1
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Huang Y, Cheng Z, Xu LP, Zhang X, Liu G. Lateral flow DNA biosensor for visual detection of nucleic acid with triple-helix DNA functionalized carbon nanotube. Anal Chim Acta 2023; 1276:341604. [PMID: 37573103 DOI: 10.1016/j.aca.2023.341604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/21/2023] [Accepted: 07/07/2023] [Indexed: 08/14/2023]
Abstract
We describe a novel lateral flow DNA biosensor (LFDB) based on carbon nanotube (CNT) and triple helix DNA (THD). The carboxylated CNT was first conjugated with amine-modified auxiliary single-stranded DNA probe (P1) by dehydration reaction and used as signal probe. A main DNA probe (P0) was introduced to react with the P1 and formed the THD on the CNT surface. Because of the large spatial effect, P1 was in an inactive state and cannot hybridize with the capture DNA probe (P2) fixed on the LFDB test area. When the target DNA was present, P0 in the triple helix DNA hybridized with the target DNA due to the stronger base action, and the decomposition of the triple helix structure exposed P1. Therefore, P1 on CNT surface was activated to hybridize with P2. The CNT along with P1 was thus captured at the test area and accumulated to show a black line, which can be observed by naked eye for qualitative analysis and recorded with a portable grayscale reader for quantitative analysis. Single-stranded DNA was used as a target to prove the feasibility of the model. Under the best experimental conditions, the THD-CNT based LFDB was able to detect the lowest DNA concentration of 15 pM, which is 2.67 times better than that of the traditional duplex CNT-based LFDB. It should be noted that the LFDB based on THD functionalized CNT can differentiate between one-base-mismatched DNA and the complementary target DNA, can detected target DNA in 10% human serum, and can be employed as a versatile platform to detect various target (proteins, small molecular) by changing the sequence of P0. This biosensor platform has enormous potential in the point-of-care detection of a rich diversity of analytes for clinical diagnosis and biomedical research.
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Affiliation(s)
- Yan Huang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
| | - Zhihao Cheng
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Li-Ping Xu
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Xueji Zhang
- School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, 518060, China.
| | - Guodong Liu
- School of Chemistry and Chemical Engineering, Linyi University, Linyi, Shandong, 276005, China.
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2
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Abdul Rashid JI, Yusof NA, Abdullah J, Shomiad Shueb RH. Strategies in the optimization of DNA hybridization conditions and its role in electrochemical detection of dengue virus (DENV) using response surface methodology (RSM). RSC Adv 2023; 13:18748-18759. [PMID: 37362605 PMCID: PMC10286818 DOI: 10.1039/d3ra00216k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/28/2023] [Indexed: 06/28/2023] Open
Abstract
In recent years, limited research has been conducted on enhancing DNA hybridization-based biosensor approaches using statistical models. This study explores the application of response surface methodology (RSM) to improve the performance of a DNA hybridization biosensor for dengue virus (DENV) detection. The biosensor is based on silicon nanowires decorated with gold nanoparticles (SiNWs/AuNPs) and utilizes methylene blue as a redox indicator. The DNA hybridization process between the immobilized DNA probe and the target DENV gene was monitored using differential pulse voltammetry (DPV) based on the reduction of methylene blue. Fourier-transform infrared spectroscopy (FTIR) and electrochemical impedance spectroscopy (EIS) were employed to confirm successful DNA hybridization events on the modified screen-printed gold electrode (SPGE) surface. Several parameters, including pH buffer, NaCl concentration, temperature, and hybridization time, were simultaneously optimized, with NaCl concentration having the most significant impact on DNA hybridization events. This study enhances the understanding of the role of each parameter in influencing DNA hybridization detection in electrochemical biosensors. The optimized biosensor demonstrated the ability to detect complementary oligonucleotide and amplified DENV gene concentrations as low as 0.0891 ng µL-1 (10 pM) and 2.8 ng µL-1, respectively. The developed biosensor shows promise for rapid clinical diagnosis of dengue virus infection.
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Affiliation(s)
- Jahwarhar Izuan Abdul Rashid
- Department of Chemistry and Biology, Centre for Defence Foundation Studies, National Defence University of Malaysia Sungai Besi Camp 57000 Kuala Lumpur Malaysia
| | - Nor Azah Yusof
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia Serdang Selangor 43400 Malaysia
| | - Jaafar Abdullah
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia Serdang Selangor 43400 Malaysia
| | - Rafidah Hanim Shomiad Shueb
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia 16150 Kubang Kerian Kelantan Malaysia
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3
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Fu X, Chen Z, Ma W, Zhang H, Mo W, Li J, Yang M. Entropy-driven dynamic self-assembled DNA dendrimers for colorimetric detection of African swine fever virus. Anal Bioanal Chem 2023; 415:1675-1685. [PMID: 36715708 DOI: 10.1007/s00216-023-04562-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/04/2023] [Accepted: 01/20/2023] [Indexed: 01/31/2023]
Abstract
Herein, we subtly engineered an amplified colorimetric biosensor for the cyclic detection of African swine fever virus DNA (ASFV-DNA), which associated the branched catalytic hairpin assembly (bCHA) amplification with G-quadruplex DNAzyme activity through triplex DNA formation. Firstly, a Y-shaped hairpin trimer was constructed for the dynamic self-assembly of DNA dendrimers. Then, in the presence of ASFV-DNA, the signal strand CP was opened, exposing the toehold regions, which would trigger the CHA cascade reaction between hairpin trimers. In the CHA cascade reaction, H1, H2, and H3 opened and bound in sequence, eventually forming the structure of DNA dendrimers. Subsequently, the obtained bCHA product was specifically recognized by the GGG repeat sequences of L1 and L2, then amplified by the synergistic effect of triplex DNA and the formation of asymmetric split G-quadruplex. Benefiting from the amplification properties of bCHA and the high peroxidase-like catalytic activity of asymmetrically split G-quadruplex DNAzymes, it could achieve effective colorimetric signal output in the presence of ASFV-DNA by means of triplex DNA formation. Under the optimal experimental conditions, this biosensor exhibited excellent sensitivity with a detection limit of 1.8 pM. Further, it was applied to the content detection of simulated samples of African swine fever, and the recoveries were 98.9 ~ 103.2%. This method has the advantages of simple operation, good selectivity, and high sensitivity, which is expected to be used for highly sensitive detection of actual samples of African swine fever virus.
