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Mi ZZ, Hu HC, Sun JJ, Wu SH. Heating promoted super sensitive electrochemical detection of p53 gene based on alkaline phosphatase and nicking endonuclease Nt.BstNBI-assisted target recycling amplification strategy at heated gold disk electrode. Anal Chim Acta 2023; 1275:341583. [PMID: 37524467 DOI: 10.1016/j.aca.2023.341583] [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: 06/03/2023] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 08/02/2023]
Abstract
An ultrasensitive electrochemical biosensor for detecting p53 gene was fabricated based on heated gold disk electrode coupling with endonuclease Nt.BstNBI-assisted target recycle amplification and alkaline phosphatase (ALP)-based electrocatalytic signal amplification. For biosensor assembling, biotinylated ssDNA capture probes were first immobilized on heated Au disk electrode (HAuDE), then combined with streptavidin-alkaline phosphatase (SA-ALP) by biotin-SA interaction. ALP could catalyze the hydrolysis of ascorbic acid 2-phosphate (AAP) to produce ascorbic acid (AA). While AA could induce the redox cycling to generate electrocatalytic oxidation current in the presence of ferrocene methanol (FcM). When capture probes hybridized with p53, Nt.BstNBI would recognize and cleave the duplexes and p53 was released for recycling. Meanwhile, the biotin group dropt from the electrode surface and subsequently SA-ALP could not adhere to the electrode. The signal difference before and after cleavage was proportional to the p53 gene concentration. Furthermore, with electrode temperature elevated, the Nt.BstNBI and ALP activities could be increased, greatly improving the sensitivity and efficiency for p53 detection. A detection limit of 9.5 × 10-17 M could be obtained (S/N = 3) with an electrode temperature of 40 °C, ca. four magnitudes lower than that at 25 °C.
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Affiliation(s)
- Zhen-Zhen Mi
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Hao-Cheng Hu
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Jian-Jun Sun
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Shao-Hua Wu
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China.
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2
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Pitikultham P, Putnin T, Pimalai D, Sathirapongsasuti N, Kitiyakara C, Jiang Q, Ding B, Japrung D. Ultrasensitive Detection of MicroRNA in Human Saliva via Rolling Circle Amplification Using a DNA-Decorated Graphene Oxide Sensor. ACS OMEGA 2023; 8:15266-15275. [PMID: 37151566 PMCID: PMC10157686 DOI: 10.1021/acsomega.3c00411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/04/2023] [Indexed: 05/09/2023]
Abstract
MicroRNAs (miRNAs) are a family of conserved small noncoding RNAs whose expression is associated with many diseases, including cancer. Salivary miRNAs are gaining popularity as noninvasive diagnostic biomarkers for cancer and other systemic disorders, but their use is limited by their low abundance and complicated detection procedure. Herein, we present a novel self-assembly approach based on rolling circle amplification (RCA) and graphene oxide (GO) for the ultrasensitive detection of miRNA21 and miRNA16 (miRNA oral cancer biomarkers in human saliva). First, target miRNA hybridizes with the RCA template. In the presence of DNA polymerase, the RCA reaction is induced and sequences matching the template are generated. Then, a nicking enzyme cuts the long ssDNA product into tiny pieces to obtain the amplified products. The DNA-decorated GO sensor was fabricated by preabsorbing the ssDNA fluorescence-labeled probe on the GO surface, resulting in fluorescence quenching. The DNA-decorated GO sensor could detect the amplified product via the self-assembly of dsDNA, leading to the desorption and recovery of the fluorescence-labeled probe. Under optimal conditions, the proposed system exhibited ultrasensitive detection; the detection limits of miRNA16 and miRNA21 were 8.81 and 3.85 fM, respectively. It showed a wide range of detection between 10 fM and 100 pM for miRNA16 and between 10 fM and 1 nM for miRNA16. It demonstrated high selectivity, distinguishing between 1- and 3-mismatch nucleotides in target miRNA. Overall, our proposed DNA-decorated GO sensor can accurately detect the salivary miRNAs and may potentially be used for the diagnosis and screening of early-stage oral cancer.
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Affiliation(s)
- Piyawat Pitikultham
- CAS
Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center
for Excellence in Nanoscience, National
Center for Nanoscience and Technology, Beijing 100190, China
- School
of Nanoscience and Technology, University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Thitirat Putnin
- National
Nanotechnology Center, National Science and Technology Department
Agency, Thailand Science Park, Pathumthani 10120, Thailand
| | - Dechnarong Pimalai
- National
Nanotechnology Center, National Science and Technology Department
Agency, Thailand Science Park, Pathumthani 10120, Thailand
| | - Nuankanya Sathirapongsasuti
- Program
in Translational Medicine, Chakri Naruebodindra Medical Institute,
Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bang Pli, Samutprakarn 10540, Thailand
| | - Chagriya Kitiyakara
- Department
of Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Qiao Jiang
- CAS
Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center
for Excellence in Nanoscience, National
Center for Nanoscience and Technology, Beijing 100190, China
- School
of Nanoscience and Technology, University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Baoquan Ding
- CAS
Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center
for Excellence in Nanoscience, National
Center for Nanoscience and Technology, Beijing 100190, China
- School
of Nanoscience and Technology, University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Deanpen Japrung
- National
Nanotechnology Center, National Science and Technology Department
Agency, Thailand Science Park, Pathumthani 10120, Thailand
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3
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Isothermal exponential amplification reactions triggered by circular templates (cEXPAR) targeting miRNA. Mol Biol Rep 2023; 50:3653-3659. [PMID: 36807240 DOI: 10.1007/s11033-023-08291-x] [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: 10/13/2022] [Accepted: 01/17/2023] [Indexed: 02/21/2023]
Abstract
BACKGROUND Isothermal exponential amplification reaction (EXPAR) is an emerging amplification technique that is most frequently used to amplify microRNA (miRNA). However, EXPAR also exhibits non-specific background amplification in the absence of the targeted sequence, which limits the attainable assay sensitivity of EXPAR. METHODS AND RESULTS A novel modified isothermal EXPAR based on circular amplification templates (cEXPAR) was developed in this study. The circular template consists of two same linear fragments that complement the target sequence, and these two linear fragments are separated by two nicking agent recognition sequences (NARS). Compared with the linear structure template, this circular template allows DNA or RNA fragments to be randomly paired with two repeated sequences and can be successfully amplified. This reaction system developed in this study could rapidly synthesize short oligonucleotide fragments (12-22 bp) through simultaneous nicking and displacement reactions. Highly sensitive chain reactions can be specifically triggered by as low as a single copy of target molecule, and non-specific amplification can be effectively eliminated in this optimized system. Moreover, the proposed approach applied to miRNA test can discriminate single-nucleotide variations between miRNAs. CONCLUSION The newly developed cEXPAR assay provides a useful alternative tool for rapid, sensitive, and highly specific detection of miRNAs.
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Cai Q, Wang F, Ge J, Xu Z, Li M, Xu H, Wang H. G-wire-based self-quenched fluorescence probe combining with target-activated isothermal cascade amplification for ultrasensitive microRNA detection. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 281:121605. [PMID: 35843057 DOI: 10.1016/j.saa.2022.121605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/11/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Herein, we reported the G-wire-based self-quenched fluorescence probe and its application in ultrasensitive microRNA (miRNA) detection by combining with target-activated isothermal cascade amplification. The terminal-single-fluorescein (FAM)-labeled G-rich oligonucletides self-assembled into G-wire nanostructures (G-wires) with K+ and Mg2+. Thereafter, the G-wires brought terminal-labeled FAM into close proximity, as a result, the self-quenched signal probe formed. Besides, when there was the target miRNA, target-activated isothermal cascade amplification converted miRNA into the copious trigger DNA. After hybridization between trigger DNA and the self-quenched probe, the G-wires were splited and forced the apart of proximate FAM, and then the self-quenched probe displayed an "on" mechanism. Therefore, the approach gave a limit of detection (LOM) of 0.82 aM to miRNA-21 and could be implemented within a wide linear range of 2 aM to 2 nM. This approach was able to distinguish the single-mismatched miRNA-21, which was selective and sensitive in detecting human spiked serum samples.
