151
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Newbigging AM, Zhang H, Le XC. Beacon-mediated exponential amplification reaction (BEAR) using a single enzyme and primer. Chem Commun (Camb) 2019; 55:10677-10680. [PMID: 31424057 DOI: 10.1039/c9cc04226a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Beacon-mediated Exponential Amplification Reaction (BEAR) enables isothermal, exponential signal amplification. BEAR uses only a single enzyme and a single primer. Detection of 0.2 amol of a mitochondrial DNA with a point mutation in less than an hour demonstrates an application of the BEAR technique for nucleic acid research.
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Affiliation(s)
- Ashley M Newbigging
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada.
| | - Hongquan Zhang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada.
| | - X Chris Le
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada.
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152
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Li W, Wang F, Chen Y, Weng X, Zhou X. A sensitive and radiolabeling-free method for pseudouridine detection. Anal Biochem 2019; 581:113350. [PMID: 31255565 DOI: 10.1016/j.ab.2019.113350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/25/2019] [Accepted: 06/26/2019] [Indexed: 01/28/2023]
Abstract
Existing methodologies for detecting Pseudouridine (Ψ) mostly use CMCT labeling or radiolabeling. Described herein is a sensitive and quantitative method for Ψ detection that does not need this labelling. This approach combines the selectivity of a 10-23 DNAzyme, which can distinguish Ψ from uridine (U), with rolling circle amplification (RCA) to increase the sensitivity of the assay.
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Affiliation(s)
- Wei Li
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, 430072, PR China
| | - Fang Wang
- Wuhan University School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yi Chen
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, 430072, PR China
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, 430072, PR China.
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute for Advanced Studies, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, 430072, PR China
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153
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Li J, Lin L, Yu J, Zhai S, Liu G, Tian L. Fabrication and Biomedical Applications of “Polymer-Like” Nucleic Acids Enzymatically Produced by Rolling Circle Amplification. ACS APPLIED BIO MATERIALS 2019; 2:4106-4120. [DOI: 10.1021/acsabm.9b00622] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jing Li
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Li Lin
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Jiantao Yu
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Shiyao Zhai
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Guoyuan Liu
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Leilei Tian
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
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154
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Sustained Release of Minor-Groove-Binding Antibiotic Netropsin from Calcium-Coated Groove-Rich DNA Particles. Pharmaceutics 2019; 11:pharmaceutics11080387. [PMID: 31382405 PMCID: PMC6724015 DOI: 10.3390/pharmaceutics11080387] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/14/2019] [Accepted: 07/22/2019] [Indexed: 12/02/2022] Open
Abstract
Control of the release properties of drugs has been considered a key factor in the development of drug delivery systems (DDSs). However, drug delivery has limitations including cytotoxicity, low loading efficiency, and burst release. To overcome these challenges, nano or micro-particles have been suggested as carrier systems to deliver chemical drugs. Herein, nano-sized DNA particles (DNAp) were manufactured to deliver netropsin, which is known to bind to DNA minor grooves. The rationally designed particles with exposed rich minor grooves were prepared by DNAp synthesis via rolling circle amplification (RCA). DNAp could load large quantities of netropsin in its minor grooves. An analytical method was also developed for the quantification of netropsin binding to DNAp by UV–visible spectrometry. Moreover, controlled release of netropsin was achieved by forming a layer of Ca2+ on the DNAp (CaDNAp). As a proof of concept, the sustained release of netropsin by CaDNAp highlights the potential of the DNAp-based delivery approach.
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155
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Fan T, Mao Y, Liu F, Zhang W, Lin JS, Yin J, Tan Y, Huang X, Jiang Y. Label-free fluorescence detection of circulating microRNAs based on duplex-specific nuclease-assisted target recycling coupled with rolling circle amplification. Talanta 2019; 200:480-486. [DOI: 10.1016/j.talanta.2019.01.038] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 01/04/2019] [Accepted: 01/09/2019] [Indexed: 11/15/2022]
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156
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Schneider GX, Gomes RR, Bombassaro A, Zamarchi K, Voidaleski MF, Costa FF, Leão ACR, Lima BJFS, Soley BS, Colombo IR, Cândido GZ, Najafzadeh MJ, Sun J, de Azevedo CMPS, Marques SG, de Hoog GS, Vicente VA. New Molecular Markers Distinguishing Fonsecaea Agents of Chromoblastomycosis. Mycopathologia 2019; 184:493-504. [PMID: 31317385 DOI: 10.1007/s11046-019-00359-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/01/2019] [Indexed: 11/28/2022]
Abstract
The species belonging to the genus Fonsecaea are the main causative agents of chromoblastomycosis. The invasive potential of Fonsecaea differs significantly among its various sibling species. Moreover, the lack of clarity on the virulence and availability of precise markers to distinguish and detect Fonsecaea species is attributed to the different ways of dissemination and pathogenicity. Therefore, the present study aimed to propose new molecular tools to differentiate between sibling species causing chromoblastomycosis. We used an infection model of chromoblastomycosis in BALB/c to study species-specific molecular markers for the in vivo detection of Fonsecaea species in biological samples. Specific primers based on the CBF5 gene were developed for Fonsecaea pedrosoi, Fonsecaea monophora, Fonsecaea nubica, and Fonsecaea pugnacius. In addition, a padlock probe was designed for F. pugnacius based on ITS sequences. We also assessed the specificity of Fonsecaea species using in silico, in vitro, and in vivo assays. The results showed that markers and probes could effectively discriminate the species in both clinical and environmental samples, enabling bioprospecting of agents of chromoblastomycosis, thereby elucidating the infection route of the disease.
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Affiliation(s)
- Gabriela X Schneider
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Renata R Gomes
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Amanda Bombassaro
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Kassiely Zamarchi
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Morgana F Voidaleski
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Flávia F Costa
- Engineering Bioprocess and Biotechnology Post-Graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil
| | - Aniele C R Leão
- Engineering Bioprocess and Biotechnology Post-Graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil
| | - Bruna J F S Lima
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Bruna S Soley
- Department of Pharmacology, Federal University of Paraná, Curitiba, Brazil
| | - Israella R Colombo
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Giovanna Z Cândido
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Mohammad J Najafzadeh
- Department of Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jiufeng Sun
- Department of Dermatology, The Second Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Conceição M P S de Azevedo
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Brazil.,Department of Medicine, Federal University of Maranhão, São Luis, Brazil
| | - Sirlei G Marques
- University Hospital, Federal University of Maranhão, São Luiz, Brazil.,Cedro Laboratory, São Luiz, Brazil
| | - G Sybren de Hoog
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Brazil. .,Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands. .,Center of Expertise in Mycology of Radboud University Medical Center, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands.
| | - Vânia A Vicente
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Pathology, Federal University of Paraná, Curitiba, Brazil.
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157
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Kong Y, Liu X, Liu C, Xue Q, Li X, Wang H. A dandelion-like liposomes-encoded magnetic bead probe-based toehold-mediated DNA circuit for the amplification detection of MiRNA. Analyst 2019; 144:4694-4701. [PMID: 31268436 DOI: 10.1039/c9an00887j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The development of facile and sensitive miRNA quantitative detection methods is a central challenge for the early diagnosis of miRNA-related diseases. Herein, we propose a strategy for a liposome-encoded magnetic bead-based DNA toehold-mediated DNA circuit for the simple and sensitive detection of miRNA based on a toehold-mediated circular strand displacement reaction (TCSDR) coupled with a personal glucometer (PGM ). In this strategy, a glucoamylase-encapsulated liposomes (GELs)-encoded magnetic bead (GELs-MB) probe is designed to integrate target binding, magnetic separation, and signal response. Upon sensing the target miRNA-21, a GELs-MB probe-based toehold-mediated circular strand displacement reaction (TCSDR) was initiated with the help of fuel-DNA, constructing a DNA circuit system, and realizing target recycling amplification and the disassembly of the liposomes. The disassembled liposomes were finally removed via magnetic separation, and the encapsulated glucoamylase was liberated to catalyze amylose hydrolysis with multiple turnovers to glucose for a PGM readout. Benefiting from target recycling amplification initiated by the toehold-mediated DNA circuit and the liposome multiple-label amplification, a small quantity of target miRNA-21 can be transformed into a large glucose signal. The strategy realized the quantification of miRNA-21 down to a level of 0.7 fM without enzymatic amplification or precise instrumentation. Moreover, the high-density GELs-MB probe allows the sensitive detection of miRNA-21 to be accomplished within 1.5 h. Furthermore, this strategy exhibits the advantages of specificity and simplicity, since a toehold-mediated strand displacement reaction, magnetic separation and portable PGM were used. Importantly, this strategy has been demonstrated to allow the high-confidence quantification of miRNA. Therefore, with the advantages of low cost, ease of use, portability, and sensitivity, the reported method holds great potential for the early diagnosis of miRNA-related diseases.