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Affiliation(s)
- Xin Fu
- State Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, 411104, China.
| | - Zhoujie Chen
- State Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, 411104, China
| | - Wenjie Ma
- State Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, 411104, China
| | - He Zhang
- State Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, 411104, China.
| | - Wenhao Mo
- State Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, 411104, China
| | - Jinyan Li
- State Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, 411104, China
| | - Mei Yang
- State Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, 411104, China
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4
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Vijayakumar S, Venkatesan S, Lin MC, Vediappen P. Highly Sensitive and Selective Detection of Melatonin in Biofluids by Antipyrine Based Fluorophore. J Fluoresc 2023; 33:383-392. [PMID: 36434443 DOI: 10.1007/s10895-022-03052-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/20/2022] [Indexed: 11/27/2022]
Abstract
A simple fluorescent based organic fluorophore was synthesized and it shows significant fluorescent intensity with melatonin (MLN). Hence, it was applicable to the detection of MLN by colorimetric and fluorimetric techniques at neutral pH. Under optimized experimental condition, the synthesized organic fluorophore detects MLN selectively in the presence of other interfering biomolecules through ICT mechanism. The melatonin sensing mechanism is supported by DFT and 1H-NMR titration. Based on the findings, this method can be applied to design a simple clinical diagnostic tool for MLN.
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Affiliation(s)
- Sathya Vijayakumar
- Department of Organic Chemistry, School of Chemistry, Madurai Kamaraj University, Madurai, 625021, Tamilnadu, India
| | - Srinivasadesikan Venkatesan
- School of Applied Science and Humanities, Department of Chemistry, Vignan's Foundation for Science, Technology and Research, Vadlamudi, Guntur, 522 213, Andhra Pradesh, India
| | - Ming-Chang Lin
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan
| | - Padmini Vediappen
- Department of Organic Chemistry, School of Chemistry, Madurai Kamaraj University, Madurai, 625021, Tamilnadu, India.
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5
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Fu Y, Si H, Chen J, Zhang W, Feng S, Xiao Z. A Novel “Turn‐On” Fluorescent Sensor for Screening Triplex DNA Binder Based upon Molecular Beacon. ChemistrySelect 2022. [DOI: 10.1002/slct.202203178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yuanxiang Fu
- School of Chemical Engineering Guizhou Institute of Technology 1st, Caiguan Road Guiyang 550003 P. R. China
| | - Hengdan Si
- School of Chemical Engineering Guizhou Institute of Technology 1st, Caiguan Road Guiyang 550003 P. R. China
| | - Juan Chen
- School of Chemical Engineering Guizhou Institute of Technology 1st, Caiguan Road Guiyang 550003 P. R. China
| | - Wenjuan Zhang
- School of Chemical Engineering Guizhou Institute of Technology 1st, Caiguan Road Guiyang 550003 P. R. China
| | - Shuang Feng
- School of Chemical Engineering Guizhou Institute of Technology 1st, Caiguan Road Guiyang 550003 P. R. China
| | - Zhiyou Xiao
- School of Chemical Engineering Guizhou Institute of Technology 1st, Caiguan Road Guiyang 550003 P. R. China
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6
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Chu X, Zhu D, Liu M, Kong L, Ai S. Moderate stability of a scissor double fluorescent triple helix molecular switch for the ultrasensitive biosensing of crop transgene. NEW J CHEM 2022. [DOI: 10.1039/d2nj00647b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Schematic of the ultrasensitive biosensing of special genes. (I: traditional molecular beacon detection method; II: scissor DFTHMS; III: three cases of BHQ-1-TFO).