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Affiliation(s)
- Qingyou Cai
- School of Teacher Education, Huzhou University, Huzhou, Zhejiang 313000, PR China
| | - Fanfan Wang
- School of Science and Engineering, Huzhou College, Huzhou, Zhejiang 313000, PR China
| | - Jingying Ge
- School of Science and Engineering, Huzhou College, Huzhou, Zhejiang 313000, PR China
| | - Zhiguo Xu
- School of Science and Engineering, Huzhou College, Huzhou, Zhejiang 313000, PR China
| | - Mei Li
- School of Science and Engineering, Huzhou College, Huzhou, Zhejiang 313000, PR China; Huzhou Key Laboratory of Medical and Environmental Applications Technologies, School of Life Sciences, Huzhou University, Zhejiang 313000, PR China.
| | - Hui Xu
- School of Science and Engineering, Huzhou College, Huzhou, Zhejiang 313000, PR China; Huzhou Key Laboratory of Medical and Environmental Applications Technologies, School of Life Sciences, Huzhou University, Zhejiang 313000, PR China
| | - Hua Wang
- Huzhou Key Laboratory of Medical and Environmental Applications Technologies, School of Life Sciences, Huzhou University, Zhejiang 313000, PR China
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5
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Concentration-Dependent Study of Nucleic Acid Blockers Used for Sequence-Specificity Enhancement in Nucleic Acids Detection. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2022. [DOI: 10.1007/s13369-022-06972-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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6
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Non-enzymatic detection of miR-21 in cancer cells using a homogeneous mix-and-read smart probe assay. Anal Biochem 2022; 645:114601. [PMID: 35182494 DOI: 10.1016/j.ab.2022.114601] [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: 10/12/2021] [Revised: 02/03/2022] [Accepted: 02/10/2022] [Indexed: 11/23/2022]
Abstract
We report a new assay system for the detection of miR-21 in cancer cells. The new assay works at room temperature and it does not involve enzymatic amplification. It consists a hairpin smart probe, designed to specifically recognize miR-21 target sequence. We tested the performance and sequence recognition capability of the smart probe to confirm desired specifications. We used the smart probe for the sequence-specific recognition of synthetic miR-21 oligonucleotides as well as mismatch sequences and we found that the probe recognizes the target sequence-specifically, while discriminating against mismatched sequences. We determined the limit of detection and limit of quantitation for the miR-21 oligonucleotides to be 1.72 nM and 5.78 nM, respectively, while the sensitivity is 6.90 × 1011 c.p.sM-1. More importantly, we showed that the smart probe-based method is also sensitive and selective for miR-21 when applied to crude extractions from MCF-7 cancer cell line at room temperature, with the results showing high fluorescence signals for the MCF-7 samples while showing much less signals for samples that did not contain miR-21. Thus, this new smart probe system constitutes a homogeneous, mix-and-read detection technique that can provide reliable diagnostics of miR-21 cancer biomarker at room temperature.
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7
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Zhao Y, Fang X, Yu H, Fu Y, Zhao Y. Universal Exponential Amplification Confers Multilocus Detection of Mutation-Prone Virus. Anal Chem 2022; 94:927-933. [PMID: 34983181 DOI: 10.1021/acs.analchem.1c03702] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yue Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xianning West Road, Xi’an, Shaanxi 710049, P. R. China
| | - Xiaoxing Fang
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xianning West Road, Xi’an, Shaanxi 710049, P. R. China
| | - Huahang Yu
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xianning West Road, Xi’an, Shaanxi 710049, P. R. China
| | - Youlan Fu
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xianning West Road, Xi’an, Shaanxi 710049, P. R. China
| | - Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xianning West Road, Xi’an, Shaanxi 710049, P. R. China
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8
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Chen M, Duan R, Xu S, Duan Z, Yuan Q, Xia F, Huang F. Photoactivated DNA Walker Based on DNA Nanoflares for Signal-Amplified MicroRNA Imaging in Single Living Cells. Anal Chem 2021; 93:16264-16272. [PMID: 34797071 DOI: 10.1021/acs.analchem.1c04505] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Specific and sensitive detection and imaging of cancer-related miRNA in living cells are desirable for cancer diagnosis and treatment. Because of the spatiotemporal variability of miRNA expression level during different cell cycles, signal amplification strategies that can be activated by external stimuli are required to image miRNAs on demand at desired times and selected locations. Herein, we develop a signal amplification strategy termed as the photoactivated DNA walker based on DNA nanoflares, which enables photocontrollable signal amplification imaging of cancer-related miRNA in single living cells. The developed method is achieved via combining photoactivated nucleic acid displacement reaction with the traditional exonuclease III (EXO III)-assisted DNA walker based on DNA nanoflares. This method is capable of on-demand activation of the DNA walker for dictated signal amplification imaging of cancer-related miRNA in single living cells. The developed method was demonstrated as a proof of concept to achieve photoactivated signal amplification imaging of miRNA-21 in single living HeLa cells via selective two-photon irradiation (λ = 740 nm) of single living HeLa cells by using confocal microscopy equipped with a femtosecond laser.
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Affiliation(s)
- Mengxi Chen
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Ruilin Duan
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Shijun Xu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Zhijuan Duan
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Quan Yuan
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Fujian Huang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
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9
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Li F, Li J, Dong B, Wang F, Fan C, Zuo X. DNA nanotechnology-empowered nanoscopic imaging of biomolecules. Chem Soc Rev 2021; 50:5650-5667. [DOI: 10.1039/d0cs01281e] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
DNA nanotechnology has led to the rise of DNA nanostructures, which possess programmable shapes and are capable of organizing different functional molecules and materials. A variety of DNA nanostructure-based imaging probes have been developed.
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Affiliation(s)
- Fan Li
- Institute of Molecular Medicine
- Department of Urology
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine
- Renji Hospital
- School of Medicine
| | - Jiang Li
- Bioimaging Center
- Shanghai Synchrotron Radiation Facility
- Zhangjiang Laboratory
- Shanghai Advanced Research Institute
- Chinese Academy of Sciences
| | - Baijun Dong
- Institute of Molecular Medicine
- Department of Urology
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine
- Renji Hospital
- School of Medicine
| | - Fei Wang
- Frontiers Science Center for Transformative Molecules
- School of Chemistry and Chemical Engineering
- Shanghai Jiao Tong University
- Shanghai 200240
- China
| | - Chunhai Fan
- Institute of Molecular Medicine
- Department of Urology
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine
- Renji Hospital
- School of Medicine
| | - Xiaolei Zuo
- Institute of Molecular Medicine
- Department of Urology
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine
- Renji Hospital
- School of Medicine
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10
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Affiliation(s)
- Fangfei Yin
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai China
- University of Chinese Academy of Sciences Beijing China
| | - Fei Wang
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Institute of Translational Medicine Shanghai Jiao Tong University Shanghai China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Institute of Translational Medicine Shanghai Jiao Tong University Shanghai China
- Institute of Molecular Medicine Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai China
| | - Xiaolei Zuo
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Institute of Translational Medicine Shanghai Jiao Tong University Shanghai China
- Institute of Molecular Medicine Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai China
| | - Qian Li
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Institute of Translational Medicine Shanghai Jiao Tong University Shanghai China
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11
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Duan R, Li T, Duan Z, Huang F, Xia F. Near-Infrared Light Activated Nucleic Acid Cascade Recycling Amplification for Spatiotemporally Controllable Signal Amplified mRNA Imaging. Anal Chem 2020; 92:5846-5854. [DOI: 10.1021/acs.analchem.9b05494] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Ruilin Duan
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Tao Li
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Zhijuan Duan
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Fujian Huang
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Fan Xia
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
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12
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Tian B, Minero G, Fock J, Dufva M, Hansen MF. CRISPR-Cas12a based internal negative control for nonspecific products of exponential rolling circle amplification. Nucleic Acids Res 2020; 48:e30. [PMID: 31956898 PMCID: PMC7049689 DOI: 10.1093/nar/gkaa017] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/16/2019] [Accepted: 01/03/2020] [Indexed: 12/26/2022] Open
Abstract
False-positive results cause a major problem in nucleic acid amplification, and require external blank/negative controls for every test. However, external controls usually have a simpler and lower background compared to the test sample, resulting in underestimation of false-positive risks. Internal negative controls, performed simultaneously with amplification to monitor the background level in real-time, are therefore appealing in both research and clinic. Herein, we describe a nonspecific product-activated single-stranded DNA-cutting approach based on CRISPR (clustered regularly interspaced short palindromic repeats) Cas12a (Cpf1) nuclease. The proposed approach, termed Cas12a-based internal referential indicator (CIRI), can indicate the onset of nonspecific amplification in an exponential rolling circle amplification strategy here combined with an optomagnetic readout. The capability of CIRI as an internal negative control can potentially be extended to other amplification strategies and sensors, improving the performance of nucleic acid amplification-based methodologies.
