251
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Affiliation(s)
- Richard M. Graybill
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
| | - Ryan C. Bailey
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
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252
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Ren M, Wang S, Cai C, Chen C, Chen X. A simple and sensitive resonance light scattering method based on aggregation of gold nanoparticles for selective detection of microRNA-21. RSC Adv 2016. [DOI: 10.1039/c6ra12366j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A novel resonance light scattering method based on analyte-induced aggregation of gold nanoparticles for the determination of microRNAs was developed.
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Affiliation(s)
- Ming Ren
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education
- College of Chemistry
- Xiangtan University
- Xiangtan
- China
| | - Shijun Wang
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education
- College of Chemistry
- Xiangtan University
- Xiangtan
- China
| | - Changqun Cai
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education
- College of Chemistry
- Xiangtan University
- Xiangtan
- China
| | - Chunyan Chen
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education
- College of Chemistry
- Xiangtan University
- Xiangtan
- China
| | - Xiaoming Chen
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education
- College of Chemistry
- Xiangtan University
- Xiangtan
- China
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253
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Zhou C, Wu C, Liu Y, Wang E. Effective construction of a AuNPs–DNA system for the implementation of various advanced logic gates. RSC Adv 2016. [DOI: 10.1039/c6ra21585h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Four advanced logic gates were successfully realized under enzyme-free conditions by integration of DNA and AuNPs.
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Affiliation(s)
- Chunyang Zhou
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Changtong Wu
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Yaqing Liu
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
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254
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Li Y, Zhang J, Zhao J, Zhao L, Cheng Y, Li Z. A simple molecular beacon with duplex-specific nuclease amplification for detection of microRNA. Analyst 2016; 141:1071-6. [DOI: 10.1039/c5an02312b] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A target recycling amplification method based on a simple molecular beacon and duplex-specific nuclease has been developed for microRNA detection.
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Affiliation(s)
- Yingcun Li
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- College of Chemistry and Environmental Science
- Hebei University
- Baoding 071002
| | - Jiangyan Zhang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- College of Chemistry and Environmental Science
- Hebei University
- Baoding 071002
| | - Jingjing Zhao
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- College of Chemistry and Environmental Science
- Hebei University
- Baoding 071002
| | - Likun Zhao
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- College of Chemistry and Environmental Science
- Hebei University
- Baoding 071002
| | - Yongqiang Cheng
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- College of Chemistry and Environmental Science
- Hebei University
- Baoding 071002
| | - Zhengping Li
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- College of Chemistry and Environmental Science
- Hebei University
- Baoding 071002
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255
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Zhang J, Wu DZ, Cai SX, Chen M, Xia YK, Wu F, Chen JH. An immobilization-free electrochemical impedance biosensor based on duplex-specific nuclease assisted target recycling for amplified detection of microRNA. Biosens Bioelectron 2016; 75:452-7. [DOI: 10.1016/j.bios.2015.09.006] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 08/27/2015] [Accepted: 09/03/2015] [Indexed: 12/31/2022]
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256
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Zhang S, Liu R, Xing Z, Zhang S, Zhang X. Multiplex miRNA assay using lanthanide-tagged probes and the duplex-specific nuclease amplification strategy. Chem Commun (Camb) 2016; 52:14310-14313. [DOI: 10.1039/c6cc08334j] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A multiplex ICP-MS-based miRNA assay was achieved with duplex-specific nuclease amplification using bifunctional oligonucleotide probes with lanthanide tags.
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Affiliation(s)
- Shixi Zhang
- Beijing Key Laboratory for Microanalytical Methods and Instrumentation
- Department of Chemistry
- Tsinghua University
- Beijing
- China
| | - Rui Liu
- College of Chemistry
- Sichuan University
- Chengdu
- China
| | - Zhi Xing
- Beijing Key Laboratory for Microanalytical Methods and Instrumentation
- Department of Chemistry
- Tsinghua University
- Beijing
- China
| | - Sichun Zhang
- Beijing Key Laboratory for Microanalytical Methods and Instrumentation
- Department of Chemistry
- Tsinghua University
- Beijing
- China
| | - Xinrong Zhang
- Beijing Key Laboratory for Microanalytical Methods and Instrumentation
- Department of Chemistry
- Tsinghua University
- Beijing
- China
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257
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258
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Abstract
Recent advances in Au NP based optical sensing systems for various analytes based on absorption, fluorescence and SERS are summarized.
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Affiliation(s)
- Zhiqin Yuan
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Cho-Chun Hu
- Department of Applied Science
- National Taitung University
- Taitung 95002
- Taiwan
| | - Huan-Tsung Chang
- Department of Chemistry
- National Taiwan University
- Taipei 106
- Taiwan
| | - Chao Lu
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- China
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259
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Miao X, Li Z, Ling L. Fluorescence recognition of double-stranded DNA based on the quenching of gold nanoparticles to a fluorophore labeled DNA probe. Analyst 2016; 141:5829-5834. [DOI: 10.1039/c6an01145d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work described an ultrasensitive fluorescent sensor for sequence-specific recognition of dsDNA based on the quenching of gold nanoparticles (AuNPs) to a fluorophore labeled DNA probe.
