1
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Oh DE, Kim HB, Kim TH. Electrochemical DNA Cleavage Sensing for EcoRV Activity and Inhibition with an ERGO Electrode. BIOSENSORS 2024; 14:73. [PMID: 38391992 PMCID: PMC10886839 DOI: 10.3390/bios14020073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 02/24/2024]
Abstract
An electrochemically reduced graphene oxide (ERGO) electrode-based electrochemical assay was developed for rapid, sensitive, and straightforward analysis of both activity and inhibition of the endonuclease EcoRV. The procedure uses a DNA substrate designed for EcoRV, featuring a double-stranded DNA (dsDNA) region labeled with methylene blue (MB) and a single-stranded DNA (ssDNA) region immobilized on the ERGO surface. The ERGO electrode, immobilized with the DNA substrate, was subsequently exposed to a sample containing EcoRV. Upon enzymatic hydrolysis, the cleaved dsDNA fragments were detached from the ERGO surface, leading to a decrease in the MB concentration near the electrode. This diminished the electron transfer efficiency for MB reduction, resulting in a decreased reduction current. This assay demonstrates excellent specificity and high sensitivity, with a limit of detection (LOD) of 9.5 × 10-3 U mL-1. Importantly, it can also measure EcoRV activity in the presence of aurintricarboxylic acid, a known inhibitor, highlighting its potential for drug discovery and clinical diagnostic applications.
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Affiliation(s)
| | | | - Tae Hyun Kim
- Department of Chemistry, Soonchunhyang University, Asan 31538, Republic of Korea; (D.E.O.); (H.B.K.)
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2
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Fredrick D, Yourston L, Krasnoslobodtsev AV. Detection of cancer-associated miRNA using a fluorescence switch of AgNC@NA and guanine-rich overhang sequences. LUMINESCENCE 2023; 38:1385-1392. [PMID: 36843363 DOI: 10.1002/bio.4471] [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: 10/07/2022] [Revised: 02/03/2023] [Accepted: 02/18/2023] [Indexed: 02/28/2023]
Abstract
DNA-templated silver nanoclusters (AgNC@DNA) are a novel type of nanomaterial with advantageous optical properties. Only a few atoms in size, the fluorescence of nanoclusters can be tuned using DNA overhangs. In this study, we explored the properties of AgNCs manufactured on a short single-stranded (dC)12 when adjacent G-rich sequences (dGN , with N = 3-15) were added. The 'red' emission of AgNC@dC12 with λMAX = 660 nm dramatically changed upon the addition of a G-rich overhang with NG = 15. The pattern of the emission-excitation matrix (EEM) suggested the emergence of two new emissive states at λMAX = 575 nm and λMAX = 710 nm. The appearance of these peaks provides an effective way to design biosensors capable of detecting specific nucleic acid sequences with low fluorescence backgrounds. We used this property to construct an NA-based switch that brings AgNC and the G overhang near one another, turning 'ON' the new fluorescence peaks only when a specific miRNA sequence is present. Next, we tested this detection switch on miR-371, which is overexpressed in prostate cancer. The results presented provide evidence that this novel fluorescent switch is both sensitive and specific with a limit of detection close to 22 picomoles of the target miR-371 molecule.