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Affiliation(s)
- Xiuling Chu
- Shandong Taian Ecological Environment Monitoring Center, Taian 271000, P. R. China
| | - Desong Zhu
- Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, College of Chemistry and Material Science, Shandong Agricultural University, Taian 271018, P. R. China
| | - Min Liu
- Shandong Qingdao Ecological Environment Monitoring Center, Qingdao 266000, P. R. China
| | - Lingrang Kong
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian 271018, P. R. China
| | - Shiyun Ai
- Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, College of Chemistry and Material Science, Shandong Agricultural University, Taian 271018, P. R. China
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7
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Wang M, Zhao L, Wen Y, Wu Y, Li Y. Label-Free Fluorescent Determination of Simian Virus 40 Using Triplex DNA and G-Quadruplex/N-Methyl Mesoporphyrin IX. ANAL LETT 2021. [DOI: 10.1080/00032719.2021.1907394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Minting Wang
- Faculty of Chemistry & Environmental Science, Guangdong Ocean University, Zhanjiang, China
| | - Liting Zhao
- Faculty of Chemistry & Environmental Science, Guangdong Ocean University, Zhanjiang, China
| | - Yanmei Wen
- Faculty of Chemistry & Environmental Science, Guangdong Ocean University, Zhanjiang, China
| | - Yulian Wu
- Faculty of Chemistry & Environmental Science, Guangdong Ocean University, Zhanjiang, China
| | - Yubin Li
- Faculty of Chemistry & Environmental Science, Guangdong Ocean University, Zhanjiang, China
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8
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Dai T, Wan Y, Tian R, Wang S, Han T, Wang G. In Situ Cation Exchange Generated ZnS–Ag2S Nanoparticles for Photothermal Detection of Transcription Factor. ACS APPLIED BIO MATERIALS 2020; 3:3260-3267. [DOI: 10.1021/acsabm.0c00232] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Tianyue Dai
- College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P. R. China
| | - Yifei Wan
- College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P. R. China
| | - Ruifen Tian
- College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P. R. China
| | - Sicheng Wang
- College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P. R. China
| | - Ting Han
- College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P. R. China
| | - Guangfeng Wang
- College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P. R. China
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9
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Wen QL, Peng J, Liu AY, Wang J, Hu YL, Ling J, Cao QE. DNA bioassays based on the fluorescence 'turn off' of silver nanocluster beacon. LUMINESCENCE 2020; 35:702-708. [PMID: 31926119 DOI: 10.1002/bio.3775] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/23/2019] [Accepted: 12/30/2019] [Indexed: 12/12/2022]
Abstract
Recognition and quantification of oligonucleotide sequences play important roles in medical diagnosis. In this study, a new fluorescent oligonucleotide-stabilized silver nanocluster beacon (NCB) probe was designed for sensitive detection of oligonucleotide sequence targets. This probe contained two tailored DNA strands. One strand was a signal probe strand containing a cytosine-rich strand template for fluorescent silver nanocluster (Ag NC) synthesis and a detection sections at each end. The other strand was a fluorescence enhancing strand containing a guanine-rich section for signal enhancement at one end and a linker section complementary to one end of the signal probe strand. After synthesis of the Ag NCs and hybridization of the two strands, the fluorescence intensity of the as-prepared silver NCB was enhanced 200-fold compared with the Ag NCs. Two NCBs were designed to detect two disease-related oligonucleotide sequences, and results indicated that the two target oligonucleotide sequences in the range 50.0-600.0 and 50.0-200.0 nM could be linearly detected with detection limits of 20 and 25 nM, respectively. The developed fluorescence method using NCBs for oligonucleotide sequence detection was sensitive, facile and had potential for use in bioanalysis and diagnosis.
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Affiliation(s)
- Qiu-Lin Wen
- Functional Molecules Analysis and Biotransformation Key Laboratory of Universities in Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, China
| | - Jun Peng
- Functional Molecules Analysis and Biotransformation Key Laboratory of Universities in Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, China.,Hunan Province Geological Testing Institute, Changsha, China
| | - An-Yong Liu
- Functional Molecules Analysis and Biotransformation Key Laboratory of Universities in Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, China
| | - Jun Wang
- Functional Molecules Analysis and Biotransformation Key Laboratory of Universities in Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, China
| | - Yi-Lin Hu
- Functional Molecules Analysis and Biotransformation Key Laboratory of Universities in Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, China
| | - Jian Ling
- Functional Molecules Analysis and Biotransformation Key Laboratory of Universities in Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, China
| | - Qiu-E Cao
- Functional Molecules Analysis and Biotransformation Key Laboratory of Universities in Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, China
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10
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Lee D, Lee H, Lee G, Kim I, Lee SW, Kim W, Lee SW, Lee JH, Park J, Yoon DS. Extremely sensitive and wide-range silver ion detection via assessing the integrated surface potential of a DNA-capped gold nanoparticle. NANOTECHNOLOGY 2019; 30:085501. [PMID: 30524017 DOI: 10.1088/1361-6528/aaf66f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
With the rapid development of nanotechnology and its associated waste stream, public concern is growing over the potential toxicity exposure to heavy metal ions poses to the human body and the environment. Herein, we report an extremely sensitive Kelvin probe force microscopy (KPFM)-based platform for detecting nanotoxic materials (e.g. Ag+) accomplished by probing the integrated surface potential differences of a single gold nanoparticle on which an interaction between probe DNA and target DNA occurs. This interaction can amplify the surface potential of the nanoparticle owing to the coordination bond mediated by Ag+ (cytosine-Ag+-cytosine base pairs). Interestingly, compared with conventional methods, this platform is capable of extremely sensitive Ag+ detection (∼1 fM) in a remarkably wide-range (1 fM to 1 μM). Furthermore, this platform enables Ag+ detection in a practical sample (general drinking water), and this KPFM-based technique may have the potential to detect other toxic heavy metal ions and single nucleotide polymorphisms by designing specific DNA sequences.
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Affiliation(s)
- Dongtak Lee
- School of Biomedical Engineering, Korea University, Seoul 02841, Republic of Korea
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11
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Lu X, Zhou G, Lu Y, Li L. Stem–loop clutch probes for sequence-specific dsDNA analysis with improved single-mismatch selectivity. Chem Commun (Camb) 2019; 55:7514-7517. [DOI: 10.1039/c9cc03137e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A stem–loop clutch probe based strategy has been proposed to guide sequence-specific dsDNA analysis with enhanced single-base mismatch selectivity.