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Affiliation(s)
- Yancong Kong
- Department of Chemistry, Liaocheng University, Liaocheng, 252059, Shandong, China.
| | - Xiaowen Liu
- Department of Chemistry, Liaocheng University, Liaocheng, 252059, Shandong, China.
| | - Chunxue Liu
- Department of Chemistry, Liaocheng University, Liaocheng, 252059, Shandong, China.
| | - Qingwang Xue
- Department of Chemistry, Liaocheng University, Liaocheng, 252059, Shandong, China.
| | - Xia Li
- Department of Chemistry, Liaocheng University, Liaocheng, 252059, Shandong, China.
| | - Huaisheng Wang
- Department of Chemistry, Liaocheng University, Liaocheng, 252059, Shandong, China.
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158
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Liu L, Yang D, Liu G. Signal amplification strategies for paper-based analytical devices. Biosens Bioelectron 2019; 136:60-75. [DOI: 10.1016/j.bios.2019.04.043] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/15/2019] [Accepted: 04/21/2019] [Indexed: 12/26/2022]
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159
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Ultrasensitive Real-Time Rolling Circle Amplification Detection Enhanced by Nicking-Induced Tandem-Acting Polymerases. Anal Chem 2019; 91:10102-10109. [DOI: 10.1021/acs.analchem.9b02073] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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160
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Jiang Y, Li S, Qiu Z, Le T, Zou S, Cao X. Rolling circle amplification and its application in microfluidic systems for
Escherichia coli
O157:H7 detections. J Food Saf 2019. [DOI: 10.1111/jfs.12671] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Yuqian Jiang
- Department of Chemical and Biological EngineeringUniversity of Ottawa Ottawa Ontario Canada
- Measurement Science and StandardsNational Research Council Canada Ottawa Ontario Canada
| | - Shuying Li
- Department of Chemical and Biological EngineeringUniversity of Ottawa Ottawa Ontario Canada
- Measurement Science and StandardsNational Research Council Canada Ottawa Ontario Canada
| | - Zhenyu Qiu
- Division of Advanced FabricationsNanchang Institute of Technology Nanchang Jiangxi Province China
| | - Tao Le
- College of Life ScienceChongqing Normal University Shapingba Chongqing China
| | - Shan Zou
- Measurement Science and StandardsNational Research Council Canada Ottawa Ontario Canada
| | - Xudong Cao
- Department of Chemical and Biological EngineeringUniversity of Ottawa Ottawa Ontario Canada
- Ottawa‐Carleton Institute of Biomedical EngineeringUniversity of Ottawa Ottawa Ontario Canada
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161
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Yuan Y, Gu Z, Yao C, Luo D, Yang D. Nucleic Acid-Based Functional Nanomaterials as Advanced Cancer Therapeutics. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900172. [PMID: 30972963 DOI: 10.1002/smll.201900172] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/04/2019] [Indexed: 06/09/2023]
Abstract
Nucleic acid-based functional nanomaterials (NAFN) have been widely used as emerging drug delivery nanocarriers for cancer therapeutics. Considerable works have demonstrated that NAFN can effectively load and protect therapeutic agents, and particularly enable targeting delivery to the tumor site and stimuli-responsive release. These outstanding performances are due to NAFN's unique properties including inherent biological functions and sequence programmability as well as biocompatibility and biodegradability. In this Review, the recent progress on NAFN as advanced cancer therapeutics is highlighted. Three main cancer therapy approaches are categorized including chemo-, immuno-, and gene-therapy. Examples are presented to show how NAFN are rationally and exquisitely designed to address problems in cancer therapy. The challenges and future development of NAFN are also discussed toward future more practical biomedical applications.
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Affiliation(s)
- Ye Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Zi Gu
- School of Chemical Engineering and Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Chi Yao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Dan Luo
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, 14853, USA
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, P. R. China
| | - Dayong Yang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
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162
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Sharafdarkolaee SH, Gill P, Motovali-Bashi M, Sharafdarkolaee FH. Isothermal Amplification Methods for the SNP Genotyping. Curr Mol Med 2019; 19:461-472. [PMID: 31131752 DOI: 10.2174/1566524019666190527083947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 06/30/2018] [Accepted: 04/23/2019] [Indexed: 12/20/2022]
Abstract
The demands for genotyping techniques with acceptable precision, accuracy, cost-effectiveness in high throughput formats made driving forces for continuous development of novel technologies. A wide range of mutation detection techniques based on polymerase chain reaction (PCR) have been introduced. The best alternatives were the isothermal amplification technologies that those did not require a thermal cycler. In this review, we aimed to describe the most known isothermal amplification techniques for SNP genotyping.
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Affiliation(s)
| | - Pooria Gill
- Nanomedicine Group, Immunogenetics Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.,The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Majid Motovali-Bashi
- Department of Genetics, Faculty of Sciences, University of Isfahan, Isfahan, Iran
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163
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Xu M, Ye J, Yang D, Abdullah Al-Maskri AA, Hu H, Jung C, Cai S, Zeng S. Ultrasensitive detection of miRNA via one-step rolling circle-quantitative PCR (RC-qPCR). Anal Chim Acta 2019; 1077:208-215. [PMID: 31307711 DOI: 10.1016/j.aca.2019.05.028] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/21/2019] [Accepted: 05/13/2019] [Indexed: 12/19/2022]
Abstract
A novel microRNA (miRNA) quantification method has been developed using one-step rolling circle-quantitative PCR (RC-qPCR) analysis. Vent (exo-) DNA polymerase is firstly utilized to combine a rolling circle amplification (RCA) and qPCR in one step with high sensitivity and specificity in our RC-qPCR assay. Before performing the RC-qPCR, a padlock probe is ligated only when it is perfectly hybridized with miRNA. This ligation-based miRNA assay is highly specific for mature miRNAs, discriminating among related miRNAs that differ by as little as one nucleotide. It exhibits a dynamic range of seven orders of magnitude with a detection limit of 500 aM, and could be also used for the quantification of other small RNA molecules such as short interfering RNAs (siRNAs).
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Affiliation(s)
- Mingcheng Xu
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jiawei Ye
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Dan Yang
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Abdu Ahmed Abdullah Al-Maskri
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Haihong Hu
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Cheulhee Jung
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Sheng Cai
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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164
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Song H, Zhang Y, Cheng P, Chen X, Luo Y, Xu W. A rapidly self-assembling soft-brush DNA hydrogel based on RCA products. Chem Commun (Camb) 2019; 55:5375-5378. [PMID: 30994649 DOI: 10.1039/c9cc01022j] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A rapid self-assembly strategy was developed for fabricating a novel soft-brush DNA hydrogel in one minute by introducing a pair of L-type probes into the RCA products. The L-type probes with universality achieved a controllable size and morphology of the DNA hydrogel, providing deeper insight into variability and probability in functional biomaterials.
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Affiliation(s)
- Huan Song
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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165
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Liu M, Yin Q, Chang Y, Zhang Q, Brennan JD, Li Y. In Vitro Selection of Circular DNA Aptamers for Biosensing Applications. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901192] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Meng Liu
- School of Environmental Science and Technology Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education) Dalian University of Technology Dalian 116024 China
| | - Qingxin Yin
- School of Environmental Science and Technology Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education) Dalian University of Technology Dalian 116024 China
| | - Yangyang Chang
- School of Environmental Science and Technology Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education) Dalian University of Technology Dalian 116024 China
| | - Qiang Zhang
- Biointerfaces Institute McMaster University 1280 Main Street West Hamilton Ontario L8S4O3 Canada
- School of Life Science and Biotechnology Dalian University of Technology Dalian 116024 China
| | - John D. Brennan
- Biointerfaces Institute McMaster University 1280 Main Street West Hamilton Ontario L8S4O3 Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton Ontario L8S4K1 Canada
- Biointerfaces Institute McMaster University 1280 Main Street West Hamilton Ontario L8S4O3 Canada
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166
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Liu M, Yin Q, Chang Y, Zhang Q, Brennan JD, Li Y. In Vitro Selection of Circular DNA Aptamers for Biosensing Applications. Angew Chem Int Ed Engl 2019; 58:8013-8017. [PMID: 31020784 DOI: 10.1002/anie.201901192] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/17/2019] [Indexed: 01/01/2023]
Abstract
We report on the first effort to select DNA aptamers from a circular DNA library, which resulted in the discovery of two high-affinity circular DNA aptamers that recognize the glutamate dehydrogenase (GDH) from Clostridium difficile, an established antigen for diagnosing Clostridium difficile infection (CDI). One aptamer binds effectively in both the circular and linear forms, the other is functional only in the circular configuration. Interestingly, these two aptamers recognize different epitopes on GDH, demonstrating the advantage of selecting aptamers from circular DNA libraries. A sensitive diagnostic test was developed to take advantage of the high stability of circular DNA aptamers in biological samples and their compatibility with rolling circle amplification. This test is capable of identifying patients with active CDI using stool samples. This work represents a significant step forward towards demonstrating the practical utility of DNA aptamers in clinical diagnosis.
