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Hu X, Wang Y, Liu H, Wang J, Tan Y, Wang F, Yuan Q, Tan W. Naked eye detection of multiple tumor-related mRNAs from patients with photonic-crystal micropattern supported dual-modal upconversion bioprobes. Chem Sci 2016; 8:466-472. [PMID: 28616133 PMCID: PMC5458711 DOI: 10.1039/c6sc03401b] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 08/19/2016] [Indexed: 01/10/2023] Open
Abstract
We have designed a biochip-based mRNA detection device by combining a hydrophilic–hydrophobic micropattern with upconversion luminescence (UCL) probes.
Development of a portable device for the detection of multiple mRNAs is a significant need in the early diagnosis of cancer. We have designed a biochip-based mRNA detection device by combining a hydrophilic–hydrophobic micropattern with upconversion luminescence (UCL) probes. The device achieves highly sensitive detection, using the naked eye, of multiple mRNAs among patient samples. The high sensitivity is attributed to enrichment of the target concentration and a fluorescence enhancement effect. In addition, since the photonic crystal (PC) dot biochip is functionalized with dual-wavelength excitation UCL probes, two kinds of mRNAs in the heterogeneous biological samples are detected simultaneously, and the corresponding luminescence signals are captured using an unmodified camera phone. The biochip-based mRNA detection device reported here demonstrates that multiple mRNAs extracted from patient samples can be simultaneously and sensitively detected in a visual way without sophisticated instrumentation. Therefore, this device is promising for real-time detection of multiple biomarkers in patient samples, and it is anticipated that it will provide a powerful tool for convenient early diagnosis of cancer.
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Affiliation(s)
- Xiaoxia Hu
- Key Laboratory of Analytical Chemistry for Biology and Medicine , Ministry of Education , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Yingqian 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 .
| | - Haoyang 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 .
| | - Jie 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 .
| | - Yaning Tan
- Key Laboratory of Analytical Chemistry for Biology and Medicine , Ministry of Education , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Fubing Wang
- Department of Laboratory Medicine & Center for Gene Diagnosis , Zhongnan Hospital , Wuhan University , Wuhan , P. R. China
| | - Quan Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine , Ministry of Education , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory , State Key Laboratory of Chemo/Bio-Sensing and Chemometrics , College of Biology and College of Chemistry and Chemical Engineering , Hunan University , Changsha , P. R. China.,Department of Chemistry , Center for Research at the Bio/Nano Interface , Health Cancer Center , UF Genetics Institute , McKnight Brain Institute , University of Florida , Gainesville , USA
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2
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Liu M, Zhang W, Zhang Q, Brennan JD, Li Y. Biosensing by Tandem Reactions of Structure Switching, Nucleolytic Digestion, and DNA Amplification of a DNA Assembly. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503182] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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3
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Liu M, Zhang W, Zhang Q, Brennan JD, Li Y. Biosensing by Tandem Reactions of Structure Switching, Nucleolytic Digestion, and DNA Amplification of a DNA Assembly. Angew Chem Int Ed Engl 2015; 54:9637-41. [PMID: 26119600 DOI: 10.1002/anie.201503182] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/28/2015] [Indexed: 12/20/2022]
Abstract
ϕ29 DNA polymerase (ϕ29DP) is able to carry out repetitive rounds of DNA synthesis using a circular DNA template by rolling circle amplification (RCA). It also has the ability to execute 3'-5' digestion of single-stranded but not double-stranded DNA. A biosensor engineering strategy is presented that takes advantage of these two properties of ϕ29DP coupled with structure-switching DNA aptamers. The design employs a DNA assembly made of a circular DNA template, a DNA aptamer, and a pre-primer. The DNA assembly is unable to undergo RCA in the absence of cognate target owing to the formation of duplex structures. The presence of the target, however, triggers a structure-switching event that causes nucleolytic conversion of the pre-primer by ϕ29DP into a mature primer to facilitate RCA. This method relays target detection by the aptamer to the production of massive DNA amplicons, giving rise to dramatically enhanced detection sensitivity.
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Affiliation(s)
- Meng Liu
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada)
| | - Wenqing Zhang
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada)
| | - Qiang Zhang
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada)
| | - John D Brennan
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada).