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Affiliation(s)
- Dylan Fredrick
- Department of Physics, University of Nebraska Omaha, 6001 Dodge Street, Omaha, Nebraska, USA
| | - Liam Yourston
- Department of Physics, University of Nebraska Omaha, 6001 Dodge Street, Omaha, Nebraska, USA
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3
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Yan X, Shu Q, Zhao K, Xiao Y, Ai F, Zheng X. Chemiluminescence "signal-on-off" dual signals ratio biosensor based on single-stranded DNA functions as guy wires to detect EcoR V. Talanta 2021; 235:122749. [PMID: 34517617 DOI: 10.1016/j.talanta.2021.122749] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 07/25/2021] [Accepted: 07/27/2021] [Indexed: 11/29/2022]
Abstract
Signal output mode is the important part of biosensor. In general, "signal on" and "signal off" are two common output modes. The development of dual signals-based ratio analysis as a powerful diagnostic tool has attracted widespread attention in the biosensor field in recent years. Dual signals ratio sensors with "signal on" and "signal off" are more favored because of their low background signal and better sensitivity and selectivity. In this study, inspired by the idea that EcoR V can cut specific sites of DNA to produce two corresponding fragments, and by using the capturing probe as guy wires, a reliable and sensitive method for EcoR V assay is developed based on the ratio of dual chemiluminescence (CL) signals for the first time. In particular, in the existence of the objective EcoR V, the substrate DNA would be degraded into two double stranded oligonucleotides with blunt ends which include the sequence I and the sequence II, then they can separately compete with two different corresponding capture probes on magnetic beads (MBs). One of capture probe hybridized with the sequence I containing more guanine (G) bases that reacted with the phenylglyoxal (PG) to produce chemical reaction which triggered a positive CL signal output I + CL as "signal-on"; another capture probe is priority to hybridize the sequence II, which triggered the weaker reporter DNA linked with horseradish peroxidase (HRP) probe to fall off the MBs, thereby outputting a negative CL signal I-CL as "signal-off". By comparing the linear relation and the correlation coefficient, the I-CL/I + CL ratio method has better linear relation (0.01-10 U/mL) and higher sensitivity (0.0045 U/mL). In addition, this developed strategy of high selectivity which can directly detect low concentration of target EcoR V in human serum, and thus this dual ratio biosensor might offer a promising detection approach for clinical diagnostics.
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Affiliation(s)
- Xiluan Yan
- School of Resources, Environmental, and Chemical Engineering, Nanchang University, Nanchang, 330031, China
| | - Qinglei Shu
- School of Resources, Environmental, and Chemical Engineering, Nanchang University, Nanchang, 330031, China
| | - Kun Zhao
- School of Resources, Environmental, and Chemical Engineering, Nanchang University, Nanchang, 330031, China
| | - Yipi Xiao
- Department of Orthopedics, Hongdu Traditional Chinese Medicine Hospital, Nanchang, 330031, China
| | - Fanrong Ai
- School of Mechanical and Electrical Engineering, Nanchang University, Nanchang, 330031, China
| | - Xiangjuan Zheng
- College of Chemistry, Nanchang University, Nanchang, 330031, China.
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4
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Chen ZP, Zhang HM, Yang P, Yuan R, Li Y, Liang WB. No-nonspecific recognition-based amplification strategy for endonuclease activity screening with dual-color DNA nano-clew. Biosens Bioelectron 2021; 190:113446. [PMID: 34166945 DOI: 10.1016/j.bios.2021.113446] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 06/09/2021] [Accepted: 06/15/2021] [Indexed: 10/21/2022]
Abstract
The inevitable nonspecific recognition severely restricted widely used nucleic acid amplification strategies, which has become an urgent problem in current scientific research. Herein, we developed a novel no-nonspecific recognition-based amplification strategy to construct dual-color dye loaded nano-clew as ultrabright illuminant for screening endonuclease activity with Escherichia coliRY13 I (EcoR I) as a model, which overcame some major drawbacks such as nonspecific recognition and photobleaching. Typically, the target endonuclease induces cleavage of the customized dumbbell-shape substrate (DSS) to generate two same triggers that can initiate the rolling circle amplification (RCA) to prepare long single-strand DNA (lssDNA), which could self-assemble into irregular DNA nano-clew based on the electrostatic interactions with Mg2+ to furtherly capture the donor and accepter fluorophore proximately, constructing the dye loaded nano-clew with dual-color fluorescence (FL) emission to resist photobleaching. Importantly, in absence of EcoR I, even if the DSS could combine with circular template a little, the reaction system performed hardly RCA reaction due to no cohesive terminus, resulting an extremely low background fluorescence signal because of the prevention of nonspecific RCA reaction. As expected, the proposed sensing platform with a low limit of detection (LOD) of 3.4 × 10-7 U/μL was demonstrated to work well for endonuclease inhibitors screening also. Furthermore, the proposed no-nonspecific recognition strategy could be readily extended to various DNA or RNA enzymes such as DNA methyltransferase, DNA repair-related enzymes and polynucleotide kinase just by simply changing the recognition sequence in the DNA substrate, performing great potential of endonucleases-related clinical diagnosis and drugs discovery.
