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Zhao H, Yan Y, Chen M, Hu T, Wu K, Liu H, Ma C. Exonuclease III-assisted signal amplification strategy for sensitive fluorescence detection of polynucleotide kinase based on poly(thymine)-templated copper nanoparticles. Analyst 2020; 144:6689-6697. [PMID: 31598619 DOI: 10.1039/c9an01659g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A sensitive and label-free fluorometric method has been developed for the determination of polynucleotide kinase (PNK) activity, by employing exonuclease III (Exo III)-assisted cyclic signal amplification and poly(thymine)-templated copper nanoparticles (polyT-CuNPs). In the presence of PNK, cDNA with 5'-hydroxyl termini was phosphorylated and then hybridized with tDNA to form the cDNA/tDNA duplex, which subsequently triggered the λ exonuclease cleavage reaction, eventually resulting in the release of tDNA. The released tDNA could unfold the hairpin structure of HP DNA to generate partially complementary duplex (tDNA/HP DNA), wherein the HP DNA possessed T-rich sequences (T30) and tDNA recognition sequence. With the help of Exo III digestion, the tDNA was able to initiate the cycle for the generation of T-rich sequences, the template for the formation of fluorescent CuNPs. Conversely, the cDNA could not be cleaved by λ exonuclease without PNK and individual HP DNA could not be hydrolyzed by Exo III. The T-rich sequence was caged in HP DNA, resulting in a weak fluorescence signal. Under optimized conditions, the fluorescence intensity was linearly correlated to a concentration range of 0.001 to 1 U mL-1 with a low detection limit of 2 × 10-4 U mL-1. Considering the intriguing analytical performance, this approach could be explored to screen T4 PNK inhibitors and hold promising applications in drug discovery and disease therapy.
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Affiliation(s)
- Han Zhao
- School of Life Sciences, Central South University, Changsha 410013, China.
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2
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Tian R, Li Y, Bai J. Hierarchical assembled nanomaterial paper based analytical devices for simultaneously electrochemical detection of microRNAs. Anal Chim Acta 2019; 1058:89-96. [DOI: 10.1016/j.aca.2019.01.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 12/28/2018] [Accepted: 01/24/2019] [Indexed: 12/17/2022]
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Cui YX, Feng XN, Li XY, Zhang YP, Tang AN, Kong DM. Trifunctional integrated DNA-based universal sensing platform for detection of diverse biomolecules in one-pot isothermal exponential amplification mode. Chem Commun (Camb) 2019; 55:7603-7606. [DOI: 10.1039/c9cc03758f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Template constructed with only a short single-stranded DNA is necessary; it is first recognized by the target enzyme, then multiple amplification cycles are initiated, achieving ultra-high sensitivity by a one-pot isothermal reaction.
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Affiliation(s)
- Yun-Xi Cui
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Centre for Analytical Sciences
- College of Chemistry
- Nankai University
| | - Xue-Nan Feng
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Centre for Analytical Sciences
- College of Chemistry
- Nankai University
| | - Xiao-Yu Li
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Centre for Analytical Sciences
- College of Chemistry
- Nankai University
| | - Yu-Peng Zhang
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Centre for Analytical Sciences
- College of Chemistry
- Nankai University
| | - An-Na Tang
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Centre for Analytical Sciences
- College of Chemistry
- Nankai University
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- Research Centre for Analytical Sciences
- College of Chemistry
- Nankai University
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Ma L, Zhang M, Yang A, Wang Q, Qu F, Qu F, Kong RM. Sensitive fluorescence detection of heparin based on self-assembly of mesoporous silica nanoparticle–gold nanoclusters with emission enhancement characteristics. Analyst 2018; 143:5388-5394. [PMID: 30295305 DOI: 10.1039/c8an01556b] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Sensitive fluorescence detection of heparin based on self-assembly of mesoporous silica nanoparticle–gold nanoclusters with emission enhancement characteristics was reported.
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Affiliation(s)
- Lin Ma
- College of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu
- P. R. China
| | - Mengyue Zhang
- College of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu
- P. R. China
| | - Aijun Yang
- Center for Reproductive medicine
- Affiliated Hospital of Jining Medical University
- Jining
- P. R. China
| | - Qin Wang
- Center for Reproductive medicine
- Affiliated Hospital of Jining Medical University
- Jining
- P. R. China
| | - Fei Qu
- College of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu
- P. R. China
| | - Fengli Qu
- College of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu
- P. R. China
| | - Rong-Mei Kong
- College of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu
- P. R. China
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Zhang X, Kong R, Tan Q, Qu F, Qu F. A label-free fluorescence turn-on assay for glutathione detection by using MnO 2 nanosheets assisted aggregation-induced emission-silica nanospheres. Talanta 2017; 169:1-7. [DOI: 10.1016/j.talanta.2017.03.050] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 03/08/2017] [Accepted: 03/16/2017] [Indexed: 12/12/2022]
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Wang LJ, Zhang Q, Tang B, Zhang CY. Single-Molecule Detection of Polynucleotide Kinase Based on Phosphorylation-Directed Recovery of Fluorescence Quenched by Au Nanoparticles. Anal Chem 2017; 89:7255-7261. [PMID: 28585816 DOI: 10.1021/acs.analchem.7b01783] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
5'-Polynucleotide kinase such as T4 polynucleotide kinase (T4 PNK) may catalyze the phosphorylation of 5'-hydroxyl termini in nucleic acids, playing a crucial role in DNA replication, DNA recombination, and DNA damage repair. Here, we demonstrate for the first time single-molecule detection of PNK based on phosphorylation-directed recovery of fluorescence quenched by Au nanoparticle (AuNP) in combination with lambda exonuclease-mediated cleavage reaction. In the presence of PNK, the γ-phosphate group from adenosine triphosphate (ATP) is transferred to 5'-hydroxyl terminus, resulting in 5'-phosphorylation of the hairpin probe. The phosphorylated hairpin probes may function as the substrates of lambda exonuclease and enable the removal of 5' mononucleotides from the stem, leading to the unfolding of hairpin structure and the formation of binding probes. The resultant binding probes may specifically hybridize with the AuNP-modified capture probes, forming double-strand DNA (dsDNA) duplexes with 5'-phosphate groups as the substrates of lambda exonuclease and subsequently leading to the cleavage of capture probes and the liberation of Cy5 molecules and the binding probes. The released binding probes may further hybridize with new capture probes, inducing cycles of digestion-release-hybridization and consequently the release of numerous Cy5 molecules. Through simply monitoring Cy5 molecules with total internal reflection fluorescence (TIRF)-based imaging, PNK activity can be quantitatively measured. This assay is very sensitive with a limit of detection of 9.77 × 10-8 U/μL, and it may be further used to screen the PNK inhibitors and measure PNK in cancer cell extracts.