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Affiliation(s)
- Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024, China
| | - Qingxin Yin
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024, China
| | - Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024, China
| | - Qiang Zhang
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4O3, Canada.,School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - John D Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4O3, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4K1, Canada.,Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4O3, Canada
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167
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Wang J, Wang Y, Liu S, Wang H, Zhang X, Song X, Yu J, Huang J. Primer remodeling amplification-activated multisite-catalytic hairpin assembly enabling the concurrent formation of Y-shaped DNA nanotorches for the fluorescence assay of ochratoxin A. Analyst 2019; 144:3389-3397. [PMID: 30990481 DOI: 10.1039/c9an00316a] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA can be configured into unique high-order structures due to its significantly high programmability, such as a three-way junction-based structure (denoted Y-shaped DNA), for further applications. Herein, we report a label-free fluorescent signal-on biosensor based on the target-driven primer remodeling rolling circle amplification (RCA)-activated multisite-catalytic hairpin assembly (CHA) enabling the concurrent formation of Y-shaped DNA nanotorches (Y-DNTs) for ultrasensitive detection of ochratoxin A (OTA). Two kinds of masterfully-designed probes, termed Complex I and II, were pre-prepared by the combination of a circular template (CT) with an OTA aptamer (S1), a substrate probe (S2) and hairpin probe 1 (HP1), respectively. Target OTA specifically binds to Complex I, resulting in the release of the remnant element in S2 and successive remodeling into a mature primer for RCA by phi29 DNA polymerase, thus a usable primer-CT complex is produced, which actuates primary RCA. Then, numerous Complex II probes can anneal with the first-generation RCA product (RP) with multiple sites to activate the CHA process. With the participation of endonuclease IV (Endo IV) and phi29, HP1 as a pre-primer containing a tetrahydrofuran abasic site mimic (AP site) in Complex II is converted into a mature primer to initiate additional rounds of RCA. So, countless Y-DNTs are formed concurrently containing a G-quadruplex structure that enables the N-methylmesoporphyrin IX (NMM) to be embedded, generating remarkably strong fluorescence signals. The biosensor was demonstrated to enable rapid and accurate highly efficient and selective detection of OTA with an improved detection limit of as low as 0.0002 ng mL-1 and a widened dynamic range of over 4 orders of magnitude. Meanwhile, this method was proven to be capable of being used to analyze actual samples. Therefore, this proposed strategy may be established as a useful and practical platform for the ultrasensitive detection of mycotoxins in food safety testing.
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Affiliation(s)
- Jingfeng Wang
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P.R. China.
| | - Yu Wang
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P.R. China.
| | - Su Liu
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, P.R. China
| | - Haiwang Wang
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P.R. China.
| | - Xue Zhang
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P.R. China.
| | - Xiaolei Song
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, P.R. China
| | - Jinghua Yu
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P.R. China
| | - Jiadong Huang
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P.R. China. and 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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168
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Wang J, Wang Y, Liu S, Wang H, Zhang X, Song X, Huang J. Base excision repair initiated rolling circle amplification-based fluorescent assay for screening uracil-DNA glycosylase activity using Endo IV-assisted cleavage of AP probes. Analyst 2019; 143:3951-3958. [PMID: 29999513 DOI: 10.1039/c8an00716k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Uracil-DNA glycosylase (UDG) is a crucial damage repair enzyme that initiates the cellular base excision repair pathway that maintains the integrity of the genome. Abnormal UDG activity may induce the malfunction of uracil excision repair that is directly related to a range of diseases including cancers, genotypic diseases, and human immunodeficiencies. In this work, a simple, robust and cost effective biosensing platform for the ultrasensitive detection of UDG activity is established based on the combination of base excision repair-initiated primer generation for rolling circular amplification (RCA) with Endo IV-assisted signal amplification. In the presence of target UDG, UDG can catalyze the removal of uracil on a hairpin probe (HP) leaving an apurinic/apyrimidinic (AP site) which can be cleaved by Endo IV to generate a primer for triggering the RCA reaction. Subsequently, numerous AP site-embedded signal probes, acting as fluorescence-quenched probes, combine with the RCA products to perform signal transduction and quadradic signal amplification through an Endo IV-catalyzed cleavage reaction, thus significantly enhancing the fluorescence signal, which can be used for UDG activity screening. Under optimum conditions, this biosensor exhibits improved sensitivity toward target UDG with a detection limit of as low as 9.3 × 10-5 U mL-1 and a wide detection range across 5 orders of magnitude. Additionally, our biosensor demonstrates high selectivity toward UDG for simple, rapid, and low-cost detection. Furthermore, by redesigning the modification of HP and using of suitable endonuclease enzymes, this RCA coupled with Endo IV-assisted signal amplification strategy might be applied for the detection of various other targets, such as thymine DNA glycosylase, 8-oxoguanine DNA glycosylase, DNA methyltransferase, and so on. Hence, the proposed strategy provides a useful and versatile biosensing platform for the ultrasensitive detection of UDG activity and related fundamental biomedicine research and clinical diagnosis.
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Affiliation(s)
- Jingfeng Wang
- College of Biological Sciences and Technology, University of Jinan, Jinan 250022, P.R. China.
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169
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Label-free DNA Y junction for detection of Hg2+ using exonuclease III or graphene oxide-assisted background reduction. Microchem J 2019. [DOI: 10.1016/j.microc.2018.12.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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170
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Chen Y, Tyagi D, Lyu M, Carrier AJ, Nganou C, Youden B, Wang W, Cui S, Servos M, Oakes K, He S, Zhang X. Regenerative NanoOctopus Based on Multivalent-Aptamer-Functionalized Magnetic Microparticles for Effective Cell Capture in Whole Blood. Anal Chem 2019; 91:4017-4022. [PMID: 30649851 DOI: 10.1021/acs.analchem.8b05432] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Isolation of specific rare cell subtypes from whole blood is critical in cellular analysis and important in basic and clinical research. Traditional immunomagnetic cell capture suffers from suboptimal sensitivity, specificity, and time- and cost-effectiveness. Mimicking the features of octopuses, a device termed a "NanoOctopus" was developed for cancer cell isolation in whole blood. The device consists of long multimerized aptamer DNA strands, or tentacle DNA, immobilized on magnetic microparticle surfaces. Their ultrahigh sensitivity and specificity are attributed to multivalent binding of the tentacle DNA to cell receptors without steric hindrance. The simple, quick, and noninvasive capture and release of the target cells allows for extensive downstream cellular and molecular analysis, and the time- and cost-effectiveness of fabrication and regeneration of the devices makes them attractive for industrial manufacture.
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Affiliation(s)
| | | | - Mingsheng Lyu
- Marine School , Huaihai Institute of Technology , Lianungang , 222005 , China
| | | | | | - Brian Youden
- Department of Biology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Wei Wang
- Institute of Translational Medicine , Shenzhen Second People's Hospital , First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen , 518055 , China
| | | | - Mark Servos
- Department of Biology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | | | - Shengnan He
- Institute of Translational Medicine , Shenzhen Second People's Hospital , First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen , 518055 , China
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171
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Liu L, Rong Q, Ke G, Zhang M, Li J, Li Y, Liu Y, Chen M, Zhang XB. Efficient and Reliable MicroRNA Imaging in Living Cells via a FRET-Based Localized Hairpin-DNA Cascade Amplifier. Anal Chem 2019; 91:3675-3680. [PMID: 30714362 DOI: 10.1021/acs.analchem.8b05778] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
MicroRNAs (miRNAs) play critical roles in many biological processes and are vital biomarkers for disease diagnostics. Hence, it is of significance to develop miRNA biosensors with fast responses, high sensitivity, and excellent reliability in living cells. As one kind of DNA molecular machine, DNA amplifiers are very promising for intracellular miRNA imaging due to their nonenzymatic, isothermal working principle and excellent signal-amplification ability. However, the practical application of current DNA amplifiers is still an issue because of their slow kinetics, unsatisfactory efficiency, and false-positive signals. Herein, taking advantage of the spatial-confinement effect on a three-dimensional (3D) finite DNA nanostructure, a FRET-based localized hairpin-DNA cascade amplifier (termed as localized-HDCA) is developed for the rapid, efficient, and reliable imaging of intracellular tumor-related miRNA. The localized-HDCA system consists of two metastable hairpin DNAs (H1 and H2) localized on a DNA nanocube. Benefiting from the spatial-confinement effect in the confined space of DNA nanocubes, not only was the speed of the miRNA-triggered HDCA reaction significantly accelerated (7 times faster), but also the reaction efficiency was greatly improved (2.6 times higher). In addition, the FRET-based 3D finite DNA nanocubes provide this localized-HDCA with improved cell permeability and better nuclease resistance as well as the ability to avoid false-positive signals, which guarantee reliable miRNA imaging in living cells. With these advantages, this strategy is expected to be widely applied to the development of more efficient and robust DNA molecular machines for biomedical research and clinical diagnosis.