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Affiliation(s)
- Zhao-Peng Chen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Hao-Min Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Peng Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Yan Li
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China.
| | - Wen-Bin Liang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China.
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5
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Shen YM, Tian R, Ma HY, Sun XH. A new fluorescence method for detection of famotidine based on polyethyleneimine-templated Ag nanoclusters. LUMINESCENCE 2020; 36:705-710. [PMID: 33300191 DOI: 10.1002/bio.3992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 11/30/2020] [Accepted: 12/06/2020] [Indexed: 02/03/2023]
Abstract
A rapid, simple, inexpensive fluorescence analysis method for determination of famotidine based on polyethyleneimine (PEI)-capped Ag nanoclusters (PEI-Ag NCs) was developed. The study showed that addition of famotidine could cause efficient quenching of PEI-Ag NC fluorescence, as the presence of famotidine could cause aggregation of Ag NCs and quench its fluorescence. The sensitivity and selectivity of the method were investigated and experimental conditions such as buffer type, pH, temperature, and reaction time were optimized. Under optimized conditions, the results showed a linear profile from 3.7 × 10-8 to 3.7 × 10-5 mol/L, and had a detection limit of 1.6 × 10-9 mol/L (S/N = 3).
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Affiliation(s)
- Yu-Mang Shen
- Department of Chemistry and Chemical Engineering, Yan'an University, Yan'an Key Laboratory of Analytical Technology and Detection, Yan'an, China
| | - Rui Tian
- Department of Chemistry and Chemical Engineering, Yan'an University, Yan'an Key Laboratory of Analytical Technology and Detection, Yan'an, China
| | - Hong-Yan Ma
- Department of Chemistry and Chemical Engineering, Yan'an University, Yan'an Key Laboratory of Analytical Technology and Detection, Yan'an, China
| | - Xue-Hua Sun
- Department of Chemistry and Chemical Engineering, Yan'an University, Yan'an Key Laboratory of Analytical Technology and Detection, Yan'an, China
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6
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Tang Z, Liu H, Chen M, Ma C. Label-free one-step fluorescent method for the detection of endonuclease activity based on thioflavin T/G-quadruplex. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 228:117823. [PMID: 31767417 DOI: 10.1016/j.saa.2019.117823] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 11/06/2019] [Accepted: 11/18/2019] [Indexed: 06/10/2023]
Abstract
Endonucleases, one of the basic tool enzymes of modern molecular biology and medical genetics, have also been clarified as the potential targets for antimicrobial and antiviral drugs screening. However, traditional assays to monitor endonuclease activity can be expensive, time-consuming, or laborious. In order to provide new detective platform, we proposed a novel label-free one-step fluorescent method for the detection of endonuclease activity based on cleavage-induced G-quadruplex formation. In this detection system, a simple DNA probe can spontaneously form a duplex structure with recognition sites of EcoRI and prevent the generation of the G-quadruplex. Once EcoRI is present, the recognition sites in the duplex DNA are cleavage, producing a free guanine-rich sequence to form G-quadruplex. When thioflavin T (ThT) is added, a strong fluorescence signal is given by ThT/G-quadruplex, and therefore the EcoRI activity can be detected. After systematic investigation and optimization, this method has gained a sensitive limit of detection at 0.75 U/mL, and a wide detection range between 0.75 U/mL and 120 U/mL. Furthermore, the inhibitory effect of 5-fluorouracil on EcoRI activity was verified and IC50 was calculated. Taken together, these experimental results have proven that this turn-on fluorescent method has considerable analytical performances. As far as we are concerned, this method is the first reported EcoRI assay based on ThT/G-quadruplex, and only one kind of probe and one kind of dye are involved, providing one of the simplest detective strategies on EcoRI. More importantly, the convenience and cost make this one-step method quite attractive for application transformation. Therefore, we hope this method could be a hopeful option for EcoRI activity determination, and further to help monitoring the quality of tool enzymes and promote the development of high-through automatic drug screening system.