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Affiliation(s)
- Xiangmin Miao
- School of Life Science
- Jiangsu Normal University
- Xuzhou 221116
- PR China
| | - Zongbing Li
- School of Life Science
- Jiangsu Normal University
- Xuzhou 221116
- PR China
| | - Liansheng Ling
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou 510275
- PR China
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260
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Chamorro-Garcia A, Merkoçi A. Nanobiosensors in diagnostics. Nanobiomedicine (Rij) 2016; 3:1849543516663574. [PMID: 29942385 PMCID: PMC5998262 DOI: 10.1177/1849543516663574] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 07/20/2016] [Indexed: 01/09/2023] Open
Abstract
Medical diagnosis has been greatly improved thanks to the development of new techniques capable of performing very sensitive detection and quantifying certain parameters. These parameters can be correlated with the presence of specific molecules and their quantity. Unfortunately, these techniques are demanding, expensive, and often complicated. On the other side, progress in other fields of science and technology has contributed to the rapid growth of nanotechnology. Although being an emerging discipline, nanotechnology has raised huge interest and expectations. Most of the enthusiasm comes from new possibilities and properties of nanomaterials. Biosensors (simple, robust, sensitive, cost-effective) combined with nanomaterials, also called nanobiosensors, are serving as bridge between advanced detection/diagnostics and daily/routine tests. Here we review some of the latest applications of nanobiosensors in diagnostics field.
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Affiliation(s)
- Alejandro Chamorro-Garcia
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The Barcelona Institute of Science and Technolgy, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Arben Merkoçi
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The Barcelona Institute of Science and Technolgy, Campus UAB, Bellaterra, 08193 Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
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261
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Li S, Xu L, Ma W, Wu X, Sun M, Kuang H, Wang L, Kotov NA, Xu C. Dual-Mode Ultrasensitive Quantification of MicroRNA in Living Cells by Chiroplasmonic Nanopyramids Self-Assembled from Gold and Upconversion Nanoparticles. J Am Chem Soc 2015; 138:306-12. [DOI: 10.1021/jacs.5b10309] [Citation(s) in RCA: 345] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Si Li
- State
Key Lab of Food Science and Technology, International Joint Research
Laboratory for Biointerface and Biodetection, School of Food Science
and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Liguang Xu
- State
Key Lab of Food Science and Technology, International Joint Research
Laboratory for Biointerface and Biodetection, School of Food Science
and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Wei Ma
- State
Key Lab of Food Science and Technology, International Joint Research
Laboratory for Biointerface and Biodetection, School of Food Science
and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Xiaoling Wu
- State
Key Lab of Food Science and Technology, International Joint Research
Laboratory for Biointerface and Biodetection, School of Food Science
and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Maozhong Sun
- State
Key Lab of Food Science and Technology, International Joint Research
Laboratory for Biointerface and Biodetection, School of Food Science
and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Hua Kuang
- State
Key Lab of Food Science and Technology, International Joint Research
Laboratory for Biointerface and Biodetection, School of Food Science
and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Libing Wang
- State
Key Lab of Food Science and Technology, International Joint Research
Laboratory for Biointerface and Biodetection, School of Food Science
and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Nicholas A. Kotov
- Department
of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109-2136, United States
| | - Chuanlai Xu
- State
Key Lab of Food Science and Technology, International Joint Research
Laboratory for Biointerface and Biodetection, School of Food Science
and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
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262
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He X, Zeng T, Li Z, Wang G, Ma N. Catalytic Molecular Imaging of MicroRNA in Living Cells by DNA-Programmed Nanoparticle Disassembly. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201509726] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Xuewen He
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry; Chemical Engineering and Materials Science; Soochow University; Suzhou 215123 P.R. China
| | - Tao Zeng
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry; Chemical Engineering and Materials Science; Soochow University; Suzhou 215123 P.R. China
| | - Zhi Li
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry; Chemical Engineering and Materials Science; Soochow University; Suzhou 215123 P.R. China
| | - Ganglin Wang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry; Chemical Engineering and Materials Science; Soochow University; Suzhou 215123 P.R. China
| | - Nan Ma
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry; Chemical Engineering and Materials Science; Soochow University; Suzhou 215123 P.R. China
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263
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He X, Zeng T, Li Z, Wang G, Ma N. Catalytic Molecular Imaging of MicroRNA in Living Cells by DNA-Programmed Nanoparticle Disassembly. Angew Chem Int Ed Engl 2015; 55:3073-6. [PMID: 26694689 DOI: 10.1002/anie.201509726] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Revised: 11/26/2015] [Indexed: 12/19/2022]
Abstract
Molecular imaging is an essential tool for disease diagnostics and treatment. Direct imaging of low-abundance nucleic acids in living cells remains challenging because of the relatively low sensitivity and insufficient signal-to-background ratio of conventional molecular imaging probes. Herein, we report a class of DNA-templated gold nanoparticle (GNP)-quantum dot (QD) assembly-based probes for catalytic imaging of cancer-related microRNAs (miRNA) in living cells with signal amplification capacity. We show that a single miRNA molecule could catalyze the disassembly of multiple QDs with the GNP through a DNA-programmed thermodynamically driven entropy gain process, yielding significantly amplified QD photoluminescence (PL) for miRNA imaging. By combining the robust PL of QDs with the catalytic amplification strategy, three orders of magnitude improvement in detection sensitivity is achieved in comparison with non-catalytic imaging probe, which enables facile and accurate differentiation between cancer cells and normal cells by miRNA imaging in living cells.