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Affiliation(s)
- Lu Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine , Hunan University , Changsha 410082 , China
| | - Qiming Rong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine , Hunan University , Changsha 410082 , China
| | - Guoliang Ke
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine , Hunan University , Changsha 410082 , China
| | - Meng Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine , Hunan University , Changsha 410082 , China
| | - Jin Li
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine , Hunan University , Changsha 410082 , China
| | - Yingqian Li
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine , Hunan University , Changsha 410082 , China
| | - Yongchun Liu
- College of Materials Science and Engineering , Hunan University , Changsha 410082 , China
| | - Mei Chen
- College of Materials Science and Engineering , Hunan University , Changsha 410082 , China
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine , Hunan University , Changsha 410082 , China
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172
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Wang J, Wang Y, Liu S, Wang H, Zhang X, Song X, Huang J. Duplex featured polymerase-driven concurrent strategy for detecting of ATP based on endonuclease-fueled feedback amplification. Anal Chim Acta 2019; 1060:79-87. [PMID: 30902334 DOI: 10.1016/j.aca.2019.01.047] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 01/11/2019] [Accepted: 01/23/2019] [Indexed: 12/24/2022]
Abstract
We have developed a novel amplification strategy termed Endo IV-assisted feedback amplification (EFA) taking advantages of rolling circular amplification (RCA) and Endo IV-assisted signal amplification (ESA) biosensing platform for detecting of adenosine triphosphate (ATP). Two kinds of specially programmed DNA complexes were employed into EFA system, one composed of a split aptamer fragment and a circular template, and the other composed of AP probe and the same circular template. Hence, ATP as a target induced the self-assembly of spilt aptamer fragments and initiated RCA reaction generating a linear DNA, which consists of hybridization elements with Complex II and formation elements of G-quadruplex. More importantly, the addition of endonuclease IV can cut the Complex II into two parts, and one of which can be trimming by phi29 DNA polymerase initiating the new round of RCA reaction producing more RCA products. Thus significantly enhanced fluorescent signal can be measured for ATP as expected, and our proposed strategy exhibits improved performances toward ATP ultrasensitive detection with a limit of detection (LOD) as low as 0.09 nM. Additionally, our developed biosensor demonstrates high selectivity and the superiority of simplicity towards ATP. Above these significant aspects, our proximity binding-induced RCA reaction-based fluorescent assay and Endo IV-fueled feedback signal amplification strategy presents an optimal detection performance towards ATP for potential application in related research and clinical diagnosis.
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Affiliation(s)
- Jingfeng Wang
- College of Biological Sciences and Technology, University of Jinan, Jinan, 250022, PR China
| | - Yu Wang
- College of Biological Sciences and Technology, University of Jinan, Jinan, 250022, PR China
| | - Su Liu
- College of Water Conservancy and Environment, University of Jinan, Jinan, 250022, PR China
| | - Haiwang Wang
- College of Biological Sciences and Technology, University of Jinan, Jinan, 250022, PR China
| | - Xue Zhang
- College of Biological Sciences and Technology, University of Jinan, Jinan, 250022, PR China
| | - Xiaolei Song
- College of Water Conservancy and Environment, University of Jinan, Jinan, 250022, PR China
| | - Jiadong Huang
- College of Biological Sciences and Technology, University of Jinan, Jinan, 250022, PR China; Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong, College of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China.
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173
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Gao M, Lian H, Yu L, Gong M, Ma L, Zhou Y, Yu M, Yan X. Rolling circle amplification integrated with suspension bead array for ultrasensitive multiplex immunodetection of tumor markers. Anal Chim Acta 2019; 1048:75-84. [DOI: 10.1016/j.aca.2018.10.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/28/2018] [Accepted: 10/02/2018] [Indexed: 12/14/2022]
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174
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He C, Wang M, Sun X, Zhu Y, Zhou X, Xiao S, Zhang Q, Liu F, Yu Y, Liang H, Zou G. Integrating PDA microtube waveguide system with heterogeneous CHA amplification strategy towards superior sensitive detection of miRNA. Biosens Bioelectron 2019; 129:50-57. [PMID: 30682689 DOI: 10.1016/j.bios.2019.01.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/20/2018] [Accepted: 01/04/2019] [Indexed: 12/25/2022]
Abstract
Catalytic hairpin assembly (CHA) is a typical enzyme-free amplification strategy, in which the target can catalyze two hairpin probes to form a duplex and yield multiple outputs signal. However, the non-specific hybridization of two hairpin probes in CHA circuit usually occurred even in the absence of target, causing significant background leakage and impeding its practical applications in trace miRNA analysis. Herein, we proposed a novel heterogeneous CHA (hetero-CHA) design integrating with PDA microtube waveguide system, offering the advantages to enhance the target signal, but suppress the background leakage simultaneously. In hetero-CHA strategy, single-stranded targets are enriched nearby the surface of PDA microtube, facilitating the target-triggered CHA amplification and strand displacement reactions. In contrast, double-stranded DNA complexes formed by uncatalyzed hybridizations are isolated from PDA microtube, impeding the leakage signal. By combination with condensing enrichment effect, the proposed hetero-CHA probe exhibited high selectivity and sensitivity to miRNA target, giving a detection limit as low as 3.3 fM. More importantly, the proposed hetero-CHA probe can be applied directly to distinguish the expression of miRNA-21 in clinical serum of cancer patients (including lung, breast and pancreatic) from those of healthy human beings, favoring the cancer diagnosis and therapeutic evaluation.
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Affiliation(s)
- Chenlu He
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, iChEM, University of Science and Technology of China, Hefei, Anhui 230026, PR China
| | - Mengqiao Wang
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, iChEM, University of Science and Technology of China, Hefei, Anhui 230026, PR China
| | - Xianbao Sun
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, iChEM, University of Science and Technology of China, Hefei, Anhui 230026, PR China
| | - Yu Zhu
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, iChEM, University of Science and Technology of China, Hefei, Anhui 230026, PR China
| | - Xiang Zhou
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, iChEM, University of Science and Technology of China, Hefei, Anhui 230026, PR China
| | - Shiyan Xiao
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, iChEM, University of Science and Technology of China, Hefei, Anhui 230026, PR China.
| | - Qijin Zhang
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, iChEM, University of Science and Technology of China, Hefei, Anhui 230026, PR China
| | - Funing Liu
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, iChEM, University of Science and Technology of China, Hefei, Anhui 230026, PR China
| | - Yue Yu
- Division of Gastroenterology, Affiliated Provincial Hospital, Anhui Medical University, No.17 Lu Jiang Road, Hefei, Anhui 230001, PR China
| | - Haojun Liang
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, iChEM, University of Science and Technology of China, Hefei, Anhui 230026, PR China
| | - Gang Zou
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, iChEM, University of Science and Technology of China, Hefei, Anhui 230026, PR China.
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175
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Wang X, Xu M, Huang K, Lou X, Xia F. AIEgens/Nucleic Acid Nanostructures for Bioanalytical Applications. Chem Asian J 2019; 14:689-699. [PMID: 30489015 DOI: 10.1002/asia.201801595] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 11/29/2018] [Indexed: 12/27/2022]
Abstract
DNA occupies significant roles in life processes, which include encoding the sequences of proteins and accurately transferring genetic information from generation to generation. Recent discoveries have demonstrated that a variety of biological functions are correlated with DNA's conformational transitions. The non-B form has attained great attention among the diverse forms of DNA over the past several years. The main reason for this is that a large number of studies have shown that the non-B form of DNA is associated with gross deletions, inversions, duplications, translocations as well as simple repeating sequences, which therefore causes human diseases. Consequently, the conformational transition of DNA between the B-form and the non-B form is important for biology. Conventional fluorescence probes based on the conformational transitions of DNA usually need a fluorophore and a quencher group, which suffers from the complex design of the structure and tedious synthetic procedures. Moreover, conventional fluorescence probes are subject to the aggregation-caused quenching (ACQ) effect, which limits their application toward imaging and analyte detection. Fluorogens exhibiting aggregation-induced emission (AIE) have attracted tremendous attention over the past decade. By taking advantage of this unique behavior, plenty of fluorescent switch-on probes without the incorporation of fluorescent quenchers/fluorophore pairs have been widely developed as biosensors for imaging a variety of analytes. Herein, the recent progress in bioanalytical applications on the basis of aggregation-induced emission luminogens (AIEgens)/nucleic acid nanostructures are presented and discussed.