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Affiliation(s)
- Zhenwei Tang
- School of Life Sciences, Central South University, Changsha 410013, China; Clinical Medicine Eight-year Program, Xiangya Medical School of Central South University, Changsha 410013, China
| | - Haisheng Liu
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Mingjian Chen
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Changbei Ma
- School of Life Sciences, Central South University, Changsha 410013, China.
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7
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Zhang B, Wei C. The sensitive detection of ATP and ADA based on turn-on fluorescent copper/silver nanoclusters. Anal Bioanal Chem 2020; 412:2529-2536. [PMID: 32043202 DOI: 10.1007/s00216-020-02476-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/27/2020] [Accepted: 01/31/2020] [Indexed: 11/25/2022]
Abstract
A simple turn-on fluorescence strategy is proposed for the detection of ATP based on DNA-stabilized copper/silver nanoclusters (DNA-Cu/Ag NCs). The fluorescence intensity of DNA-Cu/Ag NCs increases significantly in the presence of ATP, because the specific interaction between ATP and its aptamer causes two darkish Cu/Ag NCs to be situated at the 5' and 3' termini close to each other. A limit of detection (LOD) of 7.0 μM is found, in a linear range of 2-18 mM, and the proposed sensor is simple, sensitive, and selective. Additionally, the DNA-Cu/Ag NCs/ATP system is further developed into a sensor for ADA detection and demonstrates a linear response to ADA from 5 to 50 U/L with a LOD of 5 U/L. The proposed method is also shown to be successful in detecting ATP and ADA in a solution of fetal bovine serum.
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Affiliation(s)
- Baozhu Zhang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Molecular Science, Shanxi University, Taiyuan, 030006, Shanxi, China
- College of Chemistry and Chemical Engineering, Jinzhong University, Yuci, 030619, Shanxi, China
| | - Chunying Wei
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Molecular Science, Shanxi University, Taiyuan, 030006, Shanxi, China.
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8
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Gu J, Qiao Z, He X, Yu Y, Lei Y, Tang J, Shi H, He D, Wang K. Enzyme-free amplified detection of miRNA based on target-catalyzed hairpin assembly and DNA-stabilized fluorescent silver nanoclusters. Analyst 2020; 145:5194-5199. [DOI: 10.1039/d0an00545b] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A simple, cost-effective, sensitive, and selective strategy was developed for microRNA analysis using target-catalyzed hairpin assembly and fluorescent silver nanoclusters.
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Affiliation(s)
- Jinqing Gu
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- College of Biology
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
| | - Zhenzhen Qiao
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- College of Biology
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
| | - Xiaoxiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- College of Biology
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
| | - Yanru Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- College of Biology
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
| | - Yanli Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- College of Biology
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
| | - Jinlu Tang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- College of Biology
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
| | - Hui Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- College of Biology
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
| | - Dinggeng He
- State Key Laboratory of Developmental Biology of Freshwater Fish
- College of Life Sciences
- Hunan Normal University
- Changsha 410081
- China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- College of Biology
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
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9
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Kermani HA, Hosseini M, Dadmehr M. DNA-Templated Silver Nanoclusters for DNA Methylation Detection. Methods Mol Biol 2019; 1811:173-182. [PMID: 29926453 DOI: 10.1007/978-1-4939-8582-1_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
DNA methylation entails the covalent addition of a methyl group to C-5 position of cytosine by a family of DNA methyltransferase enzymes and has a significant role in gene regulation. Epigenetic changes such as DNA methylation of CpG islands located in the promoter region of some tumor suppressor genes are very common in human diseases such as cancer. Detection of aberrant methylation pattern could serve as an excellent diagnostic approach. It is key to develop methods for the direct and simple detection of methylated DNA or of methyltransferase activity without using antibodies, chemical modification, labeling and enzymatic treatments. In this study, we employ DNA-templated silver nanoclusters for detection of DNA methylation. This method entails use of cytosine rich DNA sequence as an effective template. By monitoring changes in fluorescence intensity, DNA methylation and DNA methyltransferase activity is detected. Upon DNA methylation, the fluorescence intensity of DNA templated Ag/NCs is decreased in a linear range when the concentration of methylated DNA is increased.