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Affiliation(s)
- Xuewen He
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, P.R. China
| | - Tao Zeng
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, P.R. China
| | - Zhi Li
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, P.R. China
| | - Ganglin Wang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, P.R. China
| | - Nan Ma
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, P.R. China.
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264
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Wang ZH, Xu CJ. Research Progress of MicroRNA in Early Detection of Ovarian Cancer. Chin Med J (Engl) 2015; 128:3363-70. [PMID: 26668153 PMCID: PMC4797514 DOI: 10.4103/0366-6999.171459] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVE This review aimed to update the progress of microRNA (miRNA) in early detection of ovarian cancer. We discussed the current clinical diagnosis methods and biomarkers of ovarian cancer, especially the methods of miRNA in early detection of ovarian cancer. DATA SOURCES We collected all relevant studies about miRNA and ovarian cancer in PubMed and CNKI from 1995 to 2015. STUDY SELECTION We included all relevant studies concerning miRNA in early detection of ovarian cancer, and excluded the duplicated articles. RESULTS miRNAs play a key role in various biological processes of ovarian cancer, such as development, proliferation, differentiation, apoptosis and metastasis, and these phenomena appear in the early-stage. Therefore, miRNA can be used as a new biomarker for early diagnosis of ovarian cancer, intervention on miRNA expression of known target genes, and potential target genes can achieve the effect of early prevention. With the development of nanoscience and technology, analysis methods of miRNA are also quickly developed, which may provide better characterization of early detection of ovarian cancer. CONCLUSIONS In the near future, miRNA therapy could be a powerful tool for ovarian cancer prevention and treatment, and combining with the new analysis technology and new nanomaterials, point-of-care tests for miRNA with high throughput, high sensitivity, and strong specificity are developed to achieve the application of diagnostic kits in screening of early ovarian cancer.
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Affiliation(s)
- Ze-Hua Wang
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, China
| | - Cong-Jian Xu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, China
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265
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Pang Y, Wang C, Wang J, Sun Z, Xiao R, Wang S. Fe₃O₄@Ag magnetic nanoparticles for microRNA capture and duplex-specific nuclease signal amplification based SERS detection in cancer cells. Biosens Bioelectron 2015; 79:574-80. [PMID: 26749099 DOI: 10.1016/j.bios.2015.12.052] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/16/2015] [Accepted: 12/17/2015] [Indexed: 01/07/2023]
Abstract
A functionalized Fe3O4@Ag magnetic nanoparticle (NP) biosensor for microRNA (miRNA) capture and ultrasensitive detection in total RNA extract from cancer cells was reported in this paper. Herein, Raman tags-DNA probes modified Fe3O4@Ag NPs were designed both as surface-enhanced Raman scattering (SERS) SERS and duplex-specific nuclease signal amplification (DSNSA) platform. Firstly, target miRNAs were captured to the surface of Fe3O4@Ag NPs through DNA/RNA hybridization. In the presence of endonuclease duplex specific nuclease (DSN), one target miRNA molecule could rehybrid thousands of DNA probes to trigger the signal-amplifying recycling. Base on the superparamagnetic of Fe3O4@Ag NPs, target miRNA let-7b can be captured, concentrated and direct quantified within a PE tube without any PCR preamplification treatment. The detection limit was 0.3fM (15 zeptomole, 50μL), nearly 3 orders of magnitude lower than conventional fluorescence based DSN biosensors for miRNA(∼100fM), even single-base difference between the let-7 family members can be discriminated. The result provides a novel proposal to combine the perfect single-base recognition and signal-amplifying ability of the endonuclease DSN with cost-effective SERS strategy for miRNA point-of-care (POC) clinical diagnostics.
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Affiliation(s)
- Yuanfeng Pang
- Capital Medical University, Department of Toxicology, No. 10 Xitoutiao, You An Men, Beijing 100069, PR China; Beijing Institute of Radiation Medicine, Beijing Key Laboratory of New Molecular Diagnosis Techniques for Infectious Dedication, 27 Taiping Road, Beijing, PR China
| | - Chongwen Wang
- Beijing Institute of Radiation Medicine, Beijing Key Laboratory of New Molecular Diagnosis Techniques for Infectious Dedication, 27 Taiping Road, Beijing, PR China; College of Life Science &Bio-Engineering, Beijing University of Technology, Beijing 100124, PR China
| | - Jing Wang
- Beijing Institute of Radiation Medicine, Beijing Key Laboratory of New Molecular Diagnosis Techniques for Infectious Dedication, 27 Taiping Road, Beijing, PR China; School of Pharmaceutical Science, Zhengzhou University, Zhengzhou 450001, PR China
| | - Zhiwei Sun
- Capital Medical University, Department of Toxicology, No. 10 Xitoutiao, You An Men, Beijing 100069, PR China.
| | - Rui Xiao
- Beijing Institute of Radiation Medicine, Beijing Key Laboratory of New Molecular Diagnosis Techniques for Infectious Dedication, 27 Taiping Road, Beijing, PR China.
| | - Shengqi Wang
- Beijing Institute of Radiation Medicine, Beijing Key Laboratory of New Molecular Diagnosis Techniques for Infectious Dedication, 27 Taiping Road, Beijing, PR China
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266
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Abstract
MicroRNA (miRNA) detection is of considerable significance in both disease diagnosis and in the study of miRNA function. The importance of miRNA itself is due to the complicated regulatory functions it plays in various life processes and its close relationship with some diseases. Traditional methods for miRNA detection do not meet the current demands, so various novel methods have been developed with a special focus on sensitivity and specificity. Herein, we summarize and discuss the newly developed miRNA detection methods.