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Affiliation(s)
- Xudong Wang
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Min Xu
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, China
| | - Kaixun Huang
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Xiaoding Lou
- 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
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China.,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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176
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Leung V, Brooks M, Emerson S, Ali M, Filipe CDM. Ready-to-use thermally stable mastermix pills for molecular biology applications. Biotechnol Prog 2018; 35:e2764. [PMID: 30536873 DOI: 10.1002/btpr.2764] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/14/2018] [Accepted: 12/06/2018] [Indexed: 11/12/2022]
Abstract
Rolling circle amplification (RCA), polymerase chain reaction (PCR), and loop-mediated isothermal amplification (LAMP), are powerful tools that can be used for gene manipulation, pathogen detection, and infectious disease diagnostics. However, these techniques require trained personnel, as the pipetting steps involved can lead to contamination and, consequently, erroneous results. Furthermore, many of the reagents used in molecular biology are thermally labile and must be kept within a cold-chain. In this article, we present a simple and cost-effective method that allows molecular biology reagents to be thermally stabilized into ready-to-use mastermixes via drying in pullulan and trehalose films. Our experimental results demonstrate that this method is capable of preserving the activity of RCA, PCR, LAMP, ligase, polynucleotide kinase, and Klenow fragment mastermixes for at least 3 months at ambient conditions. Thus, stabilizing reagents via drying in pullulan and trehalose film may allow for a drastic reduction in the number of pipetting steps and the elimination of the need for a cold chain. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2764, 2019.
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Affiliation(s)
- Vincent Leung
- Dept. of Chemical Engineering, 1280 Main Street West, McMaster University, Hamilton, L8S 4L7, Ontario, Canada
| | - Meredith Brooks
- Dept. of Chemical Engineering, 1280 Main Street West, McMaster University, Hamilton, L8S 4L7, Ontario, Canada
| | - Sophia Emerson
- Dept. of Chemical Engineering, 1280 Main Street West, McMaster University, Hamilton, L8S 4L7, Ontario, Canada
| | - Monsur Ali
- Biointerfaces Inst., McMaster University, Hamilton, L8S 4L7, Ontario, Canada
| | - Carlos D M Filipe
- Dept. of Chemical Engineering, 1280 Main Street West, McMaster University, Hamilton, L8S 4L7, Ontario, Canada
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177
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Chen J, Baker YR, Brown A, El-Sagheer AH, Brown T. Enzyme-free synthesis of cyclic single-stranded DNA constructs containing a single triazole, amide or phosphoramidate backbone linkage and their use as templates for rolling circle amplification and nanoflower formation. Chem Sci 2018; 9:8110-8120. [PMID: 30542561 PMCID: PMC6238721 DOI: 10.1039/c8sc02952k] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 08/23/2018] [Indexed: 12/31/2022] Open
Abstract
Cyclic oligonucleotides are valuable targets with a broad range of potential applications spanning molecular biology and nanotechnology. Of particular importance is their role as templates in the rolling circle amplification (RCA) reaction. We describe three different chemical cyclisation methods for the preparation of single-stranded cyclic DNA constructs. These chemical cyclisation reactions are cheaper to carry out than the enzymatic reaction, and more amenable to preparative scale purification and characterisation of the cyclic product. They can also be performed under denaturing conditions and are therefore particularly valuable for cyclic DNA templates that contain secondary structures. The resulting single-stranded cyclic DNA constructs contain a single non-canonical backbone linkage at the ligation point (triazole, amide or phosphoramidate). They were compared to unmodified cyclic DNA in rolling circle amplification reactions using φ-29 and Bst 2.0 DNA polymerase enzymes. The cyclic templates containing a phosphoramidate linkage were particularly well tolerated by φ-29 polymerase, consistently performing as well in RCA as the unmodified DNA controls. Moreover, these phosphoramidate-modified cyclic constructs can be readily produced in oligonucleotide synthesis facilities from commercially available precursors. Phosphoramidate ligation therefore holds promise as a practical, scalable method for the synthesis of fully biocompatible cyclic RCA templates. The triazole-modified cyclic templates generally gave lower and more variable yields of RCA products, a significant proportion of which were double-stranded, while the performances of the templates containing an amide linkage lie in between those of the phosphoramidate- and triazole-containing templates.
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Affiliation(s)
- Jinfeng Chen
- Chemistry Research Laboratory , University of Oxford , Oxford , OX1 3TA , UK .
| | - Ysobel R Baker
- Chemistry Research Laboratory , University of Oxford , Oxford , OX1 3TA , UK .
| | - Asha Brown
- ATDBio , Magdalen Centre , Oxford Science Park , Oxford , OX4 4GA , UK
| | - Afaf H El-Sagheer
- Chemistry Research Laboratory , University of Oxford , Oxford , OX1 3TA , UK .
- Chemistry Branch , Department of Science and Mathematics , Suez University , Suez 43721 , Egypt
| | - Tom Brown
- Chemistry Research Laboratory , University of Oxford , Oxford , OX1 3TA , UK .
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178
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Kim J, Jang D, Park H, Jung S, Kim DH, Kim WJ. Functional-DNA-Driven Dynamic Nanoconstructs for Biomolecule Capture and Drug Delivery. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1707351. [PMID: 30062803 DOI: 10.1002/adma.201707351] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 03/13/2018] [Indexed: 06/08/2023]
Abstract
The discovery of sequence-specific hybridization has allowed the development of DNA nanotechnology, which is divided into two categories: 1) structural DNA nanotechnology, which utilizes DNA as a biopolymer; and 2) dynamic DNA nanotechnology, which focuses on the catalytic reactions or displacement of DNA structures. Recently, numerous attempts have been made to combine DNA nanotechnologies with functional DNAs such as aptamers, DNAzymes, amplified DNA, polymer-conjugated DNA, and DNA loaded on functional nanoparticles for various applications; thus, the new interdisciplinary research field of "functional DNA nanotechnology" is initiated. In particular, a fine-tuned nanostructure composed of functional DNAs has shown immense potential as a programmable nanomachine by controlling DNA dynamics triggered by specific environments. Moreover, the programmability and predictability of functional DNA have enabled the use of DNA nanostructures as nanomedicines for various biomedical applications, such as cargo delivery and molecular drugs via stimuli-mediated dynamic structural changes of functional DNAs. Here, the concepts and recent case studies of functional DNA nanotechnology and nanostructures in nanomedicine are reviewed, and future prospects of functional DNA for nanomedicine are indicated.
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Affiliation(s)
- Jinhwan Kim
- Center for Self-Assembly and Complexity, Institute for Basic Science (IBS), Pohang, 37673, Korea
| | - Donghyun Jang
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Hyeongmok Park
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Sungjin Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Dae Heon Kim
- Department of Biology, Sunchon National University, Sunchon, 57922, Korea
| | - Won Jong Kim
- Center for Self-Assembly and Complexity, Institute for Basic Science (IBS), Pohang, 37673, Korea
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
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179
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Li Z, Song Y, Li A, Xu W, Zhang W. Direct observation of the wrapping/unwrapping of ssDNA around/from a SWCNT at the single-molecule level: towards tuning the binding mode and strength. NANOSCALE 2018; 10:18586-18596. [PMID: 30259027 DOI: 10.1039/c8nr06150e] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Complexation of single-stranded DNA (ssDNA) with a chiral single-walled carbon nanotube (SWCNT) exhibits surprising efficacy in CNT dispersion and sorting, optical sensing, and nanoelectronic device design. Studying the wrapping/unwrapping mechanism is challenging because an in situ method at the single-molecule level is required. Here, we developed a method based on single-molecule force spectroscopy to monitor the unwrapping/wrapping of ssDNA from/around a SWCNT. Our results reveal that the wrapping/unwrapping processes are reversible in water, and these processes occur in an equilibrium manner driven mainly by π-π interactions between DNA bases and CNTs. In phosphate buffered saline, the unwrapping process is loading rate-dependent, and ssDNA wrapping around a CNT undergoes two distinct stages dominated by both π-π interactions and hydrogen bonding. In addition, our results show that salts could further stabilize ssDNA/CNT complexes by blocking the electrostatic interactions between adjacent DNA segments and by catalyzing the formation of hydrogen bonds between DNA bases. The stability of ssDNA/CNT is dependent on the DNA sequence and CNT chirality. These results deepen our understanding of ssDNA-CNT interactions and provide effective means to tune the binding mode and strength.
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Affiliation(s)
- Zhandong Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China.
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180
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Cheng H, Liu J, Ma W, Duan S, Huang J, He X, Wang K. Low Background Cascade Signal Amplification Electrochemical Sensing Platform for Tumor-Related mRNA Quantification by Target-Activated Hybridization Chain Reaction and Electroactive Cargo Release. Anal Chem 2018; 90:12544-12552. [PMID: 30261719 DOI: 10.1021/acs.analchem.8b02470] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Herein a low background cascade signal amplification electrochemical sensing platform has been proposed for the ultrasensitive detection of mRNA (mRNA) by coupling the target-activated hybridization chain reaction and electroactive cargo release from mesoporous silica nanocontainers (MSNs). In this sensing platform, the 5'-phosphate-terminated DNA (5'-PO4 cDNA) complement to target mRNA is hybridized with the trigger DNA and anchor DNA on the surface of the MSNs, aiming at forming a double-stranded DNA gate molecule and sealing the methylene blue (MB) in the inner pores of the MSNs. In the presence of target mRNA, the 5'-PO4 cDNA is displaced from the MSNs and competitively hybridizes with mRNA, which led to the liberation of the trigger DNA and the opening of the MSNs pore. The liberated trigger DNA can be then immobilized onto the electrode surface through hybridization with the capture DNA, triggering HCR on the electrode surface. At the same time, the MB released from the MSNs will selectively intercalate into the HCR long dsDNA polymers, giving rise to significant electrochemical response. In addition, due to the λ-exonuclease (λ-Exo) cleavage reaction-assisted target recycling, more amounts of trigger DNA will be liberated and trigger HCR, and numerous MB are uncapped and intercalate into the HCR products. As proof of concept, thymidine kinase 1 (TK1) mRNA was used as a model target. Featured with amplification efficiency, label-free capability, and low background signal, the strategy could quantitatively detect TK1 mRNA down to 2.0 aM with a linear calibration range from 0.1 fM to 1 pM. We have also demonstrated the practical application of our proposed sensing platform for detecting TK1 mRNA in real samples, opening up new avenues for highly sensitive quantification of biomarkers in bioanalysis and clinical diagnosis.
