‐ku, Sendai 980‐8578 (Japan)
| | - Hisao Saneyoshi
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3‐27‐1 Rokkakubashi, Kanagawa‐ku, Yokohama 221‐8686 (Japan)
| | - Itaru Okamoto
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3‐27‐1 Rokkakubashi, Kanagawa‐ku, Yokohama 221‐8686 (Japan)
| | - Yoshiyuki Tanaka
- Laboratory of Molecular Transformation, Graduate School of Pharmaceutical Sciences, Tohoku University, 6‐3 Aza‐Aoba, Aramaki, Aoba‐ku, Sendai 980‐8578 (Japan)
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro‐cho, 770‐8514 Tokushima (Japan)
| | - Akira Ono
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3‐27‐1 Rokkakubashi, Kanagawa‐ku, Yokohama 221‐8686 (Japan)
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12
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Kondo J, Tada Y, Dairaku T, Saneyoshi H, Okamoto I, Tanaka Y, Ono A. High‐Resolution Crystal Structure of a Silver(I)–RNA Hybrid Duplex Containing Watson–Crick‐like CSilver(I)C Metallo‐Base Pairs. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507894] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Jiro Kondo
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7‐1 Kioi‐cho, Chiyoda‐ku, Tokyo 102‐8554 (Japan)
- Graduate School of Science and Technology, Sophia University, 7‐1 Kioi‐cho, Chiyoda‐ku, Tokyo 102‐8554 (Japan)
| | - Yoshinari Tada
- Graduate School of Science and Technology, Sophia University, 7‐1 Kioi‐cho, Chiyoda‐ku, Tokyo 102‐8554 (Japan)
| | - Takenori Dairaku
- Laboratory of Molecular Transformation, Graduate School of Pharmaceutical Sciences, Tohoku University, 6‐3 Aza‐Aoba, Aramaki, Aoba‐ku, Sendai 980‐8578 (Japan)
| | - Hisao Saneyoshi
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3‐27‐1 Rokkakubashi, Kanagawa‐ku, Yokohama 221‐8686 (Japan)
| | - Itaru Okamoto
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3‐27‐1 Rokkakubashi, Kanagawa‐ku, Yokohama 221‐8686 (Japan)
| | - Yoshiyuki Tanaka
- Laboratory of Molecular Transformation, Graduate School of Pharmaceutical Sciences, Tohoku University, 6‐3 Aza‐Aoba, Aramaki, Aoba‐ku, Sendai 980‐8578 (Japan)
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro‐cho, 770‐8514 Tokushima (Japan)
| | - Akira Ono
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3‐27‐1 Rokkakubashi, Kanagawa‐ku, Yokohama 221‐8686 (Japan)
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13
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Zheng J, Yang R, Shi M, Wu C, Fang X, Li Y, Li J, Tan W. Rationally designed molecular beacons for bioanalytical and biomedical applications. Chem Soc Rev 2015; 44:3036-55. [PMID: 25777303 PMCID: PMC4431697 DOI: 10.1039/c5cs00020c] [Citation(s) in RCA: 254] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nucleic acids hold promise as biomolecules for future applications in biomedicine and biotechnology. Their well-defined structures and compositions afford unique chemical properties and biological functions. Moreover, the specificity of hydrogen-bonded Watson-Crick interactions allows the construction of nucleic acid sequences with multiple functions. In particular, the development of nucleic acid probes as essential molecular engineering tools will make a significant contribution to advancements in biosensing, bioimaging and therapy. The molecular beacon (MB), first conceptualized by Tyagi and Kramer in 1996, is an excellent example of a double-stranded nucleic acid (dsDNA) probe. Although inactive in the absence of a target, dsDNA probes can report the presence of a specific target through hybridization or a specific recognition-triggered change in conformation. MB probes are typically fluorescently labeled oligonucleotides that range from 25 to 35 nucleotides (nt) in length, and their structure can be divided into three components: stem, loop and reporter. The intrinsic merit of MBs depends on predictable design, reproducibility of synthesis, simplicity of modification, and built-in signal transduction. Using resonance energy transfer (RET) for signal transduction, MBs are further endowed with increased sensitivity, rapid response and universality, making them ideal for chemical sensing, environmental monitoring and biological imaging, in contrast to other nucleic acid probes. Furthermore, integrating MBs with targeting ligands or molecular drugs can substantially support their in vivo applications in theranositics. In this review, we survey advances in bioanalytical and biomedical applications of rationally designed MBs, as they have evolved through the collaborative efforts of many researchers. We first discuss improvements to the three components of MBs: stem, loop and reporter. The current applications of MBs in biosensing, bioimaging and therapy will then be described. In particular, we emphasize recent progress in constructing MB-based biosensors in homogeneous solution or on solid surfaces. We expect that such rationally designed and functionalized MBs will open up new and exciting avenues for biological and medical research and applications.