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Affiliation(s)
- Hanie Ahmadzade Kermani
- Department of Life Science Engineering, Faculty of New Science and Technologies, University of Tehran, Tehran, Iran
| | - Morteza Hosseini
- Department of Life Science Engineering, Faculty of New Science and Technologies, University of Tehran, Tehran, Iran.
| | - Mehdi Dadmehr
- Department of Biotechnology, Payeme Noor University, Tehran, Iran
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10
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Sang F, Li G, Li J, Pan J, Zhang Z, Zhang X. A hairpin-type DNA probe for direct colorimetric detection of endonuclease activity and inhibition based on the deaggregation of gold nanoparticles. Mikrochim Acta 2019; 186:100. [DOI: 10.1007/s00604-018-3164-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 12/09/2018] [Indexed: 12/13/2022]
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11
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Kim S, Gang J. The detection of a mismatched DNA by using hairpin DNA-templated silver nanoclusters. Anal Biochem 2018; 549:171-173. [DOI: 10.1016/j.ab.2018.03.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 03/26/2018] [Accepted: 03/27/2018] [Indexed: 01/08/2023]
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12
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A molecular beacon based on DNA-templated silver nanoclusters for the highly sensitive and selective multiplexed detection of virulence genes. Talanta 2017; 181:24-31. [PMID: 29426508 DOI: 10.1016/j.talanta.2017.12.049] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/30/2017] [Accepted: 12/14/2017] [Indexed: 10/18/2022]
Abstract
In this work, we develop a fluorescent molecular beacon based on the DNA-templated silver nanoclusters (DNA-Ag NCs). The skillfully designed molecular beacon can be conveniently used for detection of diverse virulence genes as long as the corresponding recognition sequences are embedded. Importantly, the constructed detection system allows simultaneous detection of multiple nucleic acids, which is attributed to non-overlapping emission spectra of the as-synthesized silver nanoclusters. Based on the target-induced fluorescence enhancement, three infectious disease-related genes HIV, H1N1, and H5N1 are detected, and the corresponding detection limits are 3.53, 0.12 and 3.95nM, respectively. This design allows specific, versatile and simultaneous detection of diverse targets with easy operation and low cost.
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13
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Ahn JK, Kim HY, Baek S, Park HG. A new s-adenosylhomocysteine hydrolase-linked method for adenosine detection based on DNA-templated fluorescent Cu/Ag nanoclusters. Biosens Bioelectron 2017; 93:330-334. [DOI: 10.1016/j.bios.2016.08.058] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/09/2016] [Accepted: 08/18/2016] [Indexed: 01/26/2023]
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14
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Huang X, Liu Y, Yung B, Xiong Y, Chen X. Nanotechnology-Enhanced No-Wash Biosensors for in Vitro Diagnostics of Cancer. ACS NANO 2017; 11:5238-5292. [PMID: 28590117 DOI: 10.1021/acsnano.7b02618] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
In vitro biosensors have been an integral component for early diagnosis of cancer in the clinic. Among them, no-wash biosensors, which only depend on the simple mixing of the signal generating probes and the sample solution without additional washing and separation steps, have been found to be particularly attractive. The outstanding advantages of facile, convenient, and rapid response of no-wash biosensors are especially suitable for point-of-care testing (POCT). One fast-growing field of no-wash biosensor design involves the usage of nanomaterials as signal amplification carriers or direct signal generating elements. The analytical capacity of no-wash biosensors with respect to sensitivity or limit of detection, specificity, stability, and multiplexing detection capacity is largely improved because of their large surface area, excellent optical, electrical, catalytic, and magnetic properties. This review provides a comprehensive overview of various nanomaterial-enhanced no-wash biosensing technologies and focuses on the analysis of the underlying mechanism of these technologies applied for the early detection of cancer biomarkers ranging from small molecules to proteins, and even whole cancerous cells. Representative examples are selected to demonstrate the proof-of-concept with promising applications for in vitro diagnostics of cancer. Finally, a brief discussion of common unresolved issues and a perspective outlook on the field are provided.