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Affiliation(s)
- Hong Cheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering , Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province , Changsha 410082 , China
| | - Jinquan Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering , Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province , Changsha 410082 , China
| | - Wenjie Ma
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering , Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province , Changsha 410082 , China
| | - Shuangdi Duan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering , Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province , Changsha 410082 , China
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering , Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province , Changsha 410082 , China
| | - Xiaoxiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering , Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province , Changsha 410082 , China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering , Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province , Changsha 410082 , China
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181
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Lee IJ, Goo NI, Kim DE. Label/quencher-free detection of single-nucleotide changes in DNA using isothermal amplification and G-quadruplexes. Analyst 2018; 141:6503-6506. [PMID: 27827492 DOI: 10.1039/c6an01600f] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We report an analytical method that exploits the interaction between G-quadruplexes and thioflavin T (ThT), for detecting mutant DNA species containing single-base changes. This system is a label/quencher-free fluorescence enhancement system based on rolling circle amplification (RCA)-responsive G-quadruplex formation, which enables a highly selective detection of T790M SNPs in the gene encoding the epidermal growth factor receptor, EGFR.
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Affiliation(s)
- Il Joon Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea.
| | - Nam-In Goo
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea.
| | - Dong-Eun Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea.
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182
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Target-induced aptamer displacement on gold nanoparticles and rolling circle amplification for ultrasensitive live Salmonella typhimurium electrochemical biosensing. J Electroanal Chem (Lausanne) 2018. [DOI: 10.1016/j.jelechem.2018.07.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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183
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Zhu C, Liu M, Li X, Zhang X, Chen J. A new electrochemical aptasensor for sensitive assay of a protein based on the dual-signaling electrochemical ratiometric method and DNA walker strategy. Chem Commun (Camb) 2018; 54:10359-10362. [PMID: 30152501 DOI: 10.1039/c8cc05829f] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Herein, a new electrochemical aptamer-based biosensor for highly sensitive assay of thrombin has been developed based on the dual-signaling electrochemical ratiometric method and the DNA walker strategy, and shows a low detection limit of about 56 fM.
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Affiliation(s)
- Caixia Zhu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China.
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184
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SUN YH, WEI J, WANG ZX, MENG XY. Study on Interaction of G-rich Oligonucleotides Modified Gold Nanoparticles with Cells. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2018. [DOI: 10.1016/s1872-2040(18)61109-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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185
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Liu M, Zhang Q, Kannan B, Botton GA, Yang J, Soleymani L, Brennan JD, Li Y. Self-Assembled Functional DNA Superstructures as High-Density and Versatile Recognition Elements for Printed Paper Sensors. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806489] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Meng Liu
- Department of Biochemistry and Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton Ontario L8S4K1 Canada
- School of Environmental Science and Technology; Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education); Dalian University of Technology; Dalian 116024 China
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton Ontario L8S4O3 Canada
| | - Qiang Zhang
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton Ontario L8S4O3 Canada
| | - Balamurali Kannan
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton Ontario L8S4O3 Canada
| | - Gianluigi A. Botton
- Department of Materials Science and Engineering; McMaster University; 1280 Main Street West Hamilton Ontario L8S4K1 Canada
| | - Jie Yang
- School of Biomedical Engineering; McMaster University; 1280 Main Street West Hamilton Ontario L8S4K1 Canada
| | - Leyla Soleymani
- School of Biomedical Engineering; McMaster University; 1280 Main Street West Hamilton Ontario L8S4K1 Canada
| | - John D. Brennan
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton Ontario L8S4O3 Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton Ontario L8S4K1 Canada
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton Ontario L8S4O3 Canada
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186
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Liu M, Zhang Q, Kannan B, Botton GA, Yang J, Soleymani L, Brennan JD, Li Y. Self-Assembled Functional DNA Superstructures as High-Density and Versatile Recognition Elements for Printed Paper Sensors. Angew Chem Int Ed Engl 2018; 57:12440-12443. [PMID: 30043544 DOI: 10.1002/anie.201806489] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Indexed: 11/08/2022]
Abstract
Micrometer-sized functional nucleic acid (FNA) superstructures (denoted as 3D DNA) were examined as a unique class of biorecognition elements to produce highly functional bioactive paper surfaces. 3D DNA containing repeating sequences of either a DNA aptamer or DNAzyme was created from long-chain products of rolling circle amplification followed by salt aging. The resulting 3D DNA retained its original spherical shape upon inkjet printing and adhered strongly to the paper surface via physisorption. 3D DNA paper sensors showed resistance to degradation by nucleases, suppressed nonspecific protein adsorption, and provided a much higher surface density of functional DNA relative to monomeric FNAs, making such species ideally suited for development of paper-based biosensors.
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Affiliation(s)
- Meng Liu
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4K1, Canada.,School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024, China.,Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4O3, Canada
| | - Qiang Zhang
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4O3, Canada
| | - Balamurali Kannan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4O3, Canada
| | - Gianluigi A Botton
- Department of Materials Science and Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4K1, Canada
| | - Jie Yang
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4K1, Canada
| | - Leyla Soleymani
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4K1, Canada
| | - John D Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4O3, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4K1, Canada.,Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4O3, Canada
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187
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Reid MS, Le XC, Zhang H. Die exponentielle isotherme Amplifikation von Nukleinsäuren und Assays zur Detektion von Proteinen, Zellen, kleinen Molekülen und Enzymaktivitäten: Anwendungen für EXPAR. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712217] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Michael S. Reid
- Department of Chemistry; University of Alberta; Edmonton Alberta T6G 2G3 Kanada
| | - X. Chris Le
- Department of Chemistry; University of Alberta; Edmonton Alberta T6G 2G3 Kanada
- Department of Laboratory Medicine and Pathology; Faculty of Medicine and Dentistry, 10-102 Clinical Sciences Building; University of Alberta; Edmonton Alberta T6G 2G3 Kanada
| | - Hongquan Zhang
- Department of Laboratory Medicine and Pathology; Faculty of Medicine and Dentistry, 10-102 Clinical Sciences Building; University of Alberta; Edmonton Alberta T6G 2G3 Kanada
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188
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Reid MS, Le XC, Zhang H. Exponential Isothermal Amplification of Nucleic Acids and Assays for Proteins, Cells, Small Molecules, and Enzyme Activities: An EXPAR Example. Angew Chem Int Ed Engl 2018; 57:11856-11866. [PMID: 29704305 DOI: 10.1002/anie.201712217] [Citation(s) in RCA: 189] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 02/09/2018] [Indexed: 12/30/2022]
Abstract
Isothermal exponential amplification techniques, such as strand-displacement amplification (SDA), rolling circle amplification (RCA), loop-mediated isothermal amplification (LAMP), nucleic acid sequence based amplification (NASBA), helicase-dependent amplification (HDA), and recombinase polymerase amplification (RPA), have great potential for on-site, point-of-care, and in situ assay applications. These amplification techniques eliminate the need for temperature cycling, as required for the polymerase chain reaction (PCR), while achieving comparable amplification yields. We highlight here recent advances in the exponential amplification reaction (EXPAR) for the detection of nucleic acids, proteins, enzyme activities, cells, and metal ions. The incorporation of fluorescence, colorimetric, chemiluminescence, Raman, and electrochemical approaches enables the highly sensitive detection of a variety of targets. Remaining issues, such as undesirable background amplification resulting from nonspecific template interactions, must be addressed to further improve isothermal and exponential amplification techniques.