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Affiliation(s)
- Jing Zheng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
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14
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Del Bonis-O'Donnell JT, Fygenson DK, Pennathur S. Fluorescent silver nanocluster DNA probes for multiplexed detection using microfluidic capillary electrophoresis. Analyst 2015; 140:1609-15. [DOI: 10.1039/c4an01735h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We tune the electrophoretic mobilities of silver nanocluster DNA probes for Hepatitis A, B and C targets for single-color multiplexing by microfluidic capillary electrophoresis.
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Affiliation(s)
| | | | - Sumita Pennathur
- Department of Mechanical Engineering
- University of California Santa Barbara
- Santa Barbara
- USA
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15
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Xu H, Geng F, Wang Y, Xu M, Lai X, Qu P, Zhang Y, Liu B. A label-free fluorescent molecular switch for a DNA hybridization assay utilizing a G-quadruplex-selective auramine O. Chem Commun (Camb) 2015; 51:8622-5. [DOI: 10.1039/c5cc02624e] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A G-quadruplex molecular switch (G4-MS) assembled using auramine O and the G-rich single stranded DNA is developed for a DNA assay.
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Affiliation(s)
- Huiying Xu
- Department of Chemistry
- State Key Lab of Molecular Engineering of Polymers and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200433
- China
| | - Fenghua Geng
- Key Laboratory of Biomolecule Recognition and Sensing
- College of Chemistry and Chemical Engineering
- Shangqiu Normal University
- Shangqiu
- China
| | - Yongxiang Wang
- Key Laboratory of Biomolecule Recognition and Sensing
- College of Chemistry and Chemical Engineering
- Shangqiu Normal University
- Shangqiu
- China
| | - Maotian Xu
- Key Laboratory of Biomolecule Recognition and Sensing
- College of Chemistry and Chemical Engineering
- Shangqiu Normal University
- Shangqiu
- China
| | - Xinhe Lai
- Key Laboratory of Biomolecule Recognition and Sensing
- College of Chemistry and Chemical Engineering
- Shangqiu Normal University
- Shangqiu
- China
| | - Peng Qu
- Key Laboratory of Biomolecule Recognition and Sensing
- College of Chemistry and Chemical Engineering
- Shangqiu Normal University
- Shangqiu
- China
| | - Yintang Zhang
- Key Laboratory of Biomolecule Recognition and Sensing
- College of Chemistry and Chemical Engineering
- Shangqiu Normal University
- Shangqiu
- China
| | - Baohong Liu
- Department of Chemistry
- State Key Lab of Molecular Engineering of Polymers and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200433
- China
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16
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Nieh CC, Tseng WL. Thymine-based molecular beacon for sensing adenosine based on the inhibition of S-adenosylhomocysteine hydrolase activity. Biosens Bioelectron 2014; 61:404-9. [DOI: 10.1016/j.bios.2014.05.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/12/2014] [Accepted: 05/13/2014] [Indexed: 01/23/2023]
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17
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Xing X, Zhou Y, Liu X, Pang D, Tang H. Graphene oxide and metal-mediated base pairs based "molecular beacon" integrating with exonuclease I for fluorescence turn-on detection of biothiols. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:3412-3420. [PMID: 24788855 DOI: 10.1002/smll.201302938] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 01/18/2014] [Indexed: 06/03/2023]
Abstract
A novel fluorescence turn-on strategy, based on the resistance of metal-mediated molecular-beacons (MBs) toward nuclease digestion and the remarkable difference in the affinity of graphene oxide (GO) with MBs and the mononucleotides, is designed for the biothiols assay. Specifically, the metal-mediated base pairs facilitate the dye labeled MBs to fold into a hairpin structure preventing the digestion by exonuclease I, and thus allow the fluorescence quenching. The competition binding by biothiols removes metal ions from the base pairs, causing the nuclease reaction, and less decrease in the fluorescence is obtained after incubating with GO due to the weak affinity of the product-mononucleotides to GO. Hg(2+)-mediated MBs were firstly designed for the biothiols detection, and glutathione (GSH) was applied as the model target. Under the optimal conditions, the approach exhibits high sensitivity to GSH with a detection limit of 1.53 nM. Ag(+)-mediated MBs based sensor was also constructed to demonstrate its versatility, and cysteine was studied as the model target. The satisfactory results in the determination of biothiols in serum demonstrate that the method possesses great potential for detecting thiols in biological fluids. This new approach is expected to promote the exploitation of metal-mediated base pairs-based biosensors in biochemical and biomedical studies.