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Affiliation(s)
- Bo Tian
- Department of Health Technology, Technical University of Denmark, DTU Health Tech, Building 345C, DK-2800 Kongens Lyngby, Denmark
| | - Gabriel Antonio S Minero
- Department of Health Technology, Technical University of Denmark, DTU Health Tech, Building 345C, DK-2800 Kongens Lyngby, Denmark
| | - Jeppe Fock
- Blusense Diagnostics ApS, Fruebjergvej 3, DK-2100 Copenhagen, Denmark
| | - Martin Dufva
- Department of Health Technology, Technical University of Denmark, DTU Health Tech, Building 345C, DK-2800 Kongens Lyngby, Denmark
| | - Mikkel Fougt Hansen
- Department of Health Technology, Technical University of Denmark, DTU Health Tech, Building 345C, DK-2800 Kongens Lyngby, Denmark
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Label-free detection of microRNA: two-stage signal enhancement with hairpin assisted cascade isothermal amplification and light-up DNA-silver nanoclusters. Mikrochim Acta 2020; 187:141. [PMID: 31965324 DOI: 10.1007/s00604-019-4094-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 12/22/2019] [Indexed: 12/19/2022]
Abstract
A method is described for the determination of microRNAs via two-stage signal enhancement. This is attained by combining hairpin (HP) assisted cascade isothermal amplification with light-up DNA-Ag nanoclusters. A rationally designed dual-functional HP is used, and microRNA-21 is chosen as a model analyte. At the first stage, upon the hybridization of the microRNA-21 with HP, microRNA recycling via polymerase-displacement reaction and a circulative nicking-replication process are achieved. This generates numerous G-abundant overhang DNA sequences. In the second stage, the above-released G-abundant overhang DNA sequences hybridize with the dark green Ag NCs, and this results in the appearance of bright red fluorescence. Thanks to the two signal enhancement processes, a linear dependence between the fluorescence intensity at 616 nm and the concentration of microRNA-21 is obtained in the range from 1 pM to 20 pM with a detection limit of 0.7 pM. The strategy clearly discriminates between perfectly-matched and mismatched targets. The method was applied to the determination of microRNA-21 in a spiked serum sample. Graphical abstractSchematic representation of microRNA detection by integrating hairpin assisted cascade isothermal amplification with light-up DNA Ag nanoclusters. With microRNA, G-abundant overhang DNA sequences from amplification reaction hybridize with dark green Ag nanoclusters to produce a concentration-dependent bright red fluorescence.
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Oladepo SA, Yusuf BO. Detection of Several Homologous MicroRNAs by a Single Smart Probe System Consisting of Linear Nucleic Acid Blockers. MOLECULES (BASEL, SWITZERLAND) 2019; 24:molecules24203691. [PMID: 31615053 PMCID: PMC6832958 DOI: 10.3390/molecules24203691] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/01/2019] [Accepted: 10/05/2019] [Indexed: 11/13/2022]
Abstract
We report a universal smart probe (SP) that is capable of detecting several homologous let-7 microRNAs (miRNAs). While the SP is complementary to let-7a, and therefore, strongly binds to this target, due to sequence homology, the SP also has equal propensity to non-specifically hybridize with let-7b and let-7c, which are homologous to let-7a. The fluorescence signal of the SP was switched off in the absence of any homologous member target, but the signal was switched on when any of the three homologous members was present. With the assistance of nucleic acid blockers (NABs), this SP system can discriminate between homologous miRNAs. We show that the SP can discriminate between let-7a and the other two sequences by using linear NABs (LNABs) to block non-specific interactions between the SP and these sequences. We also found that LNABs used do not cross-react with the let-7a target due to the low LNABs:SP molar ratio of 6:1 used. Overall, this SP represents a universal probe for the recognition of a homologous miRNA family. The assay is sensitive, providing a detection limit of 6 fmol. The approach is simple, fast, usable at room temperature, and represents a general platform for the in vitro detection of homologous microRNAs by a single fluorescent hairpin probe.
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Affiliation(s)
- Sulayman A Oladepo
- Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran 31261, Saudi Arabia.
| | - Basiru O Yusuf
- Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran 31261, Saudi Arabia.
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15
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Xu J, Shi M, Huang H, Hu K, Chen W, Huang Y, Zhao S. A fluorescent aptasensor based on single oligonucleotide-mediated isothermal quadratic amplification and graphene oxide fluorescence quenching for ultrasensitive protein detection. Analyst 2019; 143:3918-3925. [PMID: 30043777 DOI: 10.1039/c8an01032c] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In this work, we have developed a novel fluorescent aptasensor based on single oligonucleotide-mediated isothermal quadratic amplification (SOIQA) and graphene oxide (GO)-mediated fluorescence quenching for the ultrasensitive detection of proteins in a homogeneous solution. The SOIQA consists of a fluorophore-labeled aptamer hairpin probe containing T7 exonuclease (T7 Exo)-resistant 5'-protruding termini and a mismatch base at its 3'-end, DNA polymerase, T7 Exo and GO. The target analyte binds with the aptamer sequences and unfolds the fluorophore-labeled aptamer hairpin probe to form a new DNA hairpin, inducing the catalytic recycling of the target analyte (assisted by DNA polymerase) and DNA sequences (aided by T7 Exo) to achieve SOIQA, which results in the digestion of numerous fluorophore-labeled aptamer hairpin probes and the generation of a large amount of mononucleotides carrying the fluorophore. These mononucleotide products cannot be adsorbed onto the GO, leading to a dramatic increase in the fluorescence intensity for the amplified detection of the target molecules. In the absence of the target analyte, however, the SOIQA reaction is inhibited and the fluorophore-labeled aptamer hairpin probe is adsorbed onto the GO, leading to an extremely low fluorescence background signal. To test the feasibility of the SOIQA systems, a protein cancer marker, carcinoembryonic antigen (CEA) was used as the model analyte. The developed aptasensor could detect CEA with a detection limit of 28.5 fg mL-1 (∼142 aM), high specificity and a broad detection range of 6 orders of magnitude. And this one-step incubation can be completed in 60 min. In addition, the approach uses only one oligonucleotide strand, and is simple. Moreover, this SOIQA sensing method is suitable for rapid and direct quantification of proteins in complex biological samples such as clinical serum. Considering the simplicity and superior sensitivity/specificity, the developed sensing method provides a promising platform for the analysis of a variety of low-abundance biomolecules.
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Affiliation(s)
- Jiayao Xu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, College of Chemistry and Pharmacy, Guangxi Normal University, Yucai Road 15, Guilin, 541004, P. R. China
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16
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Qian C, Wang R, Wu H, Ji F, Wu J. Nicking enzyme-assisted amplification (NEAA) technology and its applications: A review. Anal Chim Acta 2019; 1050:1-15. [DOI: 10.1016/j.aca.2018.10.054] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/22/2018] [Accepted: 10/23/2018] [Indexed: 01/13/2023]
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17
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Yang F, Cheng Y, Cao Y, Dong H, Lu H, Zhang K, Meng X, Liu C, Zhang X. Sensitively distinguishing intracellular precursor and mature microRNA abundance. Chem Sci 2019; 10:1709-1715. [PMID: 30842835 PMCID: PMC6368210 DOI: 10.1039/c8sc03305f] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/27/2018] [Indexed: 12/21/2022] Open
Abstract
Mature microRNAs (miRNAs) produced from precursor microRNAs (pre-miRNAs) by the RNase Dicer have showed significant potential for cancer diagnosis and prognosis due to their key regulatory roles in various pathological processes. However, discriminatory detection of low-abundance miRNAs and pre-miRNAs remains a key challenge since the mature sequence is also present in the pre-miRNA forms. Herein, we report a novel cascade reaction to sensitively distinguish miRNAs versus pre-miRNAs in living cells based on two pairs of programmable hairpin oligonucleotide probes with a simple sequence design. The programmable hairpin probes can metastably coexist until the introduction of miRNAs or pre-miRNAs, which can trigger a specific hybridization chain reaction (HCR), respectively, leading to the self-assembly of nicked DNA duplex structures and a remarkable specific fluorescence intensity increase. The system can readily and sensitively assess the miRNA or pre-miRNA abundance in a homogeneous solution. The intracellular miRNA and pre-miRNA expression level assessment in different living cells is realized. Thus, we provide a novel investigation tool for discriminatorily and accurately assessing miRNA and pre-miRNA abundance, which could be useful for the biomedical application of miRNAs.