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Affiliation(s)
- Michael S Reid
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - X Chris Le
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, 10-102 Clinical Sciences Building, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Hongquan Zhang
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, 10-102 Clinical Sciences Building, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
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189
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Yao Q, Wang Y, Wang J, Chen S, Liu H, Jiang Z, Zhang X, Liu S, Yuan Q, Zhou X. An Ultrasensitive Diagnostic Biochip Based on Biomimetic Periodic Nanostructure-Assisted Rolling Circle Amplification. ACS NANO 2018; 12:6777-6783. [PMID: 29924598 DOI: 10.1021/acsnano.8b01950] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Developing portable and sensitive devices for point of care detection of low abundance bioactive molecules is highly valuable in early diagnosis of disease. Herein, an ultrasensitive photonic crystals-assisted rolling circle amplification (PCs-RCA) biochip was constructed and further applied to circulating microRNAs (miRNAs) detection in serum. The biochip integrated the optical signal enhancement capability of biomimetic PCs surface with the thousand-fold signal amplification feature of RCA. The biomimetic PCs displayed periodic dielectric nanostructure and significantly enhanced the signal intensity of RCA reaction, leading to efficient improvement of detection sensitivity. A limit of detection (LOD) as low as 0.7 aM was obtained on the PCs-RCA biochip, and the LOD was 7 orders of magnitude lower than that of standard RCA. Moreover, the PCs-RCA biochip could discriminate a single base variation in miRNAs. Accurate quantification of ultralow-abundance circulating miRNAs in clinical serum samples was further achieved with the PCs-RCA biochip, and patients with the nonsmall cell lung carcinoma were successfully distinguished from healthy donors. The PCs-RCA biochip can detect bioactive molecules with ultrahigh sensitivity and good specificity, making it valuable in clinical disease diagnosis and health assessment.
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Affiliation(s)
- Qian Yao
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , Wuhan University , Wuhan 430072 , China
| | - Yingqian Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , Wuhan University , Wuhan 430072 , China
| | - Jie Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , Wuhan University , Wuhan 430072 , China
| | - Shaomin Chen
- Center for Gene Diagnosis , Zhongnan Hospital of Wuhan University, Wuhan University , Wuhan 430072 , China
| | - Haoyang Liu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , Wuhan University , Wuhan 430072 , China
| | - Zhuoran Jiang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , Wuhan University , Wuhan 430072 , China
| | - Xiaoe Zhang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , Wuhan University , Wuhan 430072 , China
| | - Songmei Liu
- Center for Gene Diagnosis , Zhongnan Hospital of Wuhan University, Wuhan University , Wuhan 430072 , China
| | - Quan Yuan
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , Wuhan University , Wuhan 430072 , China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , Wuhan University , Wuhan 430072 , China
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190
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Golichenari B, Nosrati R, Farokhi-Fard A, Abnous K, Vaziri F, Behravan J. Nano-biosensing approaches on tuberculosis: Defy of aptamers. Biosens Bioelectron 2018; 117:319-331. [PMID: 29933223 DOI: 10.1016/j.bios.2018.06.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/04/2018] [Accepted: 06/10/2018] [Indexed: 12/12/2022]
Abstract
Tuberculosis is a major global health problem caused by the bacterium Mycobacterium tuberculosis (Mtb) complex. According to WHO reports, 53 million TB patients died from 2000 to 2016. Therefore, early diagnosis of the disease is of great importance for global health care programs. The restrictions of traditional methods have encouraged the development of innovative methods for rapid, reliable, and cost-effective diagnosis of tuberculosis. In recent years, aptamer-based biosensors or aptasensors have drawn great attention to sensitive and accessible detection of tuberculosis. Aptamers are small short single-stranded molecules of DNA or RNA that fold to a unique form and bind to targets. Once combined with nanomaterials, nano-scale aptasensors provide powerful analytical platforms for diagnosing of tuberculosis. Various groups designed and studied aptamers specific for the whole cells of M. tuberculosis, mycobacterial proteins and IFN-γ for early diagnosis of TB. Advantages such as high specificity and strong affinity, potential for binding to a larger variety of targets, increased stability, lower costs of synthesis and storage requirements, and lower probability of contamination make aptasensors pivotal alternatives for future TB diagnostics. In recent years, the concept of SOMAmer has opened new horizons in high precision detection of tuberculosis biomarkers. This review article provides a description of the research progresses of aptamer-based and SOMAmer-based biosensors and nanobiosensors for the detection of tuberculosis.
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Affiliation(s)
- Behrouz Golichenari
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Rahim Nosrati
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Molecular Microbiology Research Center (MMRC), Shahed University, Tehran, Iran
| | - Aref Farokhi-Fard
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
| | - Javad Behravan
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Mediphage Bioceuticals, Inc., 661 University Avenue, Suite 1300, MaRS Centre, West Tower, Toronto, Canada.
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191
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Wang H, Li C, Liu X, Zhou X, Wang F. Construction of an enzyme-free concatenated DNA circuit for signal amplification and intracellular imaging. Chem Sci 2018; 9:5842-5849. [PMID: 30079197 PMCID: PMC6050587 DOI: 10.1039/c8sc01981a] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 06/05/2018] [Indexed: 12/22/2022] Open
Abstract
A rationally and modularly engineered two-layered CHA–HCR circuit was constructed for amplified biosensing and bioimaging with high performance.
Nucleic acid circuits have shown promising potential for amplified detection of biomarkers with interest in biologically important engineering applications. In this work, by properly integrating two signal amplification approaches, catalytic hairpin assembly (CHA) and hybridization chain reaction (HCR), a concatenated CHA–HCR system was established as an isothermal enzyme-free amplification strategy for highly sensitive and selective nucleic acid assay. The target catalyzes the self-assembly of CHA hairpin substrates into dsDNA products, where the split segments of HCR trigger are successively connected to drive the subsequent autonomous cross-opening of HCR hairpins, leading to the construction of HCR tandem copolymeric dsDNA nanowires. The resulting HCR copolymer brings a fluorophore donor/acceptor pair into close proximity that allows an efficient generation of FRET readout signal. Moreover, the optimized CHA–HCR circuit, upon the incorporation of an auxiliary sensing module, can be converted into a universal sensing platform for detecting cancerous biomarkers (e.g., a well-known oncogene miR-21) through a convenient easy-to-integrate procedure. The concatenated CHA–HCR amplifier enables accurate intracellular miRNA imaging in living cells, which is especially suitable for in situ amplified detection of lowly expressed endogenous analytes. The inherent synergistically accelerated recognition and hybridization features of CHA–HCR circuit contribute to the amplified detection of endogenous RNAs in living cells. The flexible and programmable nature of the homogeneous CHA–HCR system provides a versatile and robust toolbox for a wide range of research fields, such as in vivo bioimaging, clinical diagnosis and environmental monitoring.
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Affiliation(s)
- Huimin Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Chunxiao Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Xiaoqing Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Xiang Zhou
- Key Laboratory of Biomedical Polymers-Ministry of Education , College of Chemistry and Molecular Sciences , Wuhan University , 430072 Wuhan , China
| | - Fuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
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192
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Deng R, Zhang K, Wang L, Ren X, Sun Y, Li J. DNA-Sequence-Encoded Rolling Circle Amplicon for Single-Cell RNA Imaging. Chem 2018. [DOI: 10.1016/j.chempr.2018.03.003] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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193
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Schaffter SW, Green LN, Schneider J, Subramanian HKK, Schulman R, Franco E. T7 RNA polymerase non-specifically transcribes and induces disassembly of DNA nanostructures. Nucleic Acids Res 2018; 46:5332-5343. [PMID: 29718412 PMCID: PMC6007251 DOI: 10.1093/nar/gky283] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 03/28/2018] [Accepted: 04/03/2018] [Indexed: 12/18/2022] Open
Abstract
The use of proteins that bind and catalyze reactions with DNA alongside DNA nanostructures has broadened the functionality of DNA devices. DNA binding proteins have been used to specifically pattern and tune structural properties of DNA nanostructures and polymerases have been employed to directly and indirectly drive structural changes in DNA structures and devices. Despite these advances, undesired and poorly understood interactions between DNA nanostructures and proteins that bind DNA continue to negatively affect the performance and stability of DNA devices used in conjunction with enzymes. A better understanding of these undesired interactions will enable the construction of robust DNA nanostructure-enzyme hybrid systems. Here, we investigate the undesired disassembly of DNA nanotubes in the presence of viral RNA polymerases (RNAPs) under conditions used for in vitro transcription. We show that nanotubes and individual nanotube monomers (tiles) are non-specifically transcribed by T7 RNAP, and that RNA transcripts produced during non-specific transcription disassemble the nanotubes. Disassembly requires a single-stranded overhang on the nanotube tiles where transcripts can bind and initiate disassembly through strand displacement, suggesting that single-stranded domains on other DNA nanostructures could cause unexpected interactions in the presence of viral RNA polymerases.