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Affiliation(s)
- Tian Tian
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, P. R. of China.
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267
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Garafutdinov RR, Sakhabutdinova AR, Chemeris AV. [The Increase of Oligonucleotides--Gold Nanoparticles Conjugates Stability]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2015; 41:327-35. [PMID: 26502609 DOI: 10.1134/s1068162015030036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
For today the reagents based on oligonucleotides--gold nanoparticles conjugates and used for specific nucleic acids detection are actively being developed. Such molecular structures are stabilized through the bonds between thiol group in oligonucleotides and gold atoms in nanoparticle. The durability of oligonucleotides--gold nanoparticles binding affects directly on the stability of conjugates and on the possibility of further manipulations. In this paper, a method for the strengthening of oligonucleotides attachment on the gold nano-particles surface by means of anchor groups with dithiolane residues is proposed. A comparative study of the anchors molecular structure influence on the conjugates stability at conditions that typical for oligonucleotide probes was carried out.
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268
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Abstract
Isothermal amplification of nucleic acids is a simple process that rapidly and efficiently accumulates nucleic acid sequences at constant temperature. Since the early 1990s, various isothermal amplification techniques have been developed as alternatives to polymerase chain reaction (PCR). These isothermal amplification methods have been used for biosensing targets such as DNA, RNA, cells, proteins, small molecules, and ions. The applications of these techniques for in situ or intracellular bioimaging and sequencing have been amply demonstrated. Amplicons produced by isothermal amplification methods have also been utilized to construct versatile nucleic acid nanomaterials for promising applications in biomedicine, bioimaging, and biosensing. The integration of isothermal amplification into microsystems or portable devices improves nucleic acid-based on-site assays and confers high sensitivity. Single-cell and single-molecule analyses have also been implemented based on integrated microfluidic systems. In this review, we provide a comprehensive overview of the isothermal amplification of nucleic acids encompassing work published in the past two decades. First, different isothermal amplification techniques are classified into three types based on reaction kinetics. Then, we summarize the applications of isothermal amplification in bioanalysis, diagnostics, nanotechnology, materials science, and device integration. Finally, several challenges and perspectives in the field are discussed.
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Affiliation(s)
- Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Feng Chen
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Qian Li
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China.,School of Life Science & Technology, ShanghaiTech University , Shanghai 200031, China
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269
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Zhang K, Kang DK, Ali MM, Liu L, Labanieh L, Lu M, Riazifar H, Nguyen TN, Zell JA, Digman MA, Gratton E, Li J, Zhao W. Digital quantification of miRNA directly in plasma using integrated comprehensive droplet digital detection. LAB ON A CHIP 2015; 15:4217-26. [PMID: 26387763 PMCID: PMC4631652 DOI: 10.1039/c5lc00650c] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Quantification of miRNAs in blood can be potentially used for early disease detection, surveillance monitoring and drug response evaluation. However, quantitative and robust measurement of miRNAs in blood is still a major challenge in large part due to their low concentration and complicated sample preparation processes typically required in conventional assays. Here, we present the 'Integrated Comprehensive Droplet Digital Detection' (IC 3D) system where the plasma sample containing target miRNAs is encapsulated into microdroplets, enzymatically amplified and digitally counted using a novel, high-throughput 3D particle counter. Using Let-7a as a target, we demonstrate that IC 3D can specifically quantify target miRNA directly from blood plasma at extremely low concentrations ranging from 10s to 10 000 copies per mL in ≤3 hours without the need for sample processing such as RNA extraction. Using this new tool, we demonstrate that target miRNA content in colon cancer patient blood is significantly higher than that in healthy donor samples. Our IC 3D system has the potential to introduce a new paradigm for rapid, sensitive and specific detection of low-abundance biomarkers in biological samples with minimal sample processing.