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Affiliation(s)
- Fan Yang
- Beijing Advanced Innovation Center for Materials Genome Engineering , University of Science and Technology Beijing , 30 Xueyuan Road , Beijing 100083 , P. R. China . ;
- Beijing Key Laboratory for Bioengineering and Sensing Technology , Research Center for Bioengineering and Sensing Technology , School of Chemistry & Biological Engineering , University of Science & Technology Beijing , 30 Xueyuan Road , Beijing 100083 , P. R. China
| | - Yaru Cheng
- Beijing Advanced Innovation Center for Materials Genome Engineering , University of Science and Technology Beijing , 30 Xueyuan Road , Beijing 100083 , P. R. China . ;
- Beijing Key Laboratory for Bioengineering and Sensing Technology , Research Center for Bioengineering and Sensing Technology , School of Chemistry & Biological Engineering , University of Science & Technology Beijing , 30 Xueyuan Road , Beijing 100083 , P. R. China
| | - Yu Cao
- Beijing Advanced Innovation Center for Materials Genome Engineering , University of Science and Technology Beijing , 30 Xueyuan Road , Beijing 100083 , P. R. China . ;
- Beijing Key Laboratory for Bioengineering and Sensing Technology , Research Center for Bioengineering and Sensing Technology , School of Chemistry & Biological Engineering , University of Science & Technology Beijing , 30 Xueyuan Road , Beijing 100083 , P. R. China
| | - Haifeng Dong
- Beijing Advanced Innovation Center for Materials Genome Engineering , University of Science and Technology Beijing , 30 Xueyuan Road , Beijing 100083 , P. R. China . ;
- Beijing Key Laboratory for Bioengineering and Sensing Technology , Research Center for Bioengineering and Sensing Technology , School of Chemistry & Biological Engineering , University of Science & Technology Beijing , 30 Xueyuan Road , Beijing 100083 , P. R. China
| | - Huiting Lu
- Beijing Advanced Innovation Center for Materials Genome Engineering , University of Science and Technology Beijing , 30 Xueyuan Road , Beijing 100083 , P. R. China . ;
- Beijing Key Laboratory for Bioengineering and Sensing Technology , Research Center for Bioengineering and Sensing Technology , School of Chemistry & Biological Engineering , University of Science & Technology Beijing , 30 Xueyuan Road , Beijing 100083 , P. R. China
| | - Kai Zhang
- Beijing Advanced Innovation Center for Materials Genome Engineering , University of Science and Technology Beijing , 30 Xueyuan Road , Beijing 100083 , P. R. China . ;
- Beijing Key Laboratory for Bioengineering and Sensing Technology , Research Center for Bioengineering and Sensing Technology , School of Chemistry & Biological Engineering , University of Science & Technology Beijing , 30 Xueyuan Road , Beijing 100083 , P. R. China
| | - Xiangdan Meng
- Beijing Advanced Innovation Center for Materials Genome Engineering , University of Science and Technology Beijing , 30 Xueyuan Road , Beijing 100083 , P. R. China . ;
- Beijing Key Laboratory for Bioengineering and Sensing Technology , Research Center for Bioengineering and Sensing Technology , School of Chemistry & Biological Engineering , University of Science & Technology Beijing , 30 Xueyuan Road , Beijing 100083 , P. R. China
| | - Conghui Liu
- Beijing Advanced Innovation Center for Materials Genome Engineering , University of Science and Technology Beijing , 30 Xueyuan Road , Beijing 100083 , P. R. China . ;
- Beijing Key Laboratory for Bioengineering and Sensing Technology , Research Center for Bioengineering and Sensing Technology , School of Chemistry & Biological Engineering , University of Science & Technology Beijing , 30 Xueyuan Road , Beijing 100083 , P. R. China
| | - Xueji Zhang
- Beijing Advanced Innovation Center for Materials Genome Engineering , University of Science and Technology Beijing , 30 Xueyuan Road , Beijing 100083 , P. R. China . ;
- Beijing Key Laboratory for Bioengineering and Sensing Technology , Research Center for Bioengineering and Sensing Technology , School of Chemistry & Biological Engineering , University of Science & Technology Beijing , 30 Xueyuan Road , Beijing 100083 , P. R. China
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18
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Zhang T, Chai H, Meng F, Guo Z, Jiang Y, Miao P. DNA-Functionalized Porous Fe 3O 4 Nanoparticles for the Construction of Self-Powered miRNA Biosensor with Target Recycling Amplification. ACS APPLIED MATERIALS & INTERFACES 2018; 10:36796-36804. [PMID: 30303365 DOI: 10.1021/acsami.8b15419] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Herein, we have developed an ultrasensitive self-powered biosensor for miRNA assay based on biofuel cells. The system is composed of indium tin oxide cathode and graphene oxide/gold nanoparticle/glucose oxidase anode. Redox probe of [Fe(CN)6]3- is entrapped inside porous Fe3O4 nanoparticles by DNA. However, in the presence of target miRNA, hybridization reaction occurs between miRNA and DNA, which initiates the release of [Fe(CN)6]3-. Moreover, duplex specific nuclease is further employed to trigger target recycling amplification. As a result, much more redox probes are released and the open circuit voltage is significantly increased. A "signal-on" self-powered biosensor for miRNA quantification is thus developed. The detection range is from 10 aM to 10 fM; meanwhile, the limit of detection is as low as 1.4 aM, which is superior to that in most reported methods. Therefore, the proposed biosensor is expected to be a powerful point-of-care tool for miRNA diagnostics, which may have wide applications in the future.
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Affiliation(s)
- Tian Zhang
- University of Science and Technology of China , Hefei 230026 , People's Republic of China
- Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Sciences , Suzhou 215163 , People's Republic of China
| | - Hua Chai
- University of Science and Technology of China , Hefei 230026 , People's Republic of China
- Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Sciences , Suzhou 215163 , People's Republic of China
| | - Fanyu Meng
- University of Science and Technology of China , Hefei 230026 , People's Republic of China
- Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Sciences , Suzhou 215163 , People's Republic of China
| | - Zhenzhen Guo
- Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Sciences , Suzhou 215163 , People's Republic of China
| | - Yu Jiang
- Department of Orthopedics , Nanjing Medical University Affiliated Wuxi Second Hospital , Wuxi 214000 , People's Republic of China
| | - Peng Miao
- University of Science and Technology of China , Hefei 230026 , People's Republic of China
- Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Sciences , Suzhou 215163 , People's Republic of China
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Oh SW, Pereira A, Zhang T, Li T, Lane A, Fu J. DNA‐Mediated Proximity‐Based Assembly Circuit for Actuation of Biochemical Reactions. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sung Won Oh
- Center for Computational and Integrative Biology Rutgers University—Camden 315 Penn Street, Science Building Camden NJ 08102 USA
| | - Adriana Pereira
- Department of Chemistry Rutgers University—Camden 315 Penn Street Camden NJ 08102 USA
| | - Ting Zhang
- Center for Computational and Integrative Biology Rutgers University—Camden 315 Penn Street, Science Building Camden NJ 08102 USA
- Department of Chemistry Rutgers University—Camden 315 Penn Street Camden NJ 08102 USA
| | - Tianran Li
- Center for Computational and Integrative Biology Rutgers University—Camden 315 Penn Street, Science Building Camden NJ 08102 USA
| | - Ariel Lane
- Department of Chemistry Rutgers University—Camden 315 Penn Street Camden NJ 08102 USA
| | - Jinglin Fu
- Center for Computational and Integrative Biology Rutgers University—Camden 315 Penn Street, Science Building Camden NJ 08102 USA
- Department of Chemistry Rutgers University—Camden 315 Penn Street Camden NJ 08102 USA
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20
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Abstract
Point-of-care and in-field technologies for rapid, sensitive and selective detection of molecular biomarkers have attracted much interest. Rugged bioassay technology capable of fast detection of markers for pathogens and genetic diseases would in particular impact the quality of health care in the developing world, but would also make possible more extensive screening in developed countries to tackle problems such as those associated with water and food quality, and tracking of infectious organisms in hospitals and clinics. Literature trends indicate an increasing interest in the use of nanomaterials, and in particular luminescent nanoparticles, for assay development. These materials may offer attributes for development of assays and sensors that could achieve improvements in analytical figures of merit, and provide practical advantages in sensitivity and stability. There is opportunity for cost-efficiency and technical simplicity by implementation of luminescent nanomaterials as the basis for transduction technology, when combined with the use of paper substrates, and the ubiquitous availability of cell phone cameras and associated infrastructure for optical detection and transmission of results. Luminescent nanoparticles have been described for a broad range of bioanalytical targets including small molecules, oligonucleotides, peptides, proteins, saccharides and whole cells (e.g., cancer diagnostics). The luminescent nanomaterials that are described herein for paper-based bioassays include metal nanoparticles, quantum dots and lanthanide-doped nanocrystals. These nanomaterials often have broad and strong absorption and narrow emission bands that improve opportunity for multiplexed analysis, and can be designed to provide emission at wavelengths that are efficiently processed by conventional digital cameras. Luminescent nanoparticles can be embedded in paper substrates that are designed to direct fluid flow, and the resulting combination of technologies can offer competitive analytical performance at relatively low cost.
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Affiliation(s)
- Qiang Ju
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing 211816, P.R. China. and Chemical Sensors Group, Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, ON, Canada L5L 1C6.
| | - M Omair Noor
- Chemical Sensors Group, Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, ON, Canada L5L 1C6.
| | - Ulrich J Krull
- Chemical Sensors Group, Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, ON, Canada L5L 1C6.
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21
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Oh SW, Pereira A, Zhang T, Li T, Lane A, Fu J. DNA-Mediated Proximity-Based Assembly Circuit for Actuation of Biochemical Reactions. Angew Chem Int Ed Engl 2018; 57:13086-13090. [PMID: 30129087 DOI: 10.1002/anie.201806749] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/25/2018] [Indexed: 01/09/2023]
Abstract
Smart nanodevices that integrate molecular recognition and signal production hold great promise for the point-of-care (POC) diagnostic applications. Herein, the development of a DNA-mediated proximity assembly of biochemical reactions, which was capable of sensing various bio-targets and reporting easy-to-read signals is reported. The circuit was composed of a DNA hairpin-locked catalytic cofactor with inhibited activity. Specific molecular inputs can trigger a conformational switch of the DNA locks through the mechanisms of toehold displacement and aptamer switching, exposing an active cofactor. The subsequent assembly of an enzyme/cofactor pair actuated a reaction to produce colorimetric or fluorescence signals for detecting target molecules. The developed system could be potentially applied to smart biosensing in molecular diagnostics and POC tests.