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Affiliation(s)
- Xing Lu
- College of Biological
- Chemical Sciences and Engineering
- Jiaxing University
- Jiaxing 314001
- China
| | - Guobao Zhou
- College of Biological
- Chemical Sciences and Engineering
- Jiaxing University
- Jiaxing 314001
- China
| | - Yixia Lu
- College of Biological
- Chemical Sciences and Engineering
- Jiaxing University
- Jiaxing 314001
- China
| | - Lei Li
- College of Biological
- Chemical Sciences and Engineering
- Jiaxing University
- Jiaxing 314001
- China
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12
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Determination of bacterial DNA based on catalytic oxidation of cysteine by G-quadruplex DNAzyme generated from asymmetric PCR: Application to the colorimetric detection of Staphylococcus aureus. Mikrochim Acta 2018; 185:410. [DOI: 10.1007/s00604-018-2935-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 07/23/2018] [Indexed: 02/01/2023]
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13
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Ma H, Li Z, Xue N, Cheng Z, Miao X. A gold nanoparticle based fluorescent probe for simultaneous recognition of single-stranded DNA and double-stranded DNA. Mikrochim Acta 2018; 185:93. [DOI: 10.1007/s00604-017-2633-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 12/22/2017] [Indexed: 12/22/2022]
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14
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Li Y, Liu S, Ling L. Sensitive Fluorescent Sensor for Recognition of HIV-1 dsDNA by Using Glucose Oxidase and Triplex DNA. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2018; 2018:8298365. [PMID: 29805840 PMCID: PMC5901486 DOI: 10.1155/2018/8298365] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 12/05/2017] [Accepted: 12/19/2017] [Indexed: 05/08/2023]
Abstract
A sensitive fluorescent sensor for sequence-specific recognition of double-stranded DNA (dsDNA) was developed on the surface of silver-coated glass slide (SCGS). Oligonucleotide-1 (Oligo-1) was designed to assemble on the surface of SCGS and act as capture DNA, and oligonucleotide-2 (Oligo-2) was designed as signal DNA. Upon addition of target HIV-1 dsDNA (Oligo-3•Oligo-4), signal DNA could bind on the surface of silver-coated glass because of the formation of C•GoC in parallel triplex DNA structure. Biotin-labeled glucose oxidase (biotin-GOx) could bind to signal DNA through the specific interaction of biotin-streptavidin, thereby GOx was attached to the surface of SCGS, which was dependent on the concentration of target HIV-1 dsDNA. GOx could catalyze the oxidation of glucose and yield H2O2, and the HPPA can be oxidized into a fluorescent product in the presence of HRP. Therefore, the concentration of target HIV-1 dsDNA could be estimated with fluorescence intensity. Under the optimum conditions, the fluorescence intensity was proportional to the concentration of target HIV-1 dsDNA over the range of 10 pM to 1000 pM, the detection limit was 3 pM. Moreover, the sensor had good sequence selectivity and practicability and might be applied for the diagnosis of HIV disease in the future.
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Affiliation(s)
- Yubin Li
- College of Chemistry and Environment, Guangdong Ocean University, Zhanjiang 524088, China
| | - Sheng Liu
- College of Chemistry and Environment, Guangdong Ocean University, Zhanjiang 524088, China
| | - Liansheng Ling
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
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15
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Das P, Pan I, Cohen E, Reches M. Self-assembly of a metallo-peptide into a drug delivery system using a “switch on” displacement strategy. J Mater Chem B 2018; 6:8228-8237. [DOI: 10.1039/c8tb01483c] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Two newly designed tripeptides and their corresponding Cu2+ conjugates self-assemble into nanometric structures of different morphologies. These self-assembled metallo-peptide networks can serve as a drug delivery platform using a fluorescent-based "Turn-On" displacement strategy.
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Affiliation(s)
- Priyadip Das
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology
- The Hebrew University of Jerusalem
- Jerusalem
- Israel
- SRM Research Institute
| | - Ieshita Pan
- Biochemistry and Molecular Biology
- Institute for Medical Research Israel-Canada
- The Hebrew University of Jerusalem
- Jerusalem
- Israel
| | - Ehud Cohen
- Biochemistry and Molecular Biology
- Institute for Medical Research Israel-Canada
- The Hebrew University of Jerusalem
- Jerusalem
- Israel
| | - Meital Reches
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology
- The Hebrew University of Jerusalem
- Jerusalem
- Israel
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16
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Liu S, Peng P, Wang H, Shi L, Li T. Thioflavin T binds dimeric parallel-stranded GA-containing non-G-quadruplex DNAs: a general approach to lighting up double-stranded scaffolds. Nucleic Acids Res 2017; 45:12080-12089. [PMID: 29059300 PMCID: PMC5716147 DOI: 10.1093/nar/gkx942] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/03/2017] [Indexed: 12/27/2022] Open
Abstract
A molecular rotor thioflavin T (ThT) is usually used as a fluorescent ligand specific for G-quadruplexes. Here, we demonstrate that ThT can tightly bind non-G-quadruplex DNAs with several GA motifs and dimerize them in a parallel double-stranded mode, accompanied by over 100-fold enhancement in the fluorescence emission of ThT. The introduction of reverse Watson–Crick T-A base pairs into these dimeric parallel-stranded DNA systems remarkably favors the binding of ThT into the pocket between G•G and A•A base pairs, where ThT is encapsulated thereby restricting its two rotary aromatic rings in the excited state. A similar mechanism is also demonstrated in antiparallel DNA duplexes where several motifs of two consecutive G•G wobble base pairs are incorporated and serve as the active pockets for ThT binding. The insight into the interactions of ThT with non-G-quadruplex DNAs allows us to introduce a new concept for constructing DNA-based sensors and devices. As proof-of-concept experiments, we design a DNA triplex containing GA motifs in its Hoogsteen hydrogen-bonded two parallel strands as a pH-driven nanoswitch and two GA-containing parallel duplexes as novel metal sensing platforms where C–C and T–T mismatches are included. This work may find further applications in biological systems (e.g. disease gene detection) where parallel duplex or triplex stretches are involved.