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Affiliation(s)
- Kaixiang Zhang
- Department of Chemistry, Beijing Key Laboratory for Analytical Methods and Instrumentation, Tsinghua University, Beijing, 100084, China
- Department of pharmaceutical Sciences, Department of Biomedical Engineering, Sue and Bill Gross Stem Cell Research Center, Chao Family Comprehensive Cancer Center, Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA, 92697, USA
| | - Dong-Ku Kang
- Department of pharmaceutical Sciences, Department of Biomedical Engineering, Sue and Bill Gross Stem Cell Research Center, Chao Family Comprehensive Cancer Center, Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA, 92697, USA
| | - M. Monsur Ali
- Department of pharmaceutical Sciences, Department of Biomedical Engineering, Sue and Bill Gross Stem Cell Research Center, Chao Family Comprehensive Cancer Center, Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA, 92697, USA
| | - Linan Liu
- Department of pharmaceutical Sciences, Department of Biomedical Engineering, Sue and Bill Gross Stem Cell Research Center, Chao Family Comprehensive Cancer Center, Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA, 92697, USA
| | - Louai Labanieh
- Department of pharmaceutical Sciences, Department of Biomedical Engineering, Sue and Bill Gross Stem Cell Research Center, Chao Family Comprehensive Cancer Center, Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA, 92697, USA
| | - Mengrou Lu
- Department of pharmaceutical Sciences, Department of Biomedical Engineering, Sue and Bill Gross Stem Cell Research Center, Chao Family Comprehensive Cancer Center, Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA, 92697, USA
| | - Hamidreza Riazifar
- Department of pharmaceutical Sciences, Department of Biomedical Engineering, Sue and Bill Gross Stem Cell Research Center, Chao Family Comprehensive Cancer Center, Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA, 92697, USA
| | - Thi N. Nguyen
- Department of pharmaceutical Sciences, Department of Biomedical Engineering, Sue and Bill Gross Stem Cell Research Center, Chao Family Comprehensive Cancer Center, Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA, 92697, USA
| | - Jason A. Zell
- Division of Hematology/Oncology, University of California Irvine Medical Center, Orange, CA 92868, USA
| | - Michelle A. Digman
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA, 92697, USA
- Centre for Bioactive Discovery in Health and Ageing, School of Science & Technology, University of New England, Armidale, Australia
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA, 92697, USA
| | - Jinghong Li
- Department of Chemistry, Beijing Key Laboratory for Analytical Methods and Instrumentation, Tsinghua University, Beijing, 100084, China
| | - Weian Zhao
- Department of pharmaceutical Sciences, Department of Biomedical Engineering, Sue and Bill Gross Stem Cell Research Center, Chao Family Comprehensive Cancer Center, Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA, 92697, USA
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270
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Affiliation(s)
- Wen Zhou
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Molecular Recognition and Biosensing, and Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Xia Gao
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Molecular Recognition and Biosensing, and Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Dingbin Liu
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Molecular Recognition and Biosensing, and Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, Maryland 20892, United States
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271
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Label-free fluorescence turn-on detection of microRNA based on duplex-specific nuclease and a perylene probe. Anal Chim Acta 2015; 895:89-94. [DOI: 10.1016/j.aca.2015.08.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 08/16/2015] [Accepted: 08/20/2015] [Indexed: 12/23/2022]
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272
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Guan W, Chen L, Rane TD, Wang TH. Droplet Digital Enzyme-Linked Oligonucleotide Hybridization Assay for Absolute RNA Quantification. Sci Rep 2015; 5:13795. [PMID: 26333806 PMCID: PMC4558716 DOI: 10.1038/srep13795] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 08/05/2015] [Indexed: 01/03/2023] Open
Abstract
We present a continuous-flow droplet-based digital Enzyme-Linked Oligonucleotide Hybridization Assay (droplet digital ELOHA) for sensitive detection and absolute quantification of RNA molecules. Droplet digital ELOHA incorporates direct hybridization and single enzyme reaction via the formation of single probe-RNA-probe (enzyme) complex on magnetic beads. It enables RNA detection without reverse transcription and PCR amplification processes. The magnetic beads are subsequently encapsulated into a large number of picoliter-sized droplets with enzyme substrates in a continuous-flow device. This device is capable of generating droplets at high-throughput. It also integrates in-line enzymatic incubation and detection of fluorescent products. Our droplet digital ELOHA is able to accurately quantify (differentiate 40% difference) as few as ~600 RNA molecules in a 1 mL sample (equivalent to 1 aM or lower) without molecular replication. The absolute quantification ability of droplet digital ELOHA is demonstrated with the analysis of clinical Neisseria gonorrhoeae 16S rRNA to show its potential value in real complex samples.
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Affiliation(s)
- Weihua Guan
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore 21218, USA.,Department of Mechanical Engineering, Johns Hopkins University, Baltimore 21218, USA
| | - Liben Chen
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore 21218, USA
| | - Tushar D Rane
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore 21218, USA
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore 21218, USA.,Department of Mechanical Engineering, Johns Hopkins University, Baltimore 21218, USA
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273
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Zhang X, Liu C, Sun L, Duan X, Li Z. Lab on a single microbead: an ultrasensitive detection strategy enabling microRNA analysis at the single-molecule level. Chem Sci 2015; 6:6213-6218. [PMID: 30090237 PMCID: PMC6054045 DOI: 10.1039/c5sc02641e] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 08/13/2015] [Indexed: 01/05/2023] Open
Abstract
A single microbead-based sensing platform has been developed, which enables the detection of microRNA at the single-molecule level.
Detection of a single nucleic acid molecule is of great significance for both fundamental biochemistry studies and clinical diagnostics. By using microRNA (miRNA) as a model target, herein, we have developed a single-microbead-based sensing (SMBS) platform, which simply enables the detection of miRNA at the single-molecule level. In this strategy, an isothermal exponential amplification reaction (EXPAR) is rationally designed towards specific miRNAs and all products of the EXPAR are integrated onto a single microbead for signal amplification and fluorescence enrichment. This pushes the detection of miRNAs down to 1 aM in a 5 μL sample, corresponding to 3 copies of the miRNA molecule. This new strategy also affords high selectivity and it is capable of distinguishing among homologous miRNA family members even with a single-base difference. Due to its ultrahigh sensitivity and selectivity, the proposed SMBS platform has been successfully applied to the detection of miRNA extracted from a single cell.