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Affiliation(s)
- Sung Won Oh
- Center for Computational and Integrative Biology, Rutgers University-Camden, 315 Penn Street, Science Building, Camden, NJ, 08102, USA
| | - Adriana Pereira
- Department of Chemistry, Rutgers University-Camden, 315 Penn Street, Camden, NJ, 08102, USA
| | - Ting Zhang
- Center for Computational and Integrative Biology, Rutgers University-Camden, 315 Penn Street, Science Building, Camden, NJ, 08102, USA
- Department of Chemistry, Rutgers University-Camden, 315 Penn Street, Camden, NJ, 08102, USA
| | - Tianran Li
- Center for Computational and Integrative Biology, Rutgers University-Camden, 315 Penn Street, Science Building, Camden, NJ, 08102, USA
| | - Ariel Lane
- Department of Chemistry, Rutgers University-Camden, 315 Penn Street, Camden, NJ, 08102, USA
| | - Jinglin Fu
- Center for Computational and Integrative Biology, Rutgers University-Camden, 315 Penn Street, Science Building, Camden, NJ, 08102, USA
- Department of Chemistry, Rutgers University-Camden, 315 Penn Street, Camden, NJ, 08102, USA
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22
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Kilic T, Erdem A, Ozsoz M, Carrara S. microRNA biosensors: Opportunities and challenges among conventional and commercially available techniques. Biosens Bioelectron 2018; 99:525-546. [DOI: 10.1016/j.bios.2017.08.007] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 08/01/2017] [Accepted: 08/04/2017] [Indexed: 12/19/2022]
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23
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Du K, Park M, Griffiths A, Carrion R, Patterson J, Schmidt H, Mathies R. Microfluidic System for Detection of Viral RNA in Blood Using a Barcode Fluorescence Reporter and a Photocleavable Capture Probe. Anal Chem 2017; 89:12433-12440. [PMID: 29073356 PMCID: PMC5990416 DOI: 10.1021/acs.analchem.7b03527] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A microfluidic sample preparation multiplexer (SPM) and assay procedure is developed to improve amplification-free detection of Ebola virus RNA from blood. While a previous prototype successfully detected viral RNA following off-chip RNA extraction from infected cells, the new device and protocol can detect Ebola virus in raw blood with clinically relevant sensitivity. The Ebola RNA is hybridized with sequence specific capture and labeling DNA probes in solution and then the complex is pulled down onto capture beads for purification and concentration. After washing, the captured RNA target is released by irradiating the photocleavable DNA capture probe with ultraviolet (UV) light. The released, labeled, and purified RNA is detected by a sensitive and compact fluorometer. Exploiting these capabilities, a detection limit of 800 attomolar (aM) is achieved without target amplification. The new SPM can run up to 80 assays in parallel using a pneumatic multiplexing architecture. Importantly, our new protocol does not require time-consuming and problematic off-chip probe conjugation and washing. This improved SPM and labeling protocol is an important step toward a useful POC device and assay.
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Affiliation(s)
- Ke Du
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - Myeongkee Park
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - Anthony Griffiths
- Department of Virology and Immunology, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, Texas 78227, United States
| | - Ricardo Carrion
- Department of Virology and Immunology, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, Texas 78227, United States
| | - Jean Patterson
- Department of Virology and Immunology, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, Texas 78227, United States
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Richard Mathies
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
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24
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Liao X, Li L, Pan J, Peng T, Ge B, Tang Q. In situ biosensor for detection miRNA in living cells based on carbon nitride nanosheets with catalytic hairpin assembly amplification. LUMINESCENCE 2017; 33:190-195. [PMID: 28929579 DOI: 10.1002/bio.3392] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 07/12/2017] [Accepted: 08/07/2017] [Indexed: 02/04/2023]
Abstract
In this study, an ultrasensitive fluorescence turn-on assay for in situ sensing of intracellular microRNA (miRNA) was developed utilizing a carbon nitride nanosheet (CNNS) and a catalytic hairpin assembly (CHA). The CHA showed favourable signal amplification for low-level biomarkers, and CNNS was an excellent candidate as a fluorescence quencher and gene vector. Moreover, the hairpin DNA of CHA could be adsorbed onto the surface of CNNS. An enzyme-free fluorescence biosensor for ultrasensitive sensing of intracellular miRNA in cells based on CHA and CNNS was designed. When faced with target miRNA, the fluorescence was recovered due to the miRNA, which could trigger cycling of CHA circuits, leading to the production of a marked enhanced fluorescence signal. Compared with traditional methods, the proposed method is convenient, with low cytotoxicity, and high specificity and ultrasensitivity. It has promising potential for detection low-level biomarkers.
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Affiliation(s)
- Xianjiu Liao
- West Guangxi Key Laboratory for Prevention and Treatment of High-incidence Diseases, Youjiang Medical University for Nationalities, Baise, People's Republic of China.,School of Integrated Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, People's Republic of China
| | - Liqing Li
- School of Integrated Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, People's Republic of China
| | - Jianbin Pan
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, People's Republic of China
| | - Tingting Peng
- West Guangxi Key Laboratory for Prevention and Treatment of High-incidence Diseases, Youjiang Medical University for Nationalities, Baise, People's Republic of China
| | - Bin Ge
- School of Integrated Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, People's Republic of China
| | - Qianli Tang
- West Guangxi Key Laboratory for Prevention and Treatment of High-incidence Diseases, Youjiang Medical University for Nationalities, Baise, People's Republic of China.,School of Integrated Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, People's Republic of China
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25
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Multiplex quantitative analysis of microRNA expression via exponential isothermal amplification and conformation-sensitive DNA separation. Sci Rep 2017; 7:11396. [PMID: 28900270 PMCID: PMC5595994 DOI: 10.1038/s41598-017-11895-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 09/01/2017] [Indexed: 12/02/2022] Open
Abstract
Expression profiling of multiple microRNAs (miRNAs) generally provides valuable information for understanding various biological processes. Thus, it is necessary to develop a sensitive and accurate miRNA assay suitable for multiplexing. Isothermal exponential amplification reaction (EXPAR) has received significant interest as an miRNA analysis method because of high amplification efficiency. However, EXPAR cannot be used for a broader range of applications owing to limitations such as complexity of probe design and lack of proper detection method for multiplex analysis. Here, we developed a sensitive and accurate multiplex miRNA profiling method using modified isothermal EXPAR combined with high-resolution capillary electrophoresis-based single-strand conformation polymorphism (CE-SSCP). To increase target miRNA specificity, a stem-loop probe was introduced instead of a linear probe in isothermal EXPAR to allow specific amplification of multiple miRNAs with minimal background signals. CE-SSCP, a conformation-dependent separation method, was used for detection. Since CE-SSCP eliminates the need for probes to have different lengths, easier designing of probes with uniform amplification efficiency was possible. Eight small RNAs comprising six miRNAs involved in Caenorhabditis elegans development and two controls were analyzed. The expression patterns obtained using our method were concordant with those reported in previous studies, thereby supporting the proposed method’s robustness and utility.
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26
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Lu Q, Ericson D, Song Y, Zhu C, Ye R, Liu S, Spernyak JA, Du D, Li H, Wu Y, Lin Y. MnO 2 Nanotube-Based NanoSearchlight for Imaging of Multiple MicroRNAs in Live Cells. ACS APPLIED MATERIALS & INTERFACES 2017; 9:23325-23332. [PMID: 28493665 PMCID: PMC5831178 DOI: 10.1021/acsami.6b15387] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Sensitive assay and imaging of multiple low-abundance microRNAs (miRNAs) in living cells remain a grand challenge. Herein, based on polyelectrolyte-induced reduction, a facile approach has been proposed to synthesize novel MnO2 nanotubes. Owing to the remarkably strong fluorescence quenching ability, low cytotoxicity, and excellent colloid stability, the as-prepared MnO2 nanotubes showed great potential for simultaneous detection and imaging of multiple miRNAs in vitro and in situ in living cells for the first time. Besides, MnO2 nanotubes can be reduced to Mn2+ by intracellular acid pH or glutathione, which may serve as an activatable contrast reagent for MRI. Therefore, the MnO2 nanotube-based probes, termed "NanoSearchlight", provide a promising, multimodal imaging tool for precise and accurate diagnosis and prognosis of cancers.