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Affiliation(s)
- Shuangna Liu
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Pai Peng
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Huihui Wang
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Lili Shi
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Tao Li
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
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17
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Hairpin probe for sequence-specific recognition of double-stranded DNA on simian virus 40. Chem Res Chin Univ 2017. [DOI: 10.1007/s40242-017-7152-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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18
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Hu Q, Wang Q, Kong J, Li L, Zhang X. Electrochemically mediated in situ growth of electroactive polymers for highly sensitive detection of double-stranded DNA without sequence-preference. Biosens Bioelectron 2017; 101:1-6. [PMID: 29031128 DOI: 10.1016/j.bios.2017.09.045] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/10/2017] [Accepted: 09/25/2017] [Indexed: 12/21/2022]
Abstract
The ability to directly detect double-stranded DNA (dsDNA) without sequence-preference continues to be a major challenge. Herein, we report an electrochemical method for the direct, highly sensitive detection of dsDNA based on the strand replacement of dsDNA by peptide nucleic acid (PNA) and the in situ growth of electroactive polymers through the surface-initiated electrochemically mediated atom transfer radical polymerization (SI-eATRP). Thiolated PNA molecules are firstly self-assembled onto gold electrode surface for the specific recognition of target dsDNA (dsDNA-T), which in turn leads to the formation of a high density of PNA/DNA heteroduplexes on the electrode surface for the subsequent attachment of ATRP initiators via the phosphate-Zr4+-carboxylate chemistry. By applying a negative potential to the electrode, the air-stable CuII deactivators can be reduced into the CuI activators so as to trigger the surface-initiated polymerization for the in situ growth of electroactive polymers. Due to the strand replacement of dsDNA by PNA, dsDNA can be directly detected without sequence-preference. Besides, the growth of polymers enables the modification of numerous electroactive probes, thereby greatly improving the electrochemical signal. Under optimal conditions, a good linearity between the electrochemical signal and the logarithm of dsDNA-T concentration over the range from 1.0 fM to 1.0nM, with a detection limit of 0.47 fM, can be obtained. Results indicate that it is highly selective, and holds high anti-interference capability in the presence of human serum samples. Therefore, this method offers great promises in providing a universal and efficient solution for the direct detection of dsDNA.
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Affiliation(s)
- Qiong Hu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, PR China
| | - Qiangwei Wang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, PR China
| | - Jinming Kong
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, PR China.
| | - Lianzhi Li
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng 252000, PR China
| | - Xueji Zhang
- Chemistry Department, College of Arts and Sciences, University of South Florida, East Fowler Ave, Tampa, FL 33620-4202, United States.
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19
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Zhang M, Li R, Wang J, Ling L. Sequence-specific recognition of HIV-1 DNA based upon nicking-assisted strand displacement amplification and triplex DNA. Sci China Chem 2017. [DOI: 10.1007/s11426-017-9112-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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20
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Zhu H, Zhang M, Zou L, Li R, Ling L. Sequence specific recognition of HIV-1 dsDNA in the large amount of normal dsDNA based upon nicking enzyme signal amplification and triplex DNA. Talanta 2017; 173:9-13. [PMID: 28602196 DOI: 10.1016/j.talanta.2017.05.043] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 05/06/2017] [Accepted: 05/14/2017] [Indexed: 11/16/2022]
Abstract
A sensitive fluorescent strategy for sequence specific recognition of HIV dsDNA was established based upon Nicking Enzyme Signal Amplification (NESA) and triplex formation. dsDNA sequence from the site 7960 to site 7991 of the HIV1 dsDNA gene was designed as target dsDNA, which was composed of two complementary strands Oligonucleotide 1 with the sequence of 3'-CTT CCT TAT CTT CTT CTT CCA CCT CTC TCT CT-5' (Oligo-1) and Oligonucleotide 2 with the sequence of 5'-GAA GGA ATA GAA GAA GAA GGT GGA GAG AGA GA-3' (Oligo-2). As a proof of concept, Oligonucleotide 5'-6-FAM-GAG GTG GAG CTG CGC GAC TCC TCC TCT CTC TCT CTC CAC CTC-BHQ-1-3'(Oligo-4) acted as molecular beacon(MB) probe, Oligonucleotide 5'-CTT CCT TAT CTT CTT CTT CCA AAA GGA GTC GCG-3' (Oligo-7) acted as assistant probe. In the presence of target dsDNA, Oligo-4 and Oligo-7 hybridized with target dsDNA through triplex formation and formed Y-shaped structure, NESA occurred with further addition of Nt.BbvCI, accompanied with the release of fluorescent DNA fragment circularly, resulted in the increase of fluorescence intensity. Under the optimum conditions, the fluorescence intensity was linear with the concentration of target dsDNA over the range from 100pM to 200nM, the linear regression equation was I = 1.266 C + 84.3 (C: nmol/L, R2 = 0.991), with a detection limit of 65pM. Moreover, the effect of coexisted other dsDNA was investigated as well, and satisfactory results were obtained.
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Affiliation(s)
- Houya Zhu
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Manjun Zhang
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Li Zou
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Ruimin Li
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Liansheng Ling
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, PR China.
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21
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Ellairaja S, Shenbagavalli K, Ponmariappan S, Vasantha VS. A green and facile approach for synthesizing imine to develop optical biosensor for wide range detection of bilirubin in human biofluids. Biosens Bioelectron 2017; 91:82-88. [DOI: 10.1016/j.bios.2016.12.026] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 12/09/2016] [Accepted: 12/10/2016] [Indexed: 10/20/2022]
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22
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Zou L, Li R, Zhang M, Luo Y, Zhou N, Wang J, Ling L. A colorimetric sensing platform based upon recognizing hybridization chain reaction products with oligonucleotide modified gold nanoparticles through triplex formation. NANOSCALE 2017; 9:1986-1992. [PMID: 28106202 DOI: 10.1039/c6nr09089c] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A novel colorimetric sensing strategy for biomolecule assay has been developed, which integrates the signal amplification of the hybridization chain reaction (HCR) with the assembly of gold nanoparticles (AuNPs) through triplex formation. In the presence of targets, the HCR process can be triggered, the HCR products are specifically recognized by triplex-forming oligonucleotide (TFO) functionalized AuNPs, accompanying the aggregation of AuNPs and a dramatic absorbance change at 522 nm. In addition, the DNA hairpin probes can form rigid triplex structures with TFO-functionalized AuNPs in the absence of targets, resulting in a negligible background signal. By taking advantage of this new biosensor platform, a broad range of targets, involving nucleic acids, small molecules and proteins, have been successfully determined with high sensitivity and selectivity, which may hold great potential for practical application.