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Affiliation(s)
- Xiaobo Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| | - Lingbo Sun
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| | - Xinrui Duan
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| | - Zhengping Li
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
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274
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Chen F, Fan C, Zhao Y. Inhibitory impact of 3'-terminal 2'-O-methylated small silencing RNA on target-primed polymerization and unbiased amplified quantification of the RNA in Arabidopsis thaliana. Anal Chem 2015; 87:8758-64. [PMID: 26244621 DOI: 10.1021/acs.analchem.5b01683] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
3'-terminal 2'-O-methylation has been found in several kinds of small silencing RNA, regarded as a protective mechanism against enzymatic 3' → 5' degradation and 3'-end uridylation. The influence of this modification on enzymatic polymerization, however, remains unknown. Herein, a systematic investigation is performed to explore this issue. We found these methylated small RNAs exhibited a suppression behavior in target-primed polymerization, revealing biased result for the manipulation of these small RNAs by conventional polymerization-based methodology. The related potential mechanism is investigated and discussed, which is probably ascribed to the big size of modified group and its close location to 3'-OH. Furthermore, two novel solutions each utilizing base-stacking hybridization and three-way junction structure have been proposed to realize unbiased recognition of small RNAs. On the basis of phosphorothioate against nicking, a creative amplified strategy, phosphorothioate-protected polymerization/binicking amplification, has also been developed for the unbiased quantification of methylated small RNA in Arabidopsis thaliana, demonstrating its promising potential for real sample analysis. Collectively, our studies uncover the polymerization inhibition by 3'-terminal 2'-O-methylated small RNAs with mechanistic discussion, and propose novel unbiased solutions for amplified quantification of small RNAs in real sample.
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Affiliation(s)
- Feng Chen
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, P. R. China
| | - Chunhai Fan
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Yuquan Road, Shanghai 201800, P. R. China
| | - Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, P. R. China
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275
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Ye S, Wu Y, Zhai X, Tang B. Asymmetric Signal Amplification for Simultaneous SERS Detection of Multiple Cancer Markers with Significantly Different Levels. Anal Chem 2015. [DOI: 10.1021/acs.analchem.5b01186] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Sujuan Ye
- College of Chemistry,
Chemical Engineering and Materials Science, Collaborative Innovation
Center of Functionalized Probes for Chemical Imaging in Universities
of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry
of Education, Shandong Provincial Key Laboratory of Clean Production
of Fine Chemicals, Shandong Normal University, Jinan 250014, P.R. China
- Key Laboratory
of Sensor Analysis of Tumor Marker Ministry of Education, College
of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P.R. China
| | - Yanying Wu
- Key Laboratory
of Sensor Analysis of Tumor Marker Ministry of Education, College
of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P.R. China
| | - Xiaomo Zhai
- Key Laboratory
of Sensor Analysis of Tumor Marker Ministry of Education, College
of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P.R. China
| | - Bo Tang
- College of Chemistry,
Chemical Engineering and Materials Science, Collaborative Innovation
Center of Functionalized Probes for Chemical Imaging in Universities
of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry
of Education, Shandong Provincial Key Laboratory of Clean Production
of Fine Chemicals, Shandong Normal University, Jinan 250014, P.R. China
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276
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Min X, Zhuang Y, Zhang Z, Jia Y, Hakeem A, Zheng F, Cheng Y, Tang BZ, Lou X, Xia F. Lab in a Tube: Sensitive Detection of MicroRNAs in Urine Samples from Bladder Cancer Patients Using a Single-Label DNA Probe with AIEgens. ACS APPLIED MATERIALS & INTERFACES 2015; 7:16813-16818. [PMID: 26180929 DOI: 10.1021/acsami.5b04821] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We demonstrate an ultrasensitive microRNA detection method based on an extremely simple probe with only fluorogens but without quencher groups. It avoids complex and difficult steps to accurately design the relative distance between the fluorogens and quencher groups in the probes. Furthermore, the assay could accomplish various detection limits by tuning the reaction temperature due to the different activity of exonuclease III corresponding to the diverse temperature. Specifically, 1 pM miR-21 can be detected in 40 min at 37 °C, and 10 aM (about 300 molecules in 50 μL) miR-21 could be discriminated in 7 days at 4 °C. The great specificity of the assay guarantees that the real 21 urine samples from the bladder cancer patients are successfully detected by our method.