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Affiliation(s)
- Li-Juan Wang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University , Jinan 250014, China
| | - Qianyi Zhang
- Nantou High School Shenzhen , Shenzhen, 518052, China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University , Jinan 250014, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University , Jinan 250014, China
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Zhang L, Liu Y, Li Y, Zhao Y, Wei W, Liu S. Sensitive electrochemical assaying of DNA methyltransferase activity based on mimic-hybridization chain reaction amplified strategy. Anal Chim Acta 2016; 933:75-81. [DOI: 10.1016/j.aca.2016.05.044] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 05/16/2016] [Accepted: 05/23/2016] [Indexed: 11/29/2022]
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8
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Tang S, Tong P, You X, Lu W, Chen J, Li G, Zhang L. Label free electrochemical sensor for Pb2+ based on graphene oxide mediated deposition of silver nanoparticles. Electrochim Acta 2016. [DOI: 10.1016/j.electacta.2015.11.040] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Abstract
Isothermal amplification of nucleic acids is a simple process that rapidly and efficiently accumulates nucleic acid sequences at constant temperature. Since the early 1990s, various isothermal amplification techniques have been developed as alternatives to polymerase chain reaction (PCR). These isothermal amplification methods have been used for biosensing targets such as DNA, RNA, cells, proteins, small molecules, and ions. The applications of these techniques for in situ or intracellular bioimaging and sequencing have been amply demonstrated. Amplicons produced by isothermal amplification methods have also been utilized to construct versatile nucleic acid nanomaterials for promising applications in biomedicine, bioimaging, and biosensing. The integration of isothermal amplification into microsystems or portable devices improves nucleic acid-based on-site assays and confers high sensitivity. Single-cell and single-molecule analyses have also been implemented based on integrated microfluidic systems. In this review, we provide a comprehensive overview of the isothermal amplification of nucleic acids encompassing work published in the past two decades. First, different isothermal amplification techniques are classified into three types based on reaction kinetics. Then, we summarize the applications of isothermal amplification in bioanalysis, diagnostics, nanotechnology, materials science, and device integration. Finally, several challenges and perspectives in the field are discussed.
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Affiliation(s)
- Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Feng Chen
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Qian Li
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China.,School of Life Science & Technology, ShanghaiTech University , Shanghai 200031, China
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Zhou L, Shen X, Sun N, Wang K, Zhang Y, Pei R. Label-free fluorescence light-up detection of T4 polynucleotide kinase activity using the split-to-intact G-quadruplex strategy by ligation-triggered and toehold-mediated strand displacement release. Analyst 2015; 140:5450-3. [DOI: 10.1039/c5an01032b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A label-free, fluorescence light-up detection method for T4 polynucleotide kinase activity has been developed using the split-to-intact G-quadruplex strategy.
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Affiliation(s)
- Lu Zhou
- Key Laboratory of Nano-Bio Interfacce
- Division of Nanobiomedicine
- Suzhou Insitute of Nano-Tech and Nano-Bionics
- Chinese Academy of Science
- Suzhou
| | - Xiaoqiang Shen
- Key Laboratory of Nano-Bio Interfacce
- Division of Nanobiomedicine
- Suzhou Insitute of Nano-Tech and Nano-Bionics
- Chinese Academy of Science
- Suzhou
| | - Na Sun
- Key Laboratory of Nano-Bio Interfacce
- Division of Nanobiomedicine
- Suzhou Insitute of Nano-Tech and Nano-Bionics
- Chinese Academy of Science
- Suzhou
| | - Kewei Wang
- Key Laboratory of Nano-Bio Interfacce
- Division of Nanobiomedicine
- Suzhou Insitute of Nano-Tech and Nano-Bionics
- Chinese Academy of Science
- Suzhou
| | - Yuanyuan Zhang
- Key Laboratory of Nano-Bio Interfacce
- Division of Nanobiomedicine
- Suzhou Insitute of Nano-Tech and Nano-Bionics
- Chinese Academy of Science
- Suzhou
| | - Renjun Pei
- Key Laboratory of Nano-Bio Interfacce
- Division of Nanobiomedicine
- Suzhou Insitute of Nano-Tech and Nano-Bionics
- Chinese Academy of Science
- Suzhou
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