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Affiliation(s)
- Qian Lu
- School of Mechanical and Material Engineering, Washington State University, Pullman, Washington 99164, United States
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, Jiangsu 211189, China
| | - Daniel Ericson
- Department of Biomedical Engineering, State University of New York at Buffalo, Buffalo, New York 14260, United States
| | - Yang Song
- School of Mechanical and Material Engineering, Washington State University, Pullman, Washington 99164, United States
| | - Chengzhou Zhu
- School of Mechanical and Material Engineering, Washington State University, Pullman, Washington 99164, United States
| | - Ranfeng Ye
- School of Mechanical and Material Engineering, Washington State University, Pullman, Washington 99164, United States
| | - Songqin Liu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, Jiangsu 211189, China
| | - Joseph A. Spernyak
- Dept. of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, New York 14263, United States
| | - Dan Du
- School of Mechanical and Material Engineering, Washington State University, Pullman, Washington 99164, United States
| | - He Li
- School of Mechanical and Material Engineering, Washington State University, Pullman, Washington 99164, United States
| | - Yun Wu
- Department of Biomedical Engineering, State University of New York at Buffalo, Buffalo, New York 14260, United States
| | - Yuehe Lin
- School of Mechanical and Material Engineering, Washington State University, Pullman, Washington 99164, United States
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27
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Zhang M, Li R, Ling L. Homogenous assay for protein detection based on proximity DNA hybridization and isothermal circular strand displacement amplification reaction. Anal Bioanal Chem 2017; 409:4079-4085. [DOI: 10.1007/s00216-017-0356-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 03/14/2017] [Accepted: 03/31/2017] [Indexed: 01/13/2023]
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28
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Duan R, Lou X, Xia F. The development of nanostructure assisted isothermal amplification in biosensors. Chem Soc Rev 2016; 45:1738-49. [PMID: 26812957 DOI: 10.1039/c5cs00819k] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Developing simple and inexpensive methods to ultrasensitively detect biomarkers is important for medical diagnosis, food analysis and environmental security. In recent years, isothermal amplifications with sensitivity, high speed, specificity, accuracy, and automation have been designed based on interdisciplinary approaches among chemistry, biology, and materials science. In this article, we summarize the advances in nanostructure assisted isothermal amplification in the past two decades for the detection of commercial biomarkers, or biomarkers extracted from cultured cells or patient samples. This article has been divided into three parts according to the ratio of target-to-signal probe in the detection strategy, namely, the N : N amplification ratio, the 1 : N amplification ratio, and the 1 : N(2) amplification ratio.
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Affiliation(s)
- Ruixue Duan
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, P. R. China.
| | - Xiaoding Lou
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, P. R. China.
| | - Fan Xia
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, P. R. China.
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29
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Huang Y, Li H, Wang L, Mao X, Li G. Highly Sensitive Protein Detection Based on Smart Hybrid Nanocomposite-Controlled Switch of DNA Polymerase Activity. ACS APPLIED MATERIALS & INTERFACES 2016; 8:28202-28207. [PMID: 27681499 DOI: 10.1021/acsami.6b09270] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
In this work, we have successfully designed a smart and flexible signal amplification method based on a newly synthesized hybrid nanocomposite with switchable enzyme activity for specific and sensitive protein detection. The smart hybrid nanocomposite synthesized here is initially loaded with quenched fluorophore and a unique aptamer-inhibited DNA polymerase. It then undergoes target protein-triggered release of the fluorophore and activation of the DNA polymerase, which can thereby promote multiple catalytic reactions and recycled use of the target protein, resulting in the generation of highly amplified signals. Therefore, a small amount of target protein can lead to a large amount of signal without being consumed. In addition, the programmable control of DNA polymerase activity may effectively reduce background signal and avoid false positive results, which may further facilitate an efficient detection of small amounts of protein. By taking the detection of human stress-induced phosphoprotein 1 (STIP1) as an example, the excellent performance of this method has been verified. Furthermore, the proposed method has been used to analyze serum STIP1 from patients of ovarian cancer, showing promising application in clinical practice.
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Affiliation(s)
- Yue Huang
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University , Nanjing 210093, P.R. China
| | - Hao Li
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University , Nanjing 210093, P.R. China
| | - Lei Wang
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University , Nanjing 210093, P.R. China
| | - Xiaoxia Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University , Shanghai 200444, P.R. China
| | - Genxi Li
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University , Nanjing 210093, P.R. China
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University , Shanghai 200444, P.R. China
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30
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Persano S, Guevara ML, Wolfram J, Blanco E, Shen H, Ferrari M, Pompa PP. Label-Free Isothermal Amplification Assay for Specific and Highly Sensitive Colorimetric miRNA Detection. ACS OMEGA 2016; 1:448-455. [PMID: 27713932 PMCID: PMC5046170 DOI: 10.1021/acsomega.6b00109] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 09/06/2016] [Indexed: 05/11/2023]
Abstract
We describe a new method for the detection of miRNA in biological samples. This technology is based on the isothermal nicking enzyme amplification reaction and subsequent hybridization of the amplification product with gold nanoparticles and magnetic microparticles (barcode system) to achieve naked-eye colorimetric detection. This platform was used to detect a specific miRNA (miRNA-10b) associated with breast cancer, and attomolar sensitivity was demonstrated. The assay was validated in cell culture lysates from breast cancer cells and in serum from a mouse model of breast cancer.
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Affiliation(s)
- Stefano Persano
- Department
of Nanomedicine, Houston Methodist Research
Institute, 6670 Bertner
Avenue, Houston 77030, Texas, United States
- Istituto
Italiano di Tecnologia (IIT), Via Morego, 30, 16163 Genova, Italy
- Università
del Salento, Via Provinciale
Monteroni, 73100 Lecce, Italy
| | - Maria L. Guevara
- Department
of Nanomedicine, Houston Methodist Research
Institute, 6670 Bertner
Avenue, Houston 77030, Texas, United States
| | - Joy Wolfram
- Department
of Nanomedicine, Houston Methodist Research
Institute, 6670 Bertner
Avenue, Houston 77030, Texas, United States
| | - Elvin Blanco
- Department
of Nanomedicine, Houston Methodist Research
Institute, 6670 Bertner
Avenue, Houston 77030, Texas, United States
| | - Haifa Shen
- Department
of Nanomedicine, Houston Methodist Research
Institute, 6670 Bertner
Avenue, Houston 77030, Texas, United States
- Department of Cell
and Developmental Biology and Department of Medicine, Weill Cornell Medicine, 1330 York Avenue, New York 10065, New York, United
States
| | - Mauro Ferrari
- Department
of Nanomedicine, Houston Methodist Research
Institute, 6670 Bertner
Avenue, Houston 77030, Texas, United States
- Department of Cell
and Developmental Biology and Department of Medicine, Weill Cornell Medicine, 1330 York Avenue, New York 10065, New York, United
States
| | - Pier Paolo Pompa
- Istituto
Italiano di Tecnologia (IIT), Via Morego, 30, 16163 Genova, Italy
- E-mail:
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31
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Xu Y, Wang Y, Liu S, Yu J, Wang H, Guo Y, Huang J. Ultrasensitive and rapid detection of miRNA with three-way junction structure-based trigger-assisted exponential enzymatic amplification. Biosens Bioelectron 2016; 81:236-241. [DOI: 10.1016/j.bios.2016.02.034] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 01/31/2016] [Accepted: 02/13/2016] [Indexed: 11/24/2022]
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32
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Aw SS, Tang MX, Teo YN, Cohen SM. A conformation-induced fluorescence method for microRNA detection. Nucleic Acids Res 2016; 44:e92. [PMID: 26951376 PMCID: PMC4889923 DOI: 10.1093/nar/gkw108] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 02/12/2016] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs play important roles in a large variety of biological systems and processes through their regulation of target mRNA expression, and show promise as clinical biomarkers. However, their small size presents challenges for tagging or direct detection. Innovation in techniques to sense and quantify microRNAs may aid research into novel aspects of microRNA biology and contribute to the development of diagnostics. By introducing an additional stem loop into the fluorescent RNA Spinach and altering its 3' and 5' ends, we have generated a new RNA, Pandan, that functions as the basis for a microRNA sensor. Pandan contains two sequence-variable stem loops that encode complementary sequence for a target microRNA of interest. In its sensor form, it requires the binding of a target microRNA in order to reconstitute the RNA scaffold for fluorophore binding and fluorescence. Binding of the target microRNA resulted in large changes in fluorescence intensity. The median fold change in fluorescence observed for the sensors tested was ∼50-fold. Pandan RNA sensors exhibit good signal-to-noise ratios, and can detect their target microRNAs within complex RNA mixtures.
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Affiliation(s)
- Sherry S Aw
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673, Singapore
| | - Melissa Xm Tang
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673, Singapore
| | - Yin Nah Teo
- Molecular Engineering Laboratory, Biomolecular Sciences Institutes, A*STAR, 61 Biopolis Drive, 138673, Singapore Division of Chemistry and Biological Chemistry, SPMS, Nanyang Technological University, 637371, Singapore
| | - Stephen M Cohen
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673, Singapore Department of Cellular and Molecular Medicine,University of Copenhagen, Blegdamsvej 3, Copenhagen 2200 N, Denmark
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33
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Kim J, Lee E, Kang YY, Mok H. Multivalent aptamer-RNA based fluorescent probes for carrier-free detection of cellular microRNA-34a in mucin1-expressing cancer cells. Chem Commun (Camb) 2016; 51:9038-41. [PMID: 25939820 DOI: 10.1039/c5cc02052b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
In this study, multivalent carrier-free aptamer-RNA based fluorescent probes (CF-probes) were designed as a simpler, more reliable, timesaving strategy for cellular miRNA detection. CF-probes spontaneously delivered into cells without the need for additional carriers and visualized target microRNA-34a specifically.