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Affiliation(s)
- Xuehong Min
- †Key Laboratory for Large-Format Battery Materials and System, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yuan Zhuang
- †Key Laboratory for Large-Format Battery Materials and System, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Zhenyu Zhang
- †Key Laboratory for Large-Format Battery Materials and System, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yongmei Jia
- †Key Laboratory for Large-Format Battery Materials and System, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Abdul Hakeem
- †Key Laboratory for Large-Format Battery Materials and System, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Fuxin Zheng
- †Key Laboratory for Large-Format Battery Materials and System, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yong Cheng
- ‡National Engineering Research Center for Nanomedicine, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Ben Zhong Tang
- §Department of Chemistry, HKUST Jockey Club Institute for Advanced Study Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology (HKUST), Clear Water Bay, Kowloon, Hong Kong, China
| | - Xiaoding Lou
- †Key Laboratory for Large-Format Battery Materials and System, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Fan Xia
- †Key Laboratory for Large-Format Battery Materials and System, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
- ‡National Engineering Research Center for Nanomedicine, Huazhong University of Science and Technology, Wuhan 430074, China
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277
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Ma JL, Yin BC, Le HN, Ye BC. Label-Free Detection of Sequence-Specific DNA Based on Fluorescent Silver Nanoclusters-Assisted Surface Plasmon-Enhanced Energy Transfer. ACS APPLIED MATERIALS & INTERFACES 2015; 7:12856-63. [PMID: 26024337 DOI: 10.1021/acsami.5b03837] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We have developed a label-free method for sequence-specific DNA detection based on surface plasmon enhanced energy transfer (SPEET) process between fluorescent DNA/AgNC string and gold nanoparticles (AuNPs). DNA/AgNC string, prepared by a single-stranded DNA template encoded two emitter-nucleation sequences at its termini and an oligo spacer in the middle, was rationally designed to produce bright fluorescence emission. The proposed method takes advantage of two strategies. The first one is the difference in binding properties of single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) toward AuNPs. The second one is SPEET process between fluorescent DNA/AgNC string and AuNPs, in which fluorescent DNA/AgNC string can be spontaneously adsorbed onto the surface of AuNPs and correspondingly AuNPs serve as "nanoquencher" to quench the fluorescence of DNA/AgNC string. In the presence of target DNA, the sensing probe hybridized with target DNA to form duplex DNA, leading to a salt-induced AuNP aggregation and subsequently weakened SPEET process between fluorescent DNA/AgNC string and AuNPs. A red-to-blue color change of AuNPs and a concomitant fluorescence increase were clearly observed in the sensing system, which had a concentration dependent manner with specific DNA. The proposed method achieved a detection limit of ∼2.5 nM, offering the following merits of simple design, convenient operation, and low experimental cost because of no chemical modification, organic dye, enzymatic reaction, or separation procedure involved.
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Affiliation(s)
| | | | | | - Bang-Ce Ye
- ‡School of Chemistry and Chemical Engineering, Shihezi University, Xinjiang, 832000, China
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278
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Li XM, Luo J, Zhang NB, Wei QL. Nucleic acid quantification using nicking–displacement, rolling circle amplification and bio-bar-code mediated triple-amplification. Anal Chim Acta 2015; 881:117-23. [DOI: 10.1016/j.aca.2015.05.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 05/05/2015] [Accepted: 05/08/2015] [Indexed: 02/07/2023]
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279
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Qiu X, Liu X, Zhang W, Zhang H, Jiang T, Fan D, Luo Y. Dynamic Monitoring of MicroRNA–DNA Hybridization Using DNAase-Triggered Signal Amplification. Anal Chem 2015; 87:6303-10. [PMID: 25962779 DOI: 10.1021/acs.analchem.5b01159] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Xiaopei Qiu
- Department
of Blood Transfusion Medicine, Southwest Hospital, the Third Military Medical University, Chongqing 400038, China
| | - Xing Liu
- Department
of Plastic Surgery, Xinqiao Hospital, the Third Military Medical University, Chongqing 400037, China
| | - Wei Zhang
- Chongqing
Institute
of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - Hong Zhang
- Department
of Blood Transfusion Medicine, Southwest Hospital, the Third Military Medical University, Chongqing 400038, China
| | - Tianlun Jiang
- Department
of Blood Transfusion Medicine, Southwest Hospital, the Third Military Medical University, Chongqing 400038, China
| | - Dongli Fan
- Department
of Plastic Surgery, Xinqiao Hospital, the Third Military Medical University, Chongqing 400037, China
| | - Yang Luo
- Department
of Blood Transfusion Medicine, Southwest Hospital, the Third Military Medical University, Chongqing 400038, China
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280
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Winz ML, Linder EC, André T, Becker J, Jäschke A. Nucleotidyl transferase assisted DNA labeling with different click chemistries. Nucleic Acids Res 2015; 43:e110. [PMID: 26013812 PMCID: PMC4787804 DOI: 10.1093/nar/gkv544] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 05/12/2015] [Indexed: 01/19/2023] Open
Abstract
Here, we present a simple, modular and efficient strategy that allows the 3′-terminal labeling of DNA, regardless of whether it has been chemically or enzymatically synthesized or isolated from natural sources. We first incorporate a range of modified nucleotides at the 3′-terminus, using terminal deoxynucleotidyl transferase. In the second step, we convert the incorporated nucleotides, using either of four highly efficient click chemistry-type reactions, namely copper-catalyzed azide-alkyne cycloaddition, strain-promoted azide-alkyne cycloaddition, Staudinger ligation or Diels-Alder reaction with inverse electron demand. Moreover, we create internal modifications, making use of either ligation or primer extension, after the nucleotidyl transferase step, prior to the click reaction. We further study the influence of linker variants on the reactivity of azides in different click reactions. We find that different click reactions exhibit distinct substrate preferences, a fact that is often overlooked, but should be considered when labeling oligonucleotides or other biomolecules with click chemistry. Finally, our findings allowed us to extend our previously published RNA labeling strategy to the use of a different copper-free click chemistry, namely the Staudinger ligation.