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada). .,Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada).
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4
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Mao Y, Liu M, Tram K, Gu J, Salena BJ, Jiang Y, Li Y. Optimal DNA templates for rolling circle amplification revealed by in vitro selection. Chemistry 2015; 21:8069-74. [PMID: 25877998 DOI: 10.1002/chem.201500994] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Indexed: 01/21/2023]
Abstract
Rolling circle amplification (RCA) has been widely used as an isothermal DNA amplification technique for diagnostic and bioanalytical applications. Because RCA involves repeated copying of the same circular DNA template by a DNA polymerase thousands of times, we hypothesized there exist DNA sequences that can function as optimal templates and produce more DNA amplicons within an allocated time. Herein we describe an in vitro selection effort conducted to search from a random sequence DNA pool for such templates for phi29 DNA polymerase, a frequently used polymerase for RCA. Diverse DNA molecules were isolated and they were characterized by richness in adenosine (A) and cytidine (C) nucleotides. The top ranked sequences exhibit superior RCA efficiency and the use of these templates for RCA results in significantly improved detection sensitivity. AC-rich sequences are expected to find useful applications for setting up effective RCA assays for biological sensing.
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Affiliation(s)
- Yu Mao
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada).,The Ministry-Province Jointly Constructed Base for State Key Laboratory, Shenzhen Key Laboratory of Chemical Biology, The Graduate School at Shenzhen, Tsinghua University, Shenzhen, Guangdong 518055 (P. R. China).,School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055 (P. R. China)
| | - Meng Liu
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada)
| | - Kha Tram
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada)
| | - Jimmy Gu
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada)
| | - Bruno J Salena
- Department of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada)
| | - Yuyang Jiang
- The Ministry-Province Jointly Constructed Base for State Key Laboratory, Shenzhen Key Laboratory of Chemical Biology, The Graduate School at Shenzhen, Tsinghua University, Shenzhen, Guangdong 518055 (P. R. China).
| | - Yingfu Li
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada).
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5
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Ran X, Pu F, Ren J, Qu X. A CuS-based chemical tongue chip for pattern recognition of proteins and antibiotic-resistant bacteria. Chem Commun (Camb) 2015; 51:2675-8. [DOI: 10.1039/c4cc08863h] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A CuS-based sensor array having high stability and selectivity for identifying analytes on a quartz chip.
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Affiliation(s)
- Xiang Ran
- Laboratory of Chemical Biology
- State Key laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Changchun
- China
| | - Fang Pu
- Laboratory of Chemical Biology
- State Key laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Changchun
- China
| | - Jinsong Ren
- Laboratory of Chemical Biology
- State Key laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Changchun
- China
| | - Xiaogang Qu
- Laboratory of Chemical Biology
- State Key laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Changchun
- China
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Wu R, Zhang S, Lyu J, Lu F, Yue X, Lv J. A visual volumetric hydrogel sensor enables quantitative and sensitive detection of copper ions. Chem Commun (Camb) 2015; 51:8078-81. [DOI: 10.1039/c5cc00744e] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A volumetric sensor design enables the precise naked-eye readout of hydrogel volume changes for quantitative and sensitive detection of copper ions.
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Affiliation(s)
- Rui Wu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
- Xi'an
- P. R. China
| | - Shenghai Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
- Xi'an
- P. R. China
| | - Jitong Lyu
- College of Chemical Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - Fang Lu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
- Xi'an
- P. R. China
| | - Xuanfeng Yue
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
- Xi'an
- P. R. China
| | - Jiagen Lv
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
- Xi'an
- P. R. China
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7
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Wang X, Chen X, Sun S, Zhang F, Zhu J. Salt-enabled visual detection of DNA. Chem Commun (Camb) 2014; 50:15744-7. [PMID: 25370740 DOI: 10.1039/c4cc06536k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report herein a label-free, salt-enabled visual detection strategy for DNA, based on the alteration of surface adhesion properties of salt solution, which can translate to the change in the size of the salt residue upon drying, with self-assembled DNA nanostructures. This environmentally friendly array assay protocol enables the achievement of a detection sensitivity comparable to classic colorimetric methods, single-base mismatch differentiation selectivity, multiple-target detection capability, RNA target detection, and a ligase chain reaction-rolling circle amplification implementation format.