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Affiliation(s)
- Jihyun Kim
- Department of Bioscience and Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 143-701, Republic of Korea.
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34
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Wang H, Wang Y, Liu S, Yu J, Xu W, Guo Y, Huang J. Target-aptamer binding triggered quadratic recycling amplification for highly specific and ultrasensitive detection of antibiotics at the attomole level. Chem Commun (Camb) 2016; 51:8377-80. [PMID: 25892458 DOI: 10.1039/c5cc01473e] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A novel electrochemical aptasensor for ultrasensitive detection of antibiotics by combining polymerase-assisted target recycling amplification with strand displacement amplification with the help of polymerase and nicking endonuclease has been reported. This work is the first time that target-aptamer binding triggered quadratic recycling amplification has been utilized for electrochemical detection of antibiotics.
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Affiliation(s)
- Hongzhi Wang
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China.
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35
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Nuclease assisted target recycling and spherical nucleic acids gold nanoparticles recruitment for ultrasensitive detection of microRNA. Electrochim Acta 2016. [DOI: 10.1016/j.electacta.2016.01.034] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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36
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Pan X, Smith CE, Zhang J, McCabe KA, Fu J, Bell CE. A Structure-Activity Analysis for Probing the Mechanism of Processive Double-Stranded DNA Digestion by λ Exonuclease Trimers. Biochemistry 2016; 54:6139-48. [PMID: 26361255 DOI: 10.1021/acs.biochem.5b00707] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
λ exonuclease (λexo) is an ATP-independent 5'-to-3' exonuclease that binds to double-stranded DNA (dsDNA) ends and processively digests the 5'-strand into mononucleotides. The crystal structure of λexo revealed that the enzyme forms a ring-shaped homotrimer with a central funnel-shaped channel for tracking along the DNA. On the basis of this structure, it was proposed that dsDNA enters the open end of the channel, the 5'-strand is digested at one of the three active sites, and the 3'-strand passes through the narrow end of the channel to emerge out the back. This model was largely confirmed by the structure of the λexo-DNA complex, which further revealed that the enzyme unwinds the DNA by 2 bp prior to cleavage, to thread the 5'-end of the DNA into the active site. On the basis of this structure, an "electrostatic ratchet" model was proposed, in which the enzyme uses a hydrophobic wedge to insert into the base pairs to unwind the DNA, a two-metal mechanism for nucleotide hydrolysis, a positively charged pocket to bind to the terminal 5'-phosphate generated after each round of cleavage, and an arginine residue (Arg-45) to bind to the minor groove of the downstream end of the DNA. To test this model, in this study we have determined the effects of 11 structure-based mutations in λexo on DNA binding and exonuclease activities in vitro, and on DNA recombination in vivo. The results are largely consistent with the model for the mechanism that was proposed on the basis of the structure and provide new insights into the roles of particular residues of the protein in promoting the reaction. In particular, a key role for Arg-45 in DNA binding is revealed.
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Affiliation(s)
| | | | | | | | - Jun Fu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University , Shanda Nanlu 27, 250100 Jinan, People's Republic of China
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37
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Zhang J, Wu DZ, Cai SX, Chen M, Xia YK, Wu F, Chen JH. An immobilization-free electrochemical impedance biosensor based on duplex-specific nuclease assisted target recycling for amplified detection of microRNA. Biosens Bioelectron 2016; 75:452-7. [DOI: 10.1016/j.bios.2015.09.006] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 08/27/2015] [Accepted: 09/03/2015] [Indexed: 12/31/2022]
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38
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Lou X, Zhang M, Zhao Z, Min X, Hakeem A, Huang F, Gao P, Xia F, Tang BZ. A photostable AIE fluorogen for lysosome-targetable imaging of living cells. J Mater Chem B 2016; 4:5412-5417. [DOI: 10.1039/c6tb01293k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We designed and synthesized a lysosome-targetable fluorescence probe, TPE-CA, which can sensitively and selectively monitor a subcellular organelle pH change.
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Affiliation(s)
- Xiaoding Lou
- Faculty of Material Science and Chemistry
- China University of Geosciences
- Wuhan 430074
- China
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica
| | - Mengshi Zhang
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology
- Wuhan 430074
- China
| | - Zujin Zhao
- State Key Laboratory of Luminescent Materials and Devices
- South China University of Technology
- Guangzhou 510640
- China
| | - Xuehong Min
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology
- Wuhan 430074
- China
| | - Abdul Hakeem
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology
- Wuhan 430074
- China
| | - Fujian Huang
- Faculty of Material Science and Chemistry
- China University of Geosciences
- Wuhan 430074
- China
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica
| | - Pengcheng Gao
- Faculty of Material Science and Chemistry
- China University of Geosciences
- Wuhan 430074
- China
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica
| | - Fan Xia
- Faculty of Material Science and Chemistry
- China University of Geosciences
- Wuhan 430074
- China
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica
| | - Ben Zhong Tang
- State Key Laboratory of Luminescent Materials and Devices
- South China University of Technology
- Guangzhou 510640
- China
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39
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40
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Nucleic acid tool enzymes-aided signal amplification strategy for biochemical analysis: status and challenges. Anal Bioanal Chem 2015; 408:2793-811. [DOI: 10.1007/s00216-015-9240-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/13/2015] [Accepted: 12/01/2015] [Indexed: 11/27/2022]
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41
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Zhang J, Li C, Zhi X, Ramón GA, Liu Y, Zhang C, Pan F, Cui D. Hairpin DNA-Templated Silver Nanoclusters as Novel Beacons in Strand Displacement Amplification for MicroRNA Detection. Anal Chem 2015; 88:1294-302. [PMID: 26675240 DOI: 10.1021/acs.analchem.5b03729] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
MicroRNA (miRNA) biomarkers display great potential for cancer diagnosis and prognosis. The development of rapid and specific methods for miRNA detection has become a hotspot. Herein, hairpin DNA-templated silver nanoclusters (AgNCs/HpDNA) were prepared and integrated into strand-displacement amplification (SDA) as a novel beacon for miRNA detection. The light-up platform was established based on guanine (G)-rich fluorescence enhancement that essentially converted the excitation/emission pair of AgNCs/HpDNAs from a shorter wavelength to a longer wavelength, and then achieved fluorescent enhancement at longer wavelength. On the basis of the validation of the method, the single and duplex detection were conducted in two plasma biomarkers (miR-16-5p and miR-19b-3p) for the diagnosis of gastric cancer. The probe (AgNCs/RED 16(7s)C) utilized for miR-16-5p detection adopted a better conformation with high specificity to recognize single-base mismatches by producing dramatically opposite signals (increase or decrease at 580 nm ex/640 nm em) while the probe (AgNCs/GRE 19b(5s)C) for miR-19b-3p generated dual signals (increase at 490 nm ex/570 nm em and decrease at 430 nm ex/530 nm em) with bright fluorescence in one reaction during the amplification, but unexpectedly was partially digested. This is for the first time to allow the generation of enhanced fluorescent AgNCs and the target recognition integrated into a single process, which offers great opportunity for specific miRNA detection in an easy and rapid way.