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Affiliation(s)
- Xiaojing Xing
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan Institute of Biotechnology, and State, Key Laboratory of Virology, Wuhan University, Wuhan, 430072, P. R. China
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18
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Technological applications arising from the interactions of DNA bases with metal ions. Curr Opin Biotechnol 2014; 28:17-24. [DOI: 10.1016/j.copbio.2013.10.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 10/26/2013] [Accepted: 10/31/2013] [Indexed: 01/03/2023]
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Dual hairpin-like molecular beacon based on coralyne-adenosine interaction for sensing melamine in dairy products. Talanta 2014; 129:398-403. [PMID: 25127611 DOI: 10.1016/j.talanta.2014.05.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 05/18/2014] [Accepted: 05/21/2014] [Indexed: 11/20/2022]
Abstract
This study presents a novel dual hairpin-like molecular beacon (MB) for the selective and sensitive detection of melamine (MA) based on the conjugation of MA and thymine. In this protocol, the coordination between coralyne and adenosine (A) leaded a dual hairpin-like MB and the fluorophore-quencher pair is close proximity resulting in the fluorescence quenching. With the addition of MA, it conjugated with thymine in the loop part of dual hairpin-like MB by triple H-bonds, triggering the dissociation of the dual hairpin-like MB. The resulting spatial separation of the fluorophore from quencher induced the enhancement in fluorescence emission. Under the optimized conditions, the sensor exhibited a wide linear range of 8×10(-9)-1.6×10(-5) M (R(2)=0.9969) towards MA, with a low detection limit of 5 nM, approximately 4000 times lower than the Drug Administration and the US Food estimated MA safety limit. The real milk samples were also investigated with a satisfying result.
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Deng X, Tang H, Jiang J. Recent progress in graphene-material-based optical sensors. Anal Bioanal Chem 2014; 406:6903-16. [DOI: 10.1007/s00216-014-7895-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 05/07/2014] [Accepted: 05/13/2014] [Indexed: 12/11/2022]
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Feng C, Dai S, Wang L. Optical aptasensors for quantitative detection of small biomolecules: a review. Biosens Bioelectron 2014; 59:64-74. [PMID: 24690563 DOI: 10.1016/j.bios.2014.03.014] [Citation(s) in RCA: 191] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/27/2014] [Accepted: 03/06/2014] [Indexed: 01/16/2023]
Abstract
Aptasensors are aptamer-based biosensors with excellent recognition capability towards a wide range of targets. Specially, there have been ever-growing interests in the development of aptasensors for the detection of small molecules. This phenomenon is contributed to two reasons. On one hand, small biomolecules play an important role in living organisms with many kinds of biological function, such as antiarrhythmic effect and vasodilator activity of adenosine. On the other hand, the concentration of small molecules can be an indicator for disease diagnosis, for example, the concentration of ATP is closely associated with cell injury and cell viability. As a potential analysis tool in the construction of aptasensors, optical analysis has attracted much more interest of researchers due to its high sensitivity, quick response and simple operation. Besides, it promises the promotion of aptasensors in performance toward a new level. Review the development of optical aptasensors for small biomolecules will give readers an overall understanding of its progress and provide some theoretical guidelines for its future development. Hence, we give a mini-review on the advance of optical aptasensors for small biomolecules. This review focuses on recent achievements in the design of various optical aptasensors for small biomolecules, containing fluorescence aptasensors, colorimetric aptasensors, chemiluminescence aptasensors and other optical aptasensors.
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Affiliation(s)
- Chunjing Feng
- Key Laboratory of Natural Products Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 250012 Jinan, PR China
| | - Shuang Dai
- Key Laboratory of Natural Products Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 250012 Jinan, PR China
| | - Lei Wang
- Key Laboratory of Natural Products Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 250012 Jinan, PR China.
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22
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Dong H, Hao K, Tian Y, Jin S, Lu H, Zhou SF, Zhang X. Label-free and ultrasensitive microRNA detection based on novel molecular beacon binding readout and target recycling amplification. Biosens Bioelectron 2014; 53:377-83. [DOI: 10.1016/j.bios.2013.09.061] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 09/10/2013] [Accepted: 09/20/2013] [Indexed: 10/26/2022]
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Abstract
Increasing interest in detecting metal ions in many chemical and biomedical fields has created demands for developing sensors and imaging agents for metal ions with high sensitivity and selectivity. This review covers recent progress in DNA-based sensors and imaging agents for metal ions. Through both combinatorial selection and rational design, a number of metal-ion-dependent DNAzymes and metal-ion-binding DNA structures that can selectively recognize specific metal ions have been obtained. By attachment of these DNA molecules with signal reporters such as fluorophores, chromophores, electrochemical tags, and Raman tags, a number of DNA-based sensors for both diamagnetic and paramagnetic metal ions have been developed for fluorescent, colorimetric, electrochemical, and surface Raman detection. These sensors are highly sensitive (with a detection limit down to 11 ppt) and selective (with selectivity up to millions-fold) toward specific metal ions. In addition, through further development to simplify the operation, such as the use of "dipstick tests", portable fluorometers, computer-readable disks, and widely available glucose meters, these sensors have been applied for on-site and real-time environmental monitoring and point-of-care medical diagnostics. The use of these sensors for in situ cellular imaging has also been reported. The generality of the combinatorial selection to obtain DNAzymes for almost any metal ion in any oxidation state and the ease of modification of the DNA with different signal reporters make DNA an emerging and promising class of molecules for metal-ion sensing and imaging in many fields of applications.