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Affiliation(s)
- Xilong Wang
- Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, State Key Laboratory of Coordination Chemistry, Nanjing National Laboratory of Microstructures, Nanjing University, Nanjing 210093, China.
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8
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Sun S, Yao H, Zhang F, Zhu J. Multiplexed DNA detection based on positional encoding/decoding with self-assembled DNA nanostructures. Chem Sci 2014; 6:930-934. [PMID: 29560179 PMCID: PMC5811145 DOI: 10.1039/c4sc02696a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 10/15/2014] [Indexed: 01/02/2023] Open
Abstract
A multiplexed DNA detection strategy with fast hybridization kinetics based on positional encoding/decoding with self-assembled DNA nanostructures has been developed.
Current multiplexed analysis methods suffer from either slow reaction kinetics (planar arrays) or complicated encoding/decoding procedures (suspension arrays). We report herein a multiplexed DNA detection strategy that addresses these issues, based on positional encoding/decoding with self-assembled DNA nanostructures. The strategy enables the acquisition of high-resolution, consistent, and quantitative assay results in a single round of a transmission electron microscopy imaging operation. Applications in polymerase chain reaction-free settings and assays of other structurally distinct targets can be anticipated through the implementation of the strategy with miniaturized femtoliter/attoliter dispensing technology and readily accessible DNA conjugate structures.
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Affiliation(s)
- Sha Sun
- Department of Polymer Science and Engineering , School of Chemistry and Chemical Engineering , State Key Laboratory of Coordination Chemistry , Nanjing National Laboratory of Microstructures , Nanjing University , Nanjing 210093 , China .
| | - Huaxin Yao
- Department of Polymer Science and Engineering , School of Chemistry and Chemical Engineering , State Key Laboratory of Coordination Chemistry , Nanjing National Laboratory of Microstructures , Nanjing University , Nanjing 210093 , China .
| | - Feifei Zhang
- Department of Polymer Science and Engineering , School of Chemistry and Chemical Engineering , State Key Laboratory of Coordination Chemistry , Nanjing National Laboratory of Microstructures , Nanjing University , Nanjing 210093 , China .
| | - Jin Zhu
- Department of Polymer Science and Engineering , School of Chemistry and Chemical Engineering , State Key Laboratory of Coordination Chemistry , Nanjing National Laboratory of Microstructures , Nanjing University , Nanjing 210093 , China .
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Cadet J, Wagner JR. Oxidatively generated base damage to cellular DNA by hydroxyl radical and one-electron oxidants: similarities and differences. Arch Biochem Biophys 2014; 557:47-54. [PMID: 24820329 DOI: 10.1016/j.abb.2014.05.001] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 04/23/2014] [Accepted: 05/01/2014] [Indexed: 01/05/2023]
Abstract
Hydroxyl radical (OH) and one-electron oxidants that may be endogenously formed through oxidative metabolism, phagocytosis, inflammation and pathological conditions constitute the main sources of oxidatively generated damage to cellular DNA. It is worth mentioning that exposure of cells to exogenous physical agents (UV light, high intensity UV laser, ionizing radiation) and chemicals may also induce oxidatively generated damage to DNA. Emphasis is placed in this short review article on the mechanistic aspects of OH and one-electron oxidant-mediated formation of single and more complex damage (tandem lesions, intra- and interstrand cross-links, DNA-protein cross-links) in cellular DNA arising from one radical hit. This concerns DNA modifications that have been accurately measured using suitable analytical methods such as high performance liquid chromatography coupled with electrospray ionization tandem mass spectrometry. Evidence is provided that OH and one-electron oxidants after generating neutral radicals and base radical cations respectively may partly induce common degradation pathways. In addition, selective oxidative reactions giving rise to specific degradation products of OH and one-electron oxidation reactions that can be used as representative biomarkers of these oxidants have been identified.
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Affiliation(s)
- Jean Cadet
- Institut Nanosciences et Cryogénie, CEA/Grenoble, F-38054 Grenoble Cedex 9, France; Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine des Sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada.
| | - J Richard Wagner
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine des Sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
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