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Affiliation(s)
- Xiaolin Huang
- State Key Laboratory of Food Science and Technology, Nanchang University , Nanchang 330047, P. R. China
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH) , Bethesda, Maryland 20892, United States
| | - Yijing Liu
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH) , Bethesda, Maryland 20892, United States
| | - Bryant Yung
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH) , Bethesda, Maryland 20892, United States
| | - Yonghua Xiong
- State Key Laboratory of Food Science and Technology, Nanchang University , Nanchang 330047, P. R. China
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH) , Bethesda, Maryland 20892, United States
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15
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A DNA-stabilized silver nanoclusters/graphene oxide-based platform for the sensitive detection of DNA through hybridization chain reaction. Biosens Bioelectron 2017; 91:374-379. [DOI: 10.1016/j.bios.2016.12.060] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/14/2016] [Accepted: 12/29/2016] [Indexed: 12/17/2022]
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16
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An electrochemiluminescence biosensor for endonuclease EcoRI detection. Biosens Bioelectron 2017; 89:585-591. [DOI: 10.1016/j.bios.2016.01.082] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 01/11/2016] [Accepted: 01/28/2016] [Indexed: 10/22/2022]
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17
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Andersen MB, Tesauro C, Gonzalez M, Kristoffersen EL, Alonso C, Rubiales G, Coletta A, Frøhlich R, Stougaard M, Ho YP, Palacios F, Knudsen BR. Advantages of an optical nanosensor system for the mechanistic analysis of a novel topoisomerase I targeting drug: a case study. NANOSCALE 2017; 9:1886-1895. [PMID: 28094391 DOI: 10.1039/c6nr06848k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The continuous need for the development of new small molecule anti-cancer drugs calls for easily accessible sensor systems for measuring the effect of vast numbers of new drugs on their potential cellular targets. Here we demonstrate the use of an optical DNA biosensor to unravel the inhibitory mechanism of a member of a new family of small molecule human topoisomerase I inhibitors, the so-called indeno-1,5-naphthyridines. By analysing human topoisomerase I catalysis on the biosensor in the absence or presence of added drug complemented with a few traditional assays, we demonstrate that the investigated member of the indeno-1,5-naphthyridine family inhibited human topoisomerase I activity by blocking enzyme-DNA dissociation. To our knowledge, this represents the first characterized example of a small molecule drug that inhibits a post-ligation step of catalysis. The elucidation of a completely new and rather surprising drug mechanism-of-action using an optical real time sensor highlights the value of this assay system in the search for new topoisomerase I targeting small molecule drugs.