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Affiliation(s)
- Yu Xiang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Fax: 217-244-3186; Tel: 217-333-2619
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Fax: 217-244-3186; Tel: 217-333-2619
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24
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Xiong Y, Wei M, Wei W, Yin L, Pu Y, Liu S. Detection of DNA damage based on metal-mediated molecular beacon and DNA strands displacement reaction. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 118:806-810. [PMID: 24152865 DOI: 10.1016/j.saa.2013.09.084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 09/12/2013] [Accepted: 09/25/2013] [Indexed: 06/02/2023]
Abstract
DNA hairpin structure probes are usually designed by forming intra-molecular duplex based on Watson-Crick hydrogen bonds. In this paper, a molecular beacon based on silver ions-mediated cytosine-Ag(+)-cytosine base pairs was used to detect DNA. The inherent characteristic of the metal ligation facilitated the design of functional probe and the adjustment of its binding strength compared to traditional DNA hairpin structure probes, which make it be used to detect DNA in a simple, rapid and easy way with the help of DNA strands displacement reaction. The method was sensitive and also possesses the good specificity to differentiate the single base mismatched DNA from the complementary DNA. It was also successfully applied to study the damage effect of classic genotoxicity chemicals such as styrene oxide and sodium arsenite on DNA, which was significant in food science, environmental science and pharmaceutical science.
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Affiliation(s)
- Yanxiang Xiong
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, Jiangsu Province, PR China
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Lin KC, Kuo CY, Nieh CC, Tseng WL. Molecular beacon-based NAND logic gate for sensing triplex DNA binders. RSC Adv 2014. [DOI: 10.1039/c4ra06158f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Molecular beacon-based NAND logic gate was simple, rapid, selective, and sensitive for probing triplex DNA binders.
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Affiliation(s)
- Kai-Cheng Lin
- Department of Emergency Medicine
- Division of Traumatology
- Kaohsiung Veterans General Hospital
- Taiwan
| | - Chia-Yin Kuo
- Department of Chemistry
- National Sun Yat-sen University
- Kaohsiung, Taiwan
| | - Chih-Chun Nieh
- Department of Chemistry
- National Sun Yat-sen University
- Kaohsiung, Taiwan
| | - Wei-Lung Tseng
- Department of Chemistry
- National Sun Yat-sen University
- Kaohsiung, Taiwan
- School of Pharmacy
- College of Pharmacy
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26
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Lin JH, Tseng WL. Design of two and three input molecular logic gates using non-Watson–Crick base pairing-based molecular beacons. Analyst 2014; 139:1436-41. [DOI: 10.1039/c3an02298f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A single, resettable, and sensitive molecular beacon has been developed to operate two-input, three-input, and set–reset logic gates.
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Affiliation(s)
- Jia-Hui Lin
- Department of Chemistry
- National Sun Yat-sen University
- Kaohsiung 80424, Taiwan
| | - Wei-Lung Tseng
- Department of Chemistry
- National Sun Yat-sen University
- Kaohsiung 80424, Taiwan
- School of Pharmacy
- College of Pharmacy
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27
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Tang J, Lu M, Tang D. Target-initiated impedimetric proximity ligation assay with DNAzyme design for in situ amplified biocatalytic precipitation. Analyst 2014; 139:2998-3001. [DOI: 10.1039/c4an00523f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A target-initiated proximity ligation assay protocol with DNAzyme formation was for the first time designed for ultrasensitive impedimetric monitoring of heavy metal ions (silver ions were used in this case) by coupling with an enzymatic biocatalytic precipitation technique.
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Affiliation(s)
- Juan Tang
- Chongqing Key Laboratory of Environmental Materials & Remediation Technologies
- Chongqing University of Arts and Sciences
- Chongqing 402160, P.R. China
- Institute of Analytical Chemistry
- Department of Chemistry
| | - Minghua Lu
- Institute of Environmental and Analytical Science
- School of Chemistry and Chemical Engineering
- Henan University
- Kaifeng 475004, P.R. China
| | - Dianping Tang
- Chongqing Key Laboratory of Environmental Materials & Remediation Technologies
- Chongqing University of Arts and Sciences
- Chongqing 402160, P.R. China
- Institute of Analytical Chemistry
- Department of Chemistry
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28
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Cui J, An M, Wang L. Nanocomposite-based rapid, visual, and selective luminescence turn-on assay for Hg2+ sensing in aqueous media. Talanta 2013; 115:512-7. [DOI: 10.1016/j.talanta.2013.05.069] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 05/28/2013] [Accepted: 05/30/2013] [Indexed: 11/25/2022]
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29
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Lu Q, Zhou Z, Mei Y, Wei W, Liu S. Detection of DNA damage by thiazole orange fluorescence probe assisted with exonuclease III. Talanta 2013; 116:958-63. [PMID: 24148501 DOI: 10.1016/j.talanta.2013.07.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 07/15/2013] [Accepted: 07/16/2013] [Indexed: 11/17/2022]
Abstract
This work reports a fluorescent dye insertion approach for detection of DNA damage. The capture DNA with overhanging 3'-terminus was immobilized on silicon surface to hybridize with target DNA. The intercalation of cyanine dye of thiazole orange (TO) to the double helix structure of DNA (dsDNA) allowed intense enhancement of fluorescence signal. The DNA damage with chemicals led to poor intercalation of TO into double helix structure, resulting in the decrease of the fluorescence signal. This signal decrease could be further enhanced by exonuclease III (Exo III). With this approach, the target DNA could be detected down to 47 fM. Seven chemicals were chosen as models to monitor DNA damage. The results suggested that the present strategy could be developed to detect DNA damage, to classify the damaging mechanism with chemicals and to estimate the toxic effect of chemicals.