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Affiliation(s)
- Samuel W Schaffter
- Department of Chemical and Biomolecular Engineering – Johns Hopkins University
| | - Leopold N Green
- Department of Mechanical Engineering – University of California - Riverside
| | - Joanna Schneider
- Department of Chemical and Biomolecular Engineering – Johns Hopkins University
| | | | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering – Johns Hopkins University
- Department of Computer Science – Johns Hopkins University
| | - Elisa Franco
- Department of Mechanical Engineering – University of California - Riverside
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194
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Lopez R, Wang R, Seelig G. A molecular multi-gene classifier for disease diagnostics. Nat Chem 2018; 10:746-754. [PMID: 29713032 DOI: 10.1038/s41557-018-0056-1] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 03/29/2018] [Indexed: 11/09/2022]
Abstract
Despite its early promise as a diagnostic and prognostic tool, gene expression profiling remains cost-prohibitive and challenging to implement in a clinical setting. Here, we introduce a molecular computation strategy for analysing the information contained in complex gene expression signatures without the need for costly instrumentation. Our workflow begins by training a computational classifier on labelled gene expression data. This in silico classifier is then realized at the molecular level to enable expression analysis and classification of previously uncharacterized samples. Classification occurs through a series of molecular interactions between RNA inputs and engineered DNA probes designed to differentially weigh each input according to its importance. We validate our technology with two applications: a classifier for early cancer diagnostics and a classifier for differentiating viral and bacterial respiratory infections based on host gene expression. Together, our results demonstrate a general and modular framework for low-cost gene expression analysis.
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Affiliation(s)
- Randolph Lopez
- Department of Bioengineering, University of Washington, Seattle, WA, USA.,Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, USA
| | - Ruofan Wang
- Department of Biology, University of Washington, Seattle, WA, USA.,Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Georg Seelig
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, USA. .,Department of Electrical Engineering, University of Washington, Seattle, WA, USA. .,Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA.
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195
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Ma Q, Gao Z. A simple and ultrasensitive fluorescence assay for single-nucleotide polymorphism. Anal Bioanal Chem 2018; 410:3093-3100. [PMID: 29644378 DOI: 10.1007/s00216-018-0874-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/11/2017] [Accepted: 01/12/2018] [Indexed: 11/30/2022]
Abstract
In this report, a simple, label-free and highly efficient nucleic acid amplification technique is developed for ultrasensitive detection of single-nucleotide polymorphism (SNP). Briefly, a designed padlock probe is first circularized by a DNA ligase when it perfectly complements to a mutant gene. Then, the mutant gene functions as a primer to initiate branched rolling circle amplification reaction (BRCA), generating a large number of branched DNA strands and a lot of pyrophosphate molecules which is equivalent to the number of nucleotides consumed. With the addition of a terpyridine-Zn(II) complex, pyrophosphate molecules can be sensitively detected owing to the formation of a fluorescent terpyridine-Zn(II)-pyrophosphate complex. The fluorescence intensity is directly associated with the content of the mutant gene in a sample solution. On the other hand, the circulation of the padlock probe is prohibited when it hybridizes with the wild-type gene. In this assay, the accumulative nature of the BRCA process produces a detection limit of 0.1 pM and an excellent selectivity factor of 1000 toward SNP. As little as 0.1% mutant in the wild-type gene can be successfully detected. The simple procedure, high sensitivity, and high selectivity of this assay offer a potentially viable alternative for routine SNP analysis. Graphical abstract A simple and label-free fluorescence assay for SNP detection by coupling BRCA with selective fluorescence detection of pyrophosphate using the terpyridine-Zn(II) complex.
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Affiliation(s)
- Qian Ma
- Department of Chemistry, National University of Singapore, 3 Science Drive 2, Singapore, 117543, Singapore
| | - Zhiqiang Gao
- Department of Chemistry, National University of Singapore, 3 Science Drive 2, Singapore, 117543, Singapore.
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196
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Jia Y, Li F. Studies of Functional Nucleic Acids Modified Light Addressable Potentiometric Sensors: X-ray Photoelectron Spectroscopy, Biochemical Assay, and Simulation. Anal Chem 2018; 90:5153-5161. [DOI: 10.1021/acs.analchem.7b05261] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Yunfang Jia
- College of Electronic Information and Optic Engineering, Nankai University, Weijin Road, Tianjin, Nankai District, 300071, China
| | - Fang Li
- College of Electronic Information and Optic Engineering, Nankai University, Weijin Road, Tianjin, Nankai District, 300071, China
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197
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Hede MS, Fjelstrup S, Lötsch F, Zoleko RM, Klicpera A, Groger M, Mischlinger J, Endame L, Veletzky L, Neher R, Simonsen AKW, Petersen E, Mombo-Ngoma G, Stougaard M, Ho YP, Labouriau R, Ramharter M, Knudsen BR. Detection of the Malaria causing Plasmodium Parasite in Saliva from Infected Patients using Topoisomerase I Activity as a Biomarker. Sci Rep 2018. [PMID: 29515150 PMCID: PMC5841400 DOI: 10.1038/s41598-018-22378-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Malaria is among the major threats to global health with the main burden of disease being in rural areas of developing countries where accurate diagnosis based on non-invasive samples is in high demand. We here present a novel molecular assay for detection of malaria parasites based on technology that may be adapted for low-resource settings. Moreover, we demonstrate the exploitation of this assay for detection of malaria in saliva. The setup relies on pump-free microfluidics enabled extraction combined with a DNA sensor substrate that is converted to a single-stranded DNA circle specifically by topoisomerase I expressed by the malaria causing Plasmodium parasite. Subsequent rolling circle amplification of the generated DNA circle in the presence of biotin conjugated deoxynucleotides resulted in long tandem repeat products that was visualized colorimetrically upon binding of horse radish peroxidase (HRP) and addition of 3,3′,5,5′-Tetramethylbenzidine that was converted to a blue colored product by HRP. The assay was directly quantitative, specific for Plasmodium parasites, and allowed detection of Plasmodium infection in a single drop of saliva from 35 out of 35 infected individuals tested. The results could be determined directly by the naked eye and documented by quantifying the color intensity using a standard paper scanner.
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Affiliation(s)
| | - Søren Fjelstrup
- Department of Molecular Biology and Genetics, University of Aarhus, Aarhus, Denmark
| | - Felix Lötsch
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.,Department of Medicine, I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | | | - Anna Klicpera
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Mirjam Groger
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Johannes Mischlinger
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.,Department of Medicine, I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria.,Institut für Tropenmedizin, Universität Tübingen, Tübingen, Germany
| | - Lilian Endame
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Luzia Veletzky
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Ronja Neher
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.,Institut für Tropenmedizin, Universität Tübingen, Tübingen, Germany
| | | | - Eskild Petersen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark.,Department of Infectious Diseases, The Royal Hospital, Muscat, Oman
| | - Ghyslain Mombo-Ngoma
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.,Institut für Tropenmedizin, Universität Tübingen, Tübingen, Germany
| | - Magnus Stougaard
- Department of Clinical Medicine, University of Aarhus, Aarhus, Denmark
| | - Yi-Ping Ho
- Division of Biomedical Engineering, Department of Electronic Engineering, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | | | - Michael Ramharter
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon.,Department of Medicine, I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria.,Institut für Tropenmedizin, Universität Tübingen, Tübingen, Germany
| | - Birgitta Ruth Knudsen
- Department of Molecular Biology and Genetics, University of Aarhus, Aarhus, Denmark.
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198
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Zhang K, Lv S, Lin Z, Li M, Tang D. Bio-bar-code-based photoelectrochemical immunoassay for sensitive detection of prostate-specific antigen using rolling circle amplification and enzymatic biocatalytic precipitation. Biosens Bioelectron 2018; 101:159-166. [DOI: 10.1016/j.bios.2017.10.031] [Citation(s) in RCA: 204] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 10/11/2017] [Accepted: 10/14/2017] [Indexed: 12/31/2022]
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199
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An aptamer-based ligation-triggered rolling circle amplification strategy for ATP detection and imaging in situ. J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2017.09.076] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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200
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Feng Q, Zhao X, Guo Y, Liu M, Wang P. Stochastic DNA walker for electrochemical biosensing sensitized with gold nanocages@graphene nanoribbons. Biosens Bioelectron 2018. [PMID: 29522905 DOI: 10.1016/j.bios.2018.02.050] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A target-driven stochastic DNA walking electrochemical biosensor sensitized with gold nanocages@graphene nanoribbons (Au NCs@GNRs) was explored for sensitive detection of target DNA. Benefited from the large surface area and excellent conductivity of Au NCs and GNRs, the proposed sensing platform not only improved the electron transfer kinetics involved in electrochemical reactions, but also enhanced the loading capability for stem-loop structural DNA segment (H). Upon the addition of target DNA, the hairpin structure of H was opened and H:target DNA duplex was formed based on toehold-mediated DNA strand displacement. In the presence of exonuclease III (Exo III), the H:target DNA duplex was digested. As a result, target DNA spontaneously dissociated from H:target DNA duplex and then hybridized with another H strand. Therefore, the continuous locomotion of target DNA unceasingly triggered new digestion process from near to far along the electrode surface, resulting in great signal amplification. The proposed strategy exhibited excellent detection performances for DNA analysis in complex matrix such as human serum, which illuminated the practical application field of the sensing platform.
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Affiliation(s)
- Qiumei Feng
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, P. R. China
| | - Xiaolei Zhao
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, P. R. China
| | - Yuehua Guo
- Surgical Comprehensive Laboratory, Affiliated Hospital of Nantong University, Nantong 226001, P. R. China
| | - Mingkai Liu
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, P. R. China.
| | - Po Wang
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, P. R. China.
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