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Affiliation(s)
- Jingpu Zhang
- Institute of Nano Biomedicine and Engineering, Key Laboratory for Thin Film and Microfabrication of the Ministry of Education, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering; ‡School of Biomedical Engineering, §National Center for Translational Medicine, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Chao Li
- Institute of Nano Biomedicine and Engineering, Key Laboratory for Thin Film and Microfabrication of the Ministry of Education, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering; ‡School of Biomedical Engineering, §National Center for Translational Medicine, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Xiao Zhi
- Institute of Nano Biomedicine and Engineering, Key Laboratory for Thin Film and Microfabrication of the Ministry of Education, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering; ‡School of Biomedical Engineering, §National Center for Translational Medicine, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Gabriel Alfranca Ramón
- Institute of Nano Biomedicine and Engineering, Key Laboratory for Thin Film and Microfabrication of the Ministry of Education, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering; ‡School of Biomedical Engineering, §National Center for Translational Medicine, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Yanlei Liu
- Institute of Nano Biomedicine and Engineering, Key Laboratory for Thin Film and Microfabrication of the Ministry of Education, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering; ‡School of Biomedical Engineering, §National Center for Translational Medicine, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Chunlei Zhang
- Institute of Nano Biomedicine and Engineering, Key Laboratory for Thin Film and Microfabrication of the Ministry of Education, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering; ‡School of Biomedical Engineering, §National Center for Translational Medicine, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Fei Pan
- Institute of Nano Biomedicine and Engineering, Key Laboratory for Thin Film and Microfabrication of the Ministry of Education, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering; ‡School of Biomedical Engineering, §National Center for Translational Medicine, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Daxiang Cui
- Institute of Nano Biomedicine and Engineering, Key Laboratory for Thin Film and Microfabrication of the Ministry of Education, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering; ‡School of Biomedical Engineering, §National Center for Translational Medicine, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, P. R. China
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42
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Wang C, Zhang H, Zeng D, Sun W, Zhang H, Aldalbahi A, Wang Y, San L, Fan C, Zuo X, Mi X. Elaborately designed diblock nanoprobes for simultaneous multicolor detection of microRNAs. NANOSCALE 2015; 7:15822-15829. [PMID: 26359758 DOI: 10.1039/c5nr04618a] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Simultaneous detection of multiple biomarkers has important prospects in the biomedical field. In this work, we demonstrated a novel strategy for the detection of multiple microRNAs (miRNAs) based on gold nanoparticles (Au NPs) and polyadenine (polyA) mediated nanoscale molecular beacon (MB) probes (denoted p-nanoMBs). Novel fluorescent labeled p-nanoMBs bearing consecutive adenines were designed, of which polyA served as an effective anchoring block binding to the surface of Au NPs, and the appended hairpin block formed an upright conformation that favored the hybridization with targets. Using the co-assembling method and the improved hybridization conformation of the hairpin probes, we achieved high selectivity for specifically distinguishing DNA targets from single-base mismatched DNA targets. We also realized multicolor detection of three different synthetic miRNAs in a wide dynamic range from 0.01 nM to 200 nM with a detection limit of 10 pM. What's more, we even detected miRNAs in a simulated serum environment, which indicated that our method could be used in complex media. Compared with the traditional method, our strategy provides a promising alternative method for the qualitative and quantitative detection of miRNAs.
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Affiliation(s)
- Chenguang Wang
- Laboratory of System Biology, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.
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43
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Huang Y, Li H, Zhang Y, Li W, Sun L, Li G. Ultrasensitive and feasibly achieved protein detection based on the integration of three signal amplification reactions via sharing a DNA sequence. Chem Commun (Camb) 2015; 51:11004-7. [PMID: 26051912 DOI: 10.1039/c5cc03700j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
This communication reports a novel strategy for the detection of proteins based on the integration of three signal amplification reactions via sharing a specially designed DNA sequence. This strategy has been demonstrated by the assay of human TNF-α in the serum of ovarian cancer patients, showing potential clinical applications.
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Affiliation(s)
- Yue Huang
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University, Nanjing 210093, P. R. China.
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44
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Xie M, Zhou S, Mao Y. Ultrasensitive Fluorescence Determination of Adenosine Deaminase using DNA-Templated Silver Nanoclusters and Isothermal Amplification. ANAL LETT 2015. [DOI: 10.1080/00032719.2015.1004076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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45
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Pan X, Yan J, Patel A, Wysocki VH, Bell CE. Mutant poisoning demonstrates a nonsequential mechanism for digestion of double-stranded DNA by λ exonuclease trimers. Biochemistry 2015; 54:942-51. [PMID: 25531139 DOI: 10.1021/bi501431w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
λ Exonuclease (λexo) is a highly processive 5'-3' exonuclease that binds double-stranded DNA (dsDNA) ends and digests the 5'-strand into mononucleotides. The enzyme forms a toroidal homotrimer with a central tapered channel for tracking along the DNA. During catalysis, dsDNA enters the open end of the channel, and the 5'-strand is digested at one of the three active sites. It is currently not known if λexo uses a sequential mechanism, in which the DNA moves from one active site to the next around the trimer for each round of catalysis or a nonsequential mechanism, in which the DNA locks onto a single active site for multiple rounds. To understand how λexo uses its three active sites, we used a mutant poisoning approach, in which a 6xHis-tagged K131A inactive mutant of λexo was mixed with untagged wild type (WT) to form hybrid trimers. Nickel-spin pull-down analysis confirmed complete subunit exchange after 1 h at 37 °C. Exonuclease assays revealed an approximately linear decrease in activity with increasing fraction of mutant, as expected for a nonsequential mechanism. By fitting the observed rates of digestion to a simple mathematical model, the individual rates of the two hybrid species of trimer were determined. This analysis showed that trimers containing only one or two WT subunits contribute significantly to the observed activity, in further agreement with a nonsequential mechanism. Finally, purification of hybrid trimer mixtures by Ni-spin chromatography, to remove the contribution from fully WT trimers, also resulted in significant levels of activity, again consistent with a nonsequential mechanism.
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Affiliation(s)
- Xinlei Pan
- Ohio State Biochemistry Program, ‡Department of Molecular and Cellular Biochemistry, and §Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States
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46
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Isothermal circular-strand-displacement polymerization of DNA and microRNA in digital microfluidic devices. Anal Bioanal Chem 2015; 407:1533-43. [PMID: 25579461 DOI: 10.1007/s00216-014-8405-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/12/2014] [Accepted: 12/10/2014] [Indexed: 12/17/2022]
Abstract
Nucleic-acid amplification is a crucial step in nucleic-acid-sequence-detection assays. The use of digital microfluidic devices to miniaturize amplification techniques reduces the required sample volume and the analysis time and offers new possibilities for process automation and integration in a single device. The recently introduced droplet polymerase-chain-reaction (PCR) amplification methods require repeated cycles of two or three temperature-dependent steps during the amplification of the nucleic-acid target sequence. In contrast, low-temperature isothermal-amplification methods have no need for thermal cycling, thus requiring simplified microfluidic-device features. Here, the combined use of digital microfluidics and molecular-beacon (MB)-assisted isothermal circular-strand-displacement polymerization (ICSDP) to detect microRNA-210 sequences is described. MicroRNA-210 has been described as the most consistently and predominantly upregulated hypoxia-inducible factor. The nmol L(-1)-pmol L(-1) detection capabilities of the method were first tested by targeting single-stranded DNA sequences from the genetically modified Roundup Ready soybean. The ability of the droplet-ICSDP method to discriminate between full-matched, single-mismatched, and unrelated sequences was also investigated. The detection of a range of nmol L(-1)-pmol L(-1) microRNA-210 solutions compartmentalized in nanoliter-sized droplets was performed, establishing the ability of the method to detect as little as 10(-18) mol of microRNA target sequences compartmentalized in 20 nL droplets. The suitability of the method for biological samples was tested by detecting microRNA-210 from transfected K562 cells.
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47
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Chiang VSC. Post- harvest consideration factors for microRNA research in cellular, tissue, serum and plasma samples. Cell Biol Int 2014; 38:1345-54. [DOI: 10.1002/cbin.10346] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 05/28/2014] [Indexed: 12/12/2022]
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48
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Wang L, Liu Y, Li J. Self-phosphorylating deoxyribozyme initiated cascade enzymatic amplification for guanosine-5'-triphosphate detection. Anal Chem 2014; 86:7907-12. [PMID: 24971649 DOI: 10.1021/ac501842t] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The self-phosphorylating deoxyribozymes identified by in vitro selection can catalyze their own phosphorylation by utilizing phosphate donor guanosine-5'-triphosphate (GTP) which plays a critical role in a majority of cellular processes. On the basis of the unique properties of self-phosphorylating deoxyribozymes, we report a novel GTP sensor coupled with λ exonuclease cleavage reaction and nicking enzyme assisted fluorescence signal amplification process. The deoxyribozymes with special catalytic and structural characteristics display good stability compared to protein and RNA enzymes. We combined these properties with enzymatic recycling cleavage strategy to build a sensor which produced enhanced fluorescence signal. Sensitive and selective detection of GTP was successfully realized with the well-designed deoxyribozyme-based sensing platform by taking advantage of the self-phosphorylating ability of the kinase deoxyribozyme, efficient digestion capacity of λ exonuclease, and enzymatic recycling amplification of nicking enzyme. The method not only provides a platform for detecting GTP but also shows great potential in analyzing a variety of targets by combining deoxyribozymes with signal amplification strategy.
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Affiliation(s)
- Lida Wang
- Department of Chemistry, Beijing Key Laboratory for Analytical Methods and Instrumentation, Tsinghua University , Beijing 100084, China
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Tian L, Cronin TM, Weizmann Y. Enhancing-effect of gold nanoparticles on DNA strand displacement amplifications and their application to an isothermal telomerase assay. Chem Sci 2014. [DOI: 10.1039/c4sc01393j] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AuNPs take the reliability of a typical isothermal DNA amplification assay to a new level of accuracy, specificity, and sensitivity.
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Affiliation(s)
- Leilei Tian
- Department of Chemistry and Institute for Biophysical Dynamics
- The University of Chicago
- Chicago, USA
| | - Timothy M. Cronin
- Department of Chemistry and Institute for Biophysical Dynamics
- The University of Chicago
- Chicago, USA
| | - Yossi Weizmann
- Department of Chemistry and Institute for Biophysical Dynamics
- The University of Chicago
- Chicago, USA
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