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Affiliation(s)
- Li Zou
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China.
| | - Ruimin Li
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China.
| | - Manjun Zhang
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China.
| | - Yanwei Luo
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China.
| | - Nian Zhou
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China.
| | - Jing Wang
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China.
| | - Liansheng Ling
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China.
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23
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Miao X, Cheng Z, Li Z, Wang P. A novel sensing platform for sensitive cholesterol detection by using positively charged gold nanoparticles. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2016.10.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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24
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Sha L, Zhang X, Wang G. A label-free and enzyme-free ultra-sensitive transcription factors biosensor using DNA-templated copper nanoparticles as fluorescent indicator and hairpin DNA cascade reaction as signal amplifier. Biosens Bioelectron 2016; 82:85-92. [DOI: 10.1016/j.bios.2016.03.066] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 03/23/2016] [Accepted: 03/25/2016] [Indexed: 11/30/2022]
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25
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Chen Z, Zhang H, Ma X, Lin Z, Zhang L, Chen G. A novel fluorescent reagent for recognition of triplex DNA with high specificity and selectivity. Analyst 2016; 140:7742-7. [PMID: 26456316 DOI: 10.1039/c5an01852h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A fluorescent agent (DMT) was screened for recognizing triplex DNA with a specific and selective characteristic, which was embedded into the triplex DNA structure. The triplex DNA was firstly formed by a complementary target sequence through two distinct and sequential events. The conditions including pH and hybridization time, fluorescent agent concentration and embedding time were optimized in the experiment. Under the optimum conditions, the fluorescence signal was enhanced up to 9-fold in comparison with the DMT embedding into the ssDNA, dsDNA and G-quadruplexes. Under the same fluorescence conditions, the changes of the fluorescence signal were also investigated by several kinds of base mismatched DNAs in the experiment. The results showed that our biosensor provided excellent discrimination efficiency toward the perfectly mismatched target DNA with no formation of triplex DNA. We preliminarily deduced the mechanism of the fluorescent reagent for recognizing triplex DNA with high specificity and selectivity.
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Affiliation(s)
- Zongbao Chen
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350002, China. and Key Laboratory of Applied Organic Chemistry, College of Jiangxi Province Department of Chemistry, Shangrao Normal University, 334001, Jiangxi, China
| | - Huimi Zhang
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350002, China.
| | - Xiaoming Ma
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350002, China.
| | - Zhenyu Lin
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350002, China.
| | - Lan Zhang
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350002, China.
| | - Guonan Chen
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350002, China.
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26
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Hu Y, Lin F, Wu T, Wang Y, Zhou XS, Shao Y. Fluorescently Sensing of DNA Triplex Assembly Using an Isoquinoline Alkaloid as Selector, Stabilizer, Inducer, and Switch-On Emitter. Chem Asian J 2016; 11:2041-8. [DOI: 10.1002/asia.201600459] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Indexed: 01/07/2023]
Affiliation(s)
- Yuehua Hu
- Institute of Physical Chemistry; Zhejiang Normal University; Jinhua 321004 Zhejiang People's Republic of China
| | - Fan Lin
- Institute of Physical Chemistry; Zhejiang Normal University; Jinhua 321004 Zhejiang People's Republic of China
| | - Tao Wu
- Institute of Physical Chemistry; Zhejiang Normal University; Jinhua 321004 Zhejiang People's Republic of China
| | - Ying Wang
- Institute of Physical Chemistry; Zhejiang Normal University; Jinhua 321004 Zhejiang People's Republic of China
| | - Xiao-Shun Zhou
- Institute of Physical Chemistry; Zhejiang Normal University; Jinhua 321004 Zhejiang People's Republic of China
| | - Yong Shao
- Institute of Physical Chemistry; Zhejiang Normal University; Jinhua 321004 Zhejiang People's Republic of China
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27
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Xiao Z, Zhu H, Xin A, Li Y, Ling L. Triplex DNA logic gate based upon switching on/off their structure by Ag(+)/cysteine. Analyst 2016; 140:7322-6. [PMID: 26359516 DOI: 10.1039/c5an01371b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The formation of intramolecular triplex DNA can be regulated by Ag(+) and Cys (cysteine), which switch off/on the fluorescence of the oligonucleotides, 5'-TAMRA-TTC TCT TCC TCT TCC TTC TGA CGA CAG TTG ACT CTT CCT TCT CCT TCT CTT-BHQ-2-3' (Oligo 1) and 3'-GAA GGA AGA GGA AGA GAA-5' (Oligo 2). Based on this principle, sensors for Ag(+) and Cys are developed. The sensor for Ag(+) has a linear range of 2.5 nM-40 nM and a detection limit of 1.8 nM, whereas the sensor for Cys has a linear range of 10.0 nM-120.0 nM and a detection limit of 8.2 nM. Furthermore, the fluorescence is reversible with the alternate addition of Ag(+) and Cys. We constructed a DNA logic gate using Ag(+) and Cys as the input, and the fluorescence intensity as the output. The DNA logic gate is simple; moreover, it has a fast response and good reversibility.
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Affiliation(s)
- Zhiyou Xiao
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China.