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Affiliation(s)
- Qian Lu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Chemistry and Chemical Engineering, Southeast University, Jiangning District 211189, Nanjing, Jiangsu Province, PR China
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30
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Cao X, Liu S, Feng Q, Wang N. Silver nanowire-based electrochemical immunoassay for sensing immunoglobulin G with signal amplification using strawberry-like ZnO nanostructures as labels. Biosens Bioelectron 2013; 49:256-62. [PMID: 23774162 DOI: 10.1016/j.bios.2013.05.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 05/20/2013] [Accepted: 05/20/2013] [Indexed: 12/17/2022]
Abstract
The quick development of nanoscience and nanotechnology has paved the way for ultrasensitive biosensing and analysis. In this work, an ultrasensitive electrochemical immunosensor was developed for the detection of human immunoglobulin G (IgG) by combining with a newly designed trace tag on a disposable immunosensor array. The array was prepared by immobilizing captured antibodies on ultralong Ag nanowires, whilst the trace tag was prepared by loading horseradish peroxidase (HRP)-labeled goat anti-human IgG (HRP-anti-IgG) on thionine (TH)-doped mesoporous ZnO nanostrawberries (MP-ZnO). With a sandwich-type immunoassay format, mainly due to crystalline framework and high surface area of the mesoporous (MP) materials, as well as the superconductivity of silver nanowires, the electrochemical signal was significantly amplified. The linear range of the developed immunosensor is 0.01-200 ng mL(-1) and the detection limit is 4 pg mL(-1) IgG, which make the hierarchically nanostructured composites very promising candidates for the next-generation sandwich-type electrochemical immunoassays.
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Affiliation(s)
- Xia Cao
- School of Biochemical and Pharmaceutical Sciences, Capital Medical University, Beijing 100069, China.
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31
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Kuo CY, Tseng WL. Adenosine-based molecular beacons as light-up probes for sensing heparin in plasma. Chem Commun (Camb) 2013; 49:4607-9. [PMID: 23563586 DOI: 10.1039/c3cc40976g] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This study presents an adenosine-based molecular beacon (MB) for the selective and sensitive detection of heparin based on the competitive binding between heparin and the MB stem to coralyne.
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Affiliation(s)
- Chia-Yin Kuo
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan
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32
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Ding J, Qin W, Zhang Y, Wang X. Potentiometric aptasensing based on target-induced conformational switch of a DNA probe using a polymeric membrane silver ion-selective electrode. Biosens Bioelectron 2013; 45:148-51. [PMID: 23466589 DOI: 10.1016/j.bios.2013.01.052] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 01/28/2013] [Accepted: 01/29/2013] [Indexed: 01/29/2023]
Abstract
In this article, we introduce a general, sensitive, facile, and label-free potentiometric assay based on metal-mediated DNA base pairs. A nucleic acid with one adenosine-5'-triphosphate (ATP) binding sequence (aptamer) in the middle and two cytosine(C)-rich sequences at the lateral portions was employed as a model. A rigid hairpin structure can be formed in the presence of Ag(+) ions, in which the C residues of the spatially separated nucleotides are linked by the ions. The strong interaction between Ag(+) ions and cytosines forms a stable C-Ag(+)-C structure, which could reduce the concentration of silver ions released from the polymeric membrane silver ion-selective electrode (ISE) at the sample-membrane interface and decrease the potential response. In the presence of its target, the aptamer (the loop sequence of the probe) binds specifically to the target via reaction incubation. Such target-binding induced aptamer conformational change prevents the formation of C-Ag(+)-C structure, leaving more silver ions at the sample-membrane interface, which can be detected by the silver ISE. ATP can be quantified in the range of 0.5-3.0 μM with a detection limit of 0.37 μM. The relative standard deviation for 5 μM ATP is 5.5%. For the proposed method, the combination of using ion fluxes of silver ions as modulating reagents and as signal reporters greatly simplifies the detection procedures. In addition, by changing the binding sequence in the middle of the probe, the present detection method will be able to explore new applications of ISE for the detection of a large variety of targets.