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Affiliation(s)
- Marie B Andersen
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
| | - Cinzia Tesauro
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
| | - María Gonzalez
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Emil L Kristoffersen
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
| | - Concepción Alonso
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Gloria Rubiales
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Andrea Coletta
- Department of Chemistry, Langelandsgade 140, Aarhus University, 8000 Aarhus C, Denmark
| | - Rikke Frøhlich
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
| | - Magnus Stougaard
- Department of Pathology, Nørrebrogade 44 building 18B, Aarhus University, Denmark
| | - Yi-Ping Ho
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark. and Interdisciplinary Nanoscience Center, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark and Division of Biomedical Engineering, Department of Electronic Engineering, The Chinese University of Hong Kong, Shatin, NT, Hong Kong, China
| | - Francisco Palacios
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Birgitta R Knudsen
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
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18
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Tao Y, Li M, Ren J, Qu X. Metal nanoclusters: novel probes for diagnostic and therapeutic applications. Chem Soc Rev 2016; 44:8636-63. [PMID: 26400655 DOI: 10.1039/c5cs00607d] [Citation(s) in RCA: 481] [Impact Index Per Article: 60.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metal nanoclusters, composed of several to a few hundred metal atoms, have received worldwide attention due to their extraordinary physical and chemical characteristics. Recently, great efforts have been devoted to the exploration of the potential diagnostic and therapeutic applications of metal nanoclusters. Here we focus on the recent advances and new horizons in this area, and introduce the rising progress on the use of metal nanoclusters for biological analysis, biological imaging, therapeutic applications, DNA assembly and logic gate construction, enzyme mimic catalysis, as well as thermometers and pH meters. Furthermore, the future challenges in the construction of biofunctional metal nanoclusters for diagnostic and therapeutic applications are also discussed. We expect that the rapidly growing interest in metal nanocluster-based theranostic applications will certainly not only fuel the excitement and stimulate research in this highly active field, but also inspire broader concerns across various disciplines.
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Affiliation(s)
- Yu Tao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China. and University of Chinese Academy of Sciences, Beijing 100039, China
| | - Mingqiang Li
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China.
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China.
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19
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Rapid restriction enzyme free detection of DNA methyltransferase activity based on DNA-templated silver nanoclusters. Anal Bioanal Chem 2016; 408:4311-8. [DOI: 10.1007/s00216-016-9522-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 03/13/2016] [Accepted: 03/24/2016] [Indexed: 01/24/2023]
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20
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Cao F, Ju E, Liu C, Pu F, Ren J, Qu X. Coupling a DNA–ligand ensemble with Ag cluster formation for the label-free and ratiometric detection of intracellular biothiols. Chem Commun (Camb) 2016; 52:5167-70. [DOI: 10.1039/c5cc10606k] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A smart nanoprobe was constructed by coupling a DNA–ligand ensemble with Ag cluster formation for the ratiometric detection of intracellular biothiols.
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Affiliation(s)
- Fangfang Cao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Enguo Ju
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Chaoqun Liu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Fang Pu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
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21
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A DNA-templated silver nanocluster probe for label-free, turn-on fluorescence-based screening of homo-adenine binding molecules. Biosens Bioelectron 2015; 64:618-24. [DOI: 10.1016/j.bios.2014.10.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 09/30/2014] [Accepted: 10/01/2014] [Indexed: 12/19/2022]
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22
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Zhang J, Shi Z, Jin Y. Enzyme-free and label-free signal amplification for monitoring endonuclease activity and inhibition via hybridization chain reaction. Analyst 2015; 140:3500-6. [DOI: 10.1039/c5an00304k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A facile and sensitive method for studying EcoRI activity and inhibition had been developed based on EcoRI-triggered hybridization chain reaction.
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Affiliation(s)
- Jing Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
| | - Zhilu Shi
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
| | - Yan Jin
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
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23
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Ma DL, Lu L, Lin S, He B, Leung CH. A G-triplex luminescent switch-on probe for the detection of mung bean nuclease activity. J Mater Chem B 2015; 3:348-352. [DOI: 10.1039/c4tb01569j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A G-triplex luminescent switch-on probe for the detection of nuclease activity.