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28
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Das P, Reches M. Single-stranded DNA detection by solvent-induced assemblies of a metallo-peptide-based complex. NANOSCALE 2016; 8:9527-36. [PMID: 26730518 DOI: 10.1039/c5nr07714a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
DNA detection is highly important for the sensitive sensing of different pathogenic bacteria and viruses. The major challenge is to create a sensor that can selectively detect very small concentrations of DNA without the need for amplification or complicated equipment. Different technologies such as optical, electrochemical and microgravimetric approaches can detect DNA fragments. Here we show, for the first time, the use of self-assembled nanostructures generated by a metallo-peptide as an optical sensing platform for DNA detection. The system can selectively detect single stranded DNA fragments by fluorescence measurements as it can discriminate even one base mismatch and can perform in the presence of other interfering proteins. This system may be useful in lab-on-a-chip applications.
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Affiliation(s)
- Priyadip Das
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel. and The Centre for Nanoscience and Nanotechnology. The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Meital Reches
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel. and The Centre for Nanoscience and Nanotechnology. The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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29
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Miao X, Li Z, Ling L. Fluorescence recognition of double-stranded DNA based on the quenching of gold nanoparticles to a fluorophore labeled DNA probe. Analyst 2016; 141:5829-5834. [DOI: 10.1039/c6an01145d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work described an ultrasensitive fluorescent sensor for sequence-specific recognition of dsDNA based on the quenching of gold nanoparticles (AuNPs) to a fluorophore labeled DNA probe.
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Affiliation(s)
- Xiangmin Miao
- School of Life Science
- Jiangsu Normal University
- Xuzhou 221116
- PR China
| | - Zongbing Li
- School of Life Science
- Jiangsu Normal University
- Xuzhou 221116
- PR China
| | - Liansheng Ling
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou 510275
- PR China
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30
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Li Z, Miao X, Xing K, Zhu A, Ling L. Enhanced electrochemical recognition of double-stranded DNA by using hybridization chain reaction and positively charged gold nanoparticles. Biosens Bioelectron 2015. [DOI: 10.1016/j.bios.2015.06.070] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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31
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Li X, Ding X, Fan J. Nicking endonuclease-assisted signal amplification of a split molecular aptamer beacon for biomolecule detection using graphene oxide as a sensing platform. Analyst 2015; 140:7918-25. [PMID: 26502364 DOI: 10.1039/c5an01759a] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Sensitive and selective detection of ultralow concentrations of specific biomolecules is important in early clinical diagnoses and biomedical applications. Many types of aptasensors have been developed for the detection of various biomolecules, but usually suffer from false positive signals and high background signals. In this work, we have developed an amplified fluorescence aptasensor platform for ultrasensitive biomolecule detection based on enzyme-assisted target-recycling signal amplification and graphene oxide. By using a split molecular aptamer beacon and a nicking enzyme, the typical problem of false positive signals can be effectively resolved. Only in the presence of a target biomolecule, the sensor system is able to generate a positive signal, which significantly improves the selectivity of the aptasensor. Moreover, using graphene oxide as a super-quencher can effectively reduce the high background signal of a sensing platform. We select vascular endothelial growth factor (VEGF) and adenosine triphosphate (ATP) as model analytes in the current proof-of-concept experiments. It is shown that under optimized conditions, our strategy exhibits high sensitivity and selectivity for the quantification of VEGF and ATP with a low detection limit (1 pM and 4 nM, respectively). In addition, this biosensor has been successfully utilized in the analysis of real biological samples.
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Affiliation(s)
- Xiang Li
- School of Environment, Henan Key Laboratory for Environmental Pollution Control, Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang, Henan 453007, P. R. China.
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32
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Hu H, Huang X, Ren J. Studies on the formation and stability of triplex DNA using fluorescence correlation spectroscopy. LUMINESCENCE 2015; 31:830-6. [DOI: 10.1002/bio.3030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Revised: 08/17/2015] [Accepted: 08/17/2015] [Indexed: 12/17/2022]
Affiliation(s)
- Hongyan Hu
- College of Chemistry & Chemical Engineering; Shanghai Jiao Tong University; Shanghai People's Republic of China
| | - Xiangyi Huang
- College of Chemistry & Chemical Engineering; Shanghai Jiao Tong University; Shanghai People's Republic of China
| | - Jicun Ren
- College of Chemistry & Chemical Engineering; Shanghai Jiao Tong University; Shanghai People's Republic of China
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33
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Li Y, Miao X, Ling L. Triplex DNA: A new platform for polymerase chain reaction-based biosensor. Sci Rep 2015; 5:13010. [PMID: 26268575 PMCID: PMC4534768 DOI: 10.1038/srep13010] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 06/10/2015] [Indexed: 01/20/2023] Open
Abstract
Non - specific PCR amplification and DNA contamination usually accompany with PCR process, to overcome these problems, here we establish a sensor for thrombin by sequence - specific recognition of the PCR product with molecular beacon through triplex formation. Probe A and probe B were designed for the sensor, upon addition of thrombin, two probes hybridized to each other and the probe B was extended in the presence of Klenow Fragment polymerase and dNTPs. The PCR amplification occurred with further addition of Taq DNA Polymerase and two primers, the PCR product was recognized by molecular beacon through triplex formation. The fluorescence intensity increased with the logarithm of the concentration of thrombin over the range from 1.0 × 10−12 M to 1.0 × 10−7 M, with a detection limit of 261 fM. Moreover, the effect of DNA contamination and non - specific amplification could be ignored completely in the proposed strategy.