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Affiliation(s)
- Jiawang Ding
- Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Yantai, Shandong 264003, PR China
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33
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Petty JT, Giri B, Miller IC, Nicholson DA, Sergev OO, Banks TM, Story SP. Silver clusters as both chromophoric reporters and DNA ligands. Anal Chem 2013; 85:2183-90. [PMID: 23330780 DOI: 10.1021/ac303531y] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Molecular silver clusters conjugated with DNA act as analyte sensors. Our studies evaluate a type of cluster-laden DNA strand whose structure and silver stoichiometry change with hybridization. The sensor strand integrates two functions: the 3' region binds target DNA strands through base recognition while the 5' sequence C(3)AC(3)AC(3)TC(3)A favors formation of a near-infrared absorbing and emitting cluster. This precursor form exclusively harbors an ∼11 silver atom cluster that absorbs at 400 nm and that condenses its single-stranded host. The 3' recognition site associates with a complementary target strand, thereby effecting a 330 nm red-shift in cluster absorption and a background-limited recovery of cluster emission at 790 nm. One factor underlying these changes is sensor unfolding and aggregation. Variations in salt and oligonucleotide concentrations control cluster development by influencing DNA association. Structural studies using fluorescence anisotropy, fluorescence correlation spectroscopy, and size exclusion chromatography show that the sensor-cluster conjugate opens and subsequently dimerizes with hybridization. A second factor contributing to the spectral and photophysical changes is cluster transformation. Empirical silver stoichiometries are preserved through hybridization, so hybridized, dimeric near-infrared conjugates host twice the amount of silver in relation to their violet absorbing predecessors. These DNA structure and net silver stoichiometry alterations provide insight into how DNA-silver conjugates recognize analytes.
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Affiliation(s)
- Jeffrey T Petty
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States.
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Anas A, Jiya J, Rameez MJ, Anand PB, Anantharaman MR, Nair S. Sequential interactions of silver-silica nanocomposite (Ag-SiO2 NC) with cell wall, metabolism and genetic stability of Pseudomonas aeruginosa, a multiple antibiotic-resistant bacterium. Lett Appl Microbiol 2012; 56:57-62. [PMID: 23083417 DOI: 10.1111/lam.12015] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 10/17/2012] [Accepted: 10/17/2012] [Indexed: 12/24/2022]
Abstract
UNLABELLED The study was carried out to understand the effect of silver-silica nanocomposite (Ag-SiO(2) NC) on the cell wall integrity, metabolism and genetic stability of Pseudomonas aeruginosa, a multiple drug-resistant bacterium. Bacterial sensitivity towards antibiotics and Ag-SiO(2) NC was studied using standard disc diffusion and death rate assay, respectively. The effect of Ag-SiO(2) NC on cell wall integrity was monitored using SDS assay and fatty acid profile analysis, while the effect on metabolism and genetic stability was assayed microscopically, using CTC viability staining and comet assay, respectively. Pseudomonas aeruginosa was found to be resistant to β-lactamase, glycopeptidase, sulfonamide, quinolones, nitrofurantoin and macrolides classes of antibiotics. Complete mortality of the bacterium was achieved with 80 μg ml(-1) concentration of Ag-SiO(2) NC. The cell wall integrity reduced with increasing time and reached a plateau of 70% in 110 min. Changes were also noticed in the proportion of fatty acids after the treatment. Inside the cytoplasm, a complete inhibition of electron transport system was achieved with 100 μg ml(-1) Ag-SiO(2) NC, followed by DNA breakage. The study thus demonstrates that Ag-SiO(2) NC invades the cytoplasm of the multiple drug-resistant P. aeruginosa by impinging upon the cell wall integrity and kills the cells by interfering with electron transport chain and the genetic stability. SIGNIFICANCE AND IMPACT OF STUDY Although the synthesis, structural characteristics and biofunction of silver nanoparticles are well understood, their application in antimicrobial therapy is still at its infancy as only a small number of microorganisms are tested to be sensitive to nanoparticles. A thorough knowledge of the mode of interaction of nanoparticles with bacteria at subcellular level is mandatory for any clinical application. The present study deals with the interactions of Ag-SiO2NC with the cell wall integrity, metabolism and genetic stability of Pseudomonas aeruginosa, which would contribute substantially in strengthening the therapeutic applications of silver nanoparticles.
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Affiliation(s)
- A Anas
- Council of Scientific and Industrial Research (CSIR), National Institute of Oceanography (NIO), Cochin, India.
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35
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Shah P, Rørvig-Lund A, Chaabane SB, Thulstrup PW, Kjaergaard HG, Fron E, Hofkens J, Yang SW, Vosch T. Design aspects of bright red emissive silver nanoclusters/DNA probes for microRNA detection. ACS NANO 2012; 6:8803-14. [PMID: 22947065 DOI: 10.1021/nn302633q] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The influence of the nucleic acid secondary structure on the fast (1 h) formation of bright red emissive silver nanoclusters (AgNCs) in a DNA sequence (DNA-12nt-RED-160), designed for the detection of a microRNA sequence (RNA-miR160), was investigated. The findings show that especially the propensity for mismatch self-dimer formation of the DNA probes can be a good indicator for the creation and stabilization of red emissive AgNCs. Also, the role of the thermal stability of the secondary DNA structures (mismatch self-dimer and hairpin monomers) and the observed AgNC red emission intensity were investigated. These findings can form the basis for a rationale to design new red emissive AgNC-based probes. As an example, a bright red emissive AgNC-based DNA probe was designed for RNA-miR172 detection. The latter opens the possibility to create a variety of AgNC-based DNA probes for the specific detection of plant and animal miRNAs.