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Affiliation(s)
- Dik-Lung Ma
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
| | - Lihua Lu
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
| | - Sheng Lin
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
| | - Bingyong He
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine
- Institute of Chinese Medical Sciences
- University of Macau
- Macao
- China
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24
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A versatile biosensing system for DNA-related enzyme activity assay via the synthesis of silver nanoclusters using enzymatically-generated DNA as template. Biosens Bioelectron 2014; 61:321-7. [DOI: 10.1016/j.bios.2014.05.038] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/06/2014] [Accepted: 05/15/2014] [Indexed: 01/24/2023]
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25
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Recent advances in the field of bionanotechnology: an insight into optoelectric bacteriorhodopsin, quantum dots, and noble metal nanoclusters. SENSORS 2014; 14:19731-66. [PMID: 25340449 PMCID: PMC4239883 DOI: 10.3390/s141019731] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 10/08/2014] [Accepted: 10/15/2014] [Indexed: 12/20/2022]
Abstract
Molecular sensors and molecular electronics are a major component of a recent research area known as bionanotechnology, which merges biology with nanotechnology. This new class of biosensors and bioelectronics has been a subject of intense research over the past decade and has found application in a wide variety of fields. The unique characteristics of these biomolecular transduction systems has been utilized in applications ranging from solar cells and single-electron transistors (SETs) to fluorescent sensors capable of sensitive and selective detection of a wide variety of targets, both organic and inorganic. This review will discuss three major systems in the area of molecular sensors and electronics and their application in unique technological innovations. Firstly, the synthesis of optoelectric bacteriorhodopsin (bR) and its application in the field of molecular sensors and electronics will be discussed. Next, this article will discuss recent advances in the synthesis and application of semiconductor quantum dots (QDs). Finally, this article will conclude with a review of the new and exciting field of noble metal nanoclusters and their application in the creation of a new class of fluorescent sensors.
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26
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Wang L, Ma K, Zhang Y. Label-free fluorometric detection of S1 nuclease activity by using polycytosine oligonucleotide-templated silver nanoclusters. Anal Biochem 2014; 468:34-8. [PMID: 25263815 DOI: 10.1016/j.ab.2014.09.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 09/09/2014] [Accepted: 09/17/2014] [Indexed: 12/22/2022]
Abstract
S1 nuclease has an important function in DNA transcription, replication, recombination, and repair. A label-free fluorescent method for the detection of S1 nuclease activity has been developed using polycytosine oligonucleotide-templated silver nanoclusters (dC12-Ag NCs). In this assay, dC12 can function as both the template for the stabilization of Ag NCs and the substrate of the S1 nuclease. Fluorescent Ag NCs could be effectively formed using dC12 as the template without S1 nuclease. In the presence of S1 nuclease, dC12 is degraded to mono- or oligonucleotide fragments, thereby resulting in a reduction in fluorescence. S1 nuclease with an activity as low as 5×10(-8)Uμl(-1) (signal/noise=3) can be determined with a linear range of 5×10(-7) to 1×10(-3)Uμl(-1). The promising application of the proposed method in S1 nuclease inhibitor screening has been demonstrated using pyrophosphate as the model inhibitor. Furthermore, the S1 nuclease concentrations in RPMI 1640 cell medium were validated. The developed method for S1 nuclease is sensitive and facile because its operation does not require any complicated DNA labeling or laborious fluorescent dye synthesis.
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Affiliation(s)
- Lihui Wang
- Key Laboratory of Applied Surface and Colloid Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Keke Ma
- Key Laboratory of Applied Surface and Colloid Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Yaodong Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China.
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27
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Zhou Y, Zhou T, Zhang M, Shi G. A DNA–scaffolded silver nanocluster/Cu2+ ensemble as a turn-on fluorescent probe for histidine. Analyst 2014; 139:3122-6. [DOI: 10.1039/c4an00487f] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A new type of rapid, sensitive, and selective fluorescence turn-on assay was developed for detection of histidine using a DNA–scaffolded silver nanocluster/Cu2+ ensemble (DNA–AgNC/Cu2+).
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Affiliation(s)
- Ying Zhou
- Department of Chemistry
- East China Normal University
- Shanghai 200241, China
| | - Tianshu Zhou
- Department of Environmental Science
- East China Normal University
- Shanghai 200241, China
| | - Min Zhang
- Department of Chemistry
- East China Normal University
- Shanghai 200241, China
| | - Guoyue Shi
- Department of Chemistry
- East China Normal University
- Shanghai 200241, China
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