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Affiliation(s)
- Yubin Li
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Xiangmin Miao
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, PR China
| | - Liansheng Ling
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
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34
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Xu L, Guo Y, Wang J, Zhou L, Zhang Y, Hong S, Wang Z, Zhang J, Pei R. A H+/Ag+Dual-Target Responsive Label-Free Light-Up Probe Based on a DNA Triplex. Chem Asian J 2015; 10:1126-9. [DOI: 10.1002/asia.201500001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Indexed: 02/03/2023]
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35
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Deng W, Xu H, Ding W, Liang H. DNA logic gate based on metallo-toehold strand displacement. PLoS One 2014; 9:e111650. [PMID: 25365381 PMCID: PMC4218789 DOI: 10.1371/journal.pone.0111650] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Accepted: 09/30/2014] [Indexed: 01/05/2023] Open
Abstract
DNA is increasingly being used as an ideal material for the construction of nanoscale structures, circuits, and machines. Toehold-mediated DNA strand displacement reactions play a very important role in these enzyme-free constructions. In this study, the concept of metallo-toehold was utilized to further develop a mechanism for strand displacement driven by Ag+ ions, in which the intercalation of cytosine-cytosine mismatched base pairs on the toeholds provides additional control by varying of the concentration of Ag+ ions. The characteristics of displacement reaction in response to different concentration of Ag+ ions are investigated by fluorescence spectral and non-denaturing polyacrylamide gel electrophoresis. The reaction can successfully occur when the concentration of Ag+ ions is suitabe; excess Ag+ ions block the reaction. Furthermore, the displacement reaction can be tuned and controlled most efficiently under the condition of two C:C mismatched base pairs placed on the six-nt toehold. Based on our research, a mechanism was developed to construct Boolean logic gate AND and OR by employing strand displacement reaction as a tool, Ag+ and Hg2+ as input.
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Affiliation(s)
- Wei Deng
- CAS Key Laboratory of Soft Matter Chemistry, Department of polymer science and engineering, University of Science and Technologyof China, Hefei, Anhui, P. R. China
| | - Huaguo Xu
- CAS Key Laboratory of Soft Matter Chemistry, Department of polymer science and engineering, University of Science and Technologyof China, Hefei, Anhui, P. R. China
| | - Wei Ding
- CAS Key Laboratory of Soft Matter Chemistry, Department of polymer science and engineering, University of Science and Technologyof China, Hefei, Anhui, P. R. China
| | - Haojun Liang
- CAS Key Laboratory of Soft Matter Chemistry, Department of polymer science and engineering, University of Science and Technologyof China, Hefei, Anhui, P. R. China
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, P. R. China
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36
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Xu N, Wang Q, Lei J, Liu L, Ju H. Label-free triple-helix aptamer as sensing platform for "signal-on" fluorescent detection of thrombin. Talanta 2014; 132:387-91. [PMID: 25476322 DOI: 10.1016/j.talanta.2014.09.031] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 09/13/2014] [Accepted: 09/18/2014] [Indexed: 11/25/2022]
Abstract
The design of a label-free aptamer for separation of recognition sequence from signal reporter is significant to ensure the high-efficiency affinity between aptamer and target. This work develops a label-free triple-helix aptamer (THA) as sensing platform for "signal-on" fluorescent detection of thrombin. THA was composed of aptamer sequence and help DNA 1 (H1), which contained the complementary sequence of hexachloro-fluorescein (HEX) labeled help DNA 2 (H2). The specific recognition event between aptamer and thrombin triggered the dismission of THA to release H1. The released H1 then reacted with the signal probe of H2/graphene oxide (GO) nanocomposite to form H1-H2 duplex, leading to the fluorescence recovery of H2 due to the detachment of H1-H2 duplex from the surface of GO. With employment of THA as a signal transducer and GO as a "superquencher", this method shows a sensitive response to thrombin with a wide concentration range from 5 to 1200 nM. The limit of detection is 1.8 nM (S/N=3) with excellent selectivity. Considering the universality of THA, the proposed aptasensor would provide a platform for homogeneous fluorescent detection of a wide range of analytes.
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Affiliation(s)
- Nan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, PR China
| | - Quanbo Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, PR China
| | - Jianping Lei
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, PR China.
| | - Lin Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, PR China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, PR China
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37
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Wang M, Leung KH, Lin S, Chan DSH, Leung CH, Ma DL. A G-quadruplex-based, label-free, switch-on luminescent detection assay for Ag+ions based on the exonuclease III-mediated digestion of C–Ag+–C DNA. J Mater Chem B 2014; 2:6467-6471. [DOI: 10.1039/c4tb01140f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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38
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Urata S, Miyahata T, Matsuura H, Kitamura Y, Ihara T. Alteration of DNAzyme Activity by Silver Ion. CHEM LETT 2014. [DOI: 10.1246/cl.140197] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Shoma Urata
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University
| | - Takaaki Miyahata
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University
| | - Hirotaka Matsuura
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University
| | - Yusuke Kitamura
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University
- CREST, Japan Science and Technology Agency
| | - Toshihiro Ihara
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University
- CREST, Japan Science and Technology Agency
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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: 0.6] [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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Zhu D, Zhu J, Zhu Y, Wang L, Jiang W. Sensitive detection of transcription factors using an Ag+-stabilized self-assembly triplex DNA molecular switch. Chem Commun (Camb) 2014; 50:14987-90. [DOI: 10.1039/c4cc06205a] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A simple, enzyme-free and sensitive new fluorescent strategy for detection of transcription factors was proposed based on a bifunctional Ag+-stabilized self-assembly triplex DNA molecular switch.
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Affiliation(s)
- Desong Zhu
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry
- Department of Chemistry
- Shandong University
- Jinan, China
| | - Jing Zhu
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry
- Department of Chemistry
- Shandong University
- Jinan, China
| | - Ye Zhu
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry
- Department of Chemistry
- Shandong University
- Jinan, China
| | - Lei Wang
- School of Pharmacy
- Shandong University
- Jinan 250012, P. R. China
| | - Wei Jiang
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry
- Department of Chemistry
- Shandong University
- Jinan, China
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