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Affiliation(s)
- Pratik Shah
- Department of Plant Biology and Biotechnology, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Copenhagen, Denmark
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Babu E, Mareeswaran PM, Rajagopal S. Highly sensitive optical biosensor for thrombin based on structure switching aptamer-luminescent silica nanoparticles. J Fluoresc 2012; 23:137-46. [PMID: 22965479 DOI: 10.1007/s10895-012-1127-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Accepted: 09/02/2012] [Indexed: 12/17/2022]
Abstract
We describe here the construction of a sensitive and selective optical sensor system for the detection of human α-thrombin. The surface functionalized luminescent [Ru(dpsphen)(3)](4-) (dpsphen-4,7-diphenyl-1,10-phenanthroline disulfonate) ion doped silica nanoparticles (SiNPs) with a size ~70 nm have been prepared. The DABCYL (2-(4-dimethylaminophenyl)diazenyl-benzoic acid) quencher labeled thrombin binding aptamer is conjugated to the surface of SiNPs using BS(3) (bis(sulfosuccinimidyl) suberate) as a cross-linker, resulting in the conformational change of aptamer to form G-quadruplex structure upon the addition of thrombin. The binding event is translated into a change in the luminescence intensity of Ru(II) complex via FRET mechanism, due to the close proximity of DABCYL quencher with SiNPs. The selective detection of thrombin using the SiNPs-aptamer system up to 4 nM is confirmed by comparing its sensitivity towards other proteins. This work demonstrates the application of simple aptamer-SiNPs conjugate as a highly sensitive system for the detection of thrombin and also it is highly sensitive towards thrombin in the presence of other proteins and complex medium such as BSA.
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Affiliation(s)
- Ethiraju Babu
- School of Chemistry, Madurai Kamaraj University, Madurai 625 021, India
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Photochemically relevant DNA-based molecular systems enabling chemical and signal transductions and their analytical applications. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2012. [DOI: 10.1016/j.jphotochemrev.2012.03.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Liu H, Wang Y, Shen A, Zhou X, Hu J. Highly selective and sensitive method for cysteine detection based on fluorescence resonance energy transfer between FAM-tagged ssDNA and graphene oxide. Talanta 2012; 93:330-5. [DOI: 10.1016/j.talanta.2012.02.044] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 02/20/2012] [Accepted: 02/22/2012] [Indexed: 11/25/2022]
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39
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Lin YH, Tseng WL. A room-temperature adenosine-based molecular beacon for highly sensitive detection of nucleic acids. Chem Commun (Camb) 2012; 48:6262-4. [PMID: 22531390 DOI: 10.1039/c2cc31382k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
This study developed a simple, sensitive, and selective molecular beacon for detecting nucleic acids at room temperature based on coralyne induced conformational change of a MB through A(2)-coralyne-A(2) coordination.
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Affiliation(s)
- Yen-Hsiu Lin
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan
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40
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Liu JM, Yan XP. Competitive aptamer bioassay for selective detection of adenosine triphosphate based on metal-paired molecular conformational switch and fluorescent gold nanoclusters. Biosens Bioelectron 2012; 36:135-41. [PMID: 22560440 DOI: 10.1016/j.bios.2012.04.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 03/29/2012] [Accepted: 04/04/2012] [Indexed: 10/28/2022]
Abstract
A competitive aptamer bioassay was developed for the selective detection of adenosine triphosphate (ATP). The proposed bioassay employed the T-Hg-T induced hairpin-structure as the molecule conformational switch (MCS), aptamer as a specific recognizer, and mercaptoundecanoic acid modified gold nanoclusters (MUA-AuNCs) as a sensitive signal reporter. The T-rich MCS ssDNA with the sequence complementary with that for the aptamer of ATP was bound with Hg(2+) to form the metal-paired hairpin-structure. Addition of the aptamer and its target biomolecule ATP resulted in a competitive aptamer bioassay. The aptamer competed with Hg(2+) to hybridize with T-rich MCS ssDNA, thereby destroyed the hairpin-structure. As a result, the Hg(2+) was released and the signal transduction was achieved. The ATP affected the interaction between aptamer and hairpin-structure, thus mediated the release of Hg(2+), which was sensitively quantified by fluorescent MUA-AuNCs. Under selected conditions, the developed method allowed sensitive and selective detection of ATP with a linear range of 100-2000 nM and a detection limit (3s) of 48 nM. The relative standard deviation for sixty replicate detections of 200 nM ATP was 2.1%, and the recoveries of the spiked ATP in urine samples ranged from 89% to 105%. The developed metal-paired MCS can be easily extended to the sensitive and selective detection of other biomolecules by changing the base sequence of hairpin structure and choosing the corresponding aptamer for the target biomolecule.
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Affiliation(s)
- Jing-Min Liu
- State Key Laboratory of Medicinal Chemical Biology, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, China
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41
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Zhang R, Ye Z, Yin Y, Wang G, Jin D, Yuan J, Piper JA. Developing Red-Emissive Ruthenium(II) Complex-Based Luminescent Probes for Cellular Imaging. Bioconjug Chem 2012; 23:725-33. [DOI: 10.1021/bc200506w] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Run Zhang
- State Key Laboratory of Fine
Chemicals, School of Chemistry, Dalian University of Technology, Dalian 116024, P. R. China
| | - Zhiqiang Ye
- State Key Laboratory of Fine
Chemicals, School of Chemistry, Dalian University of Technology, Dalian 116024, P. R. China
| | - Yuejiao Yin
- State Key Laboratory of Fine
Chemicals, School of Chemistry, Dalian University of Technology, Dalian 116024, P. R. China
| | - Guilan Wang
- State Key Laboratory of Fine
Chemicals, School of Chemistry, Dalian University of Technology, Dalian 116024, P. R. China
| | - Dayong Jin
- MQ Photonics Centre, Faculty
of Science, Macquarie University, NSW 2109,
Sydney, Australia
| | - Jingli Yuan
- State Key Laboratory of Fine
Chemicals, School of Chemistry, Dalian University of Technology, Dalian 116024, P. R. China
| | - James A. Piper
- MQ Photonics Centre, Faculty
of Science, Macquarie University, NSW 2109,
Sydney, Australia
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42
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Wang Y, Geng F, Xu H, Qu P, Zhou X, Xu M. A label-free oligonucleotide based thioflavin-T fluorescent switch for Ag+ detection with low background emission. J Fluoresc 2012; 22:925-9. [PMID: 22234459 DOI: 10.1007/s10895-011-1031-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Accepted: 12/28/2011] [Indexed: 10/14/2022]
Abstract
A novel fluorescent Ag(+) sensor was developed based on the label-free silver (I) specific oligonucleotide (SSO) and Thioflavine T (ThT) monomer-excimer switch. C-rich SSO which contain C-C mismatched base pairs can selectively bind to Ag(+) ions and the formed duplexes which constructed by C-Ag(+)-C structure are thermally stabilized without largely altering the double helical structure. ThT give very weak fluorescent in bulk solution and/or in the presence of SSO. However ThT shows high fluorescence in the presence of SSO and Ag(+) at the same time mainly because ThT excimer, which has the high quantum yield, formed and stabilized in the minor or major groove. Based on the discovery, we developed the novel Ag(+) sensor. Under the optimum condition, the selectivity of this system for Ag(+) over other metal ions in aqueous solution is remarkably high, and Ag(+) can be quantified over the dynamic range of 30-450 nM, with a limit of detection of ~16 nM and a linear correlation coefficient of 0.995.
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Affiliation(s)
- Yongxiang Wang
- Henan Key Laboratory Cultivation Base of Nanobiological Analytical Chemistry, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, China
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43
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Ji H, Dong H, Yan F, Lei J, Ding L, Gao W, Ju H. Visual Scanometric Detection of DNA through Silver Enhancement Regulated by Gold-Nanoparticle Aggregation with a Molecular Beacon as the Trigger. Chemistry 2011; 17:11344-9. [DOI: 10.1002/chem.201100563] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2011] [Indexed: 11/11/2022]
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Petty JT, Sengupta B, Story SP, Degtyareva NN. DNA sensing by amplifying the number of near-infrared emitting, oligonucleotide-encapsulated silver clusters. Anal Chem 2011; 83:5957-64. [PMID: 21702495 PMCID: PMC4201625 DOI: 10.1021/ac201321m] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A bifunctional oligonucleotide integrates in situ synthesis of a fluorogenic silver cluster with recognition of a target DNA sequence. With the template C(3)AC(3)AC(3)GC(3)A, a complex forms with 10 silver atoms that possesses electronic transitions in the near-infrared and that is detected at nanomolar concentrations using diode laser excitation. Pendant to this cluster encoding region, the recognition component binds a target DNA strand through hybridization, and decoupling of these two regions of the composite sensor renders a modular sensor for specific oligonucleotides. A target is detected using a quencher strand that bridges the cluster template and recognition components and disturbs cluster binding, as indicated by static quenching. Competitive displacement of the quencher by the target strand restores the favored cluster environment, and our key finding is that this exchange enhances emission through a proportional increase in the number of emissive clusters. DNA detection is also accomplished in serum-containing buffers by taking advantage of the high brightness of this fluorophore and the inherently low endogenous background in the near-infrared spectral region. Cluster stability in this biological environment is enhanced by supplementing the solutions with Ag(+).
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Affiliation(s)
- Jeffrey T Petty
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States.
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Silver nanoparticles fluorescence enhancement effect for determination of nucleic acids with kaempferol–Al(III). Talanta 2011; 84:1188-94. [DOI: 10.1016/j.talanta.2011.03.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2011] [Revised: 02/16/2011] [Accepted: 03/12/2011] [Indexed: 11/21/2022]
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