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Affiliation(s)
- Marie-Luise Winz
- Heidelberg University, Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Eva Christina Linder
- Heidelberg University, Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Timon André
- Heidelberg University, Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Juliane Becker
- Heidelberg University, Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Andres Jäschke
- Heidelberg University, Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
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281
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Abstract
MicroRNAs (miRNAs) are small endogenous non-coding RNAs of ~22 nucleotides that play important functions in the regulation of many biological processes, including cell proliferation, differentiation, and death. Since their expression has been in close association with the development of many diseases, recently, miRNAs have been regarded as clinically important biomarkers and drug discovery targets. However, because of the short length, high sequence similarity and low abundance of miRNAs in vivo, it is difficult to realize the sensitive and selective detection of miRNAs with conventional methods. In line with the rapid development of nanotechnology, nanomaterials have attracted great attention and have been intensively studied in biological analysis due to their unique chemical, physical and size properties. In particular, fluorimetric methodologies in combination with nanotechnology are especially rapid, sensitive and efficient. The aim of this review is to provide insight into nanomaterials-based fluorimetric methods for the detection of miRNAs, including metal nanomaterials, quantum dots (QDs), graphene oxide (GO) and silicon nanoparticles.
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282
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Lu W, Wang L, Li J, Zhao Y, Zhou Z, Shi J, Zuo X, Pan D. Quantitative investigation of the poly-adenine DNA dissociation from the surface of gold nanoparticles. Sci Rep 2015; 5:10158. [PMID: 25974839 PMCID: PMC4431394 DOI: 10.1038/srep10158] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 04/01/2015] [Indexed: 12/22/2022] Open
Abstract
In recent years, poly adenine (polyA) DNA functionalized gold nanoparticles (AuNPs) free of modifications was fabricated with high density of DNA attachment and high hybridization ability similar to those of its thiolated counterpart. This nanoconjugate utilized poly adenine as an anchoring block for binding with the AuNPs surface thereby facilitated the appended recognition block a better upright conformation for hybridization, demonstrating its great potential to be a tunable plasmonic biosensor. It's one of the key points for any of the practical applications to maintaining stable conjugation between DNA oligonucleotides and gold nanoparticles under various experimental treatments. Thus, in this research, we designed a simple but sensitive fluorescence turn-on strategy to systematically investigate and quantified the dissociation of polyA DNA on gold nanoparticles in diverse experimental conditions. DNA desorbed spontaneously as a function of elevated temperature, ion strength, buffer pH, organic solvents and keeping time. What's more, evaluating this conjugate stability as affected by the length of its polyA anchor was another crucial aspect in our study. With the improved understanding from these results, we were able to control some of our experimental conditions to maintain a good stability of this kind of polyA DNA-AuNPs nanoconjugates.
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Affiliation(s)
- Weiwen Lu
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Lihua Wang
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jiang Li
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Yun Zhao
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Ziang Zhou
- Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, US
| | | | - Xiaolei Zuo
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Dun Pan
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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283
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Shen Y, Tian F, Chen Z, Li R, Ge Q, Lu Z. Amplification-based method for microRNA detection. Biosens Bioelectron 2015; 71:322-331. [PMID: 25930002 DOI: 10.1016/j.bios.2015.04.057] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 04/17/2015] [Accepted: 04/18/2015] [Indexed: 12/20/2022]
Abstract
Over the last two decades, the study of miRNAs has attracted tremendous attention since they regulate gene expression post-transcriptionally and have been demonstrated to be dysregulated in many diseases. Detection methods with higher sensitivity, specificity and selectivity between precursors and mature microRNAs are urgently needed and widely studied. This review gave an overview of the amplification-based technologies including traditional methods, current modified methods and the cross-platforms of them combined with other techniques. Many progresses were found in the modified amplification-based microRNA detection methods, while traditional platforms could not be replaced until now. Several sample-specific normalizers had been validated, suggesting that the different normalizers should be established for different sample types and the combination of several normalizers might be more appropriate than a single universal normalizer. This systematic overview would be useful to provide comprehensive information for subsequent related studies and could reduce the un-necessary repetition in the future.
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Affiliation(s)
- Yanting Shen
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Fei Tian
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Zhenzhu Chen
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Rui Li
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Qinyu Ge
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China; State Key Laboratory of Bioelectronics, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Zuhong Lu
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China; State Key Laboratory of Bioelectronics, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
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284
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Liu Q, Shin Y, Kee JS, Kim KW, Mohamed Rafei SR, Perera AP, Tu X, Lo GQ, Ricci E, Colombel M, Chiong E, Thiery JP, Park MK. Mach-Zehnder interferometer (MZI) point-of-care system for rapid multiplexed detection of microRNAs in human urine specimens. Biosens Bioelectron 2015; 71:365-372. [PMID: 25950930 DOI: 10.1016/j.bios.2015.04.052] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 04/13/2015] [Accepted: 04/17/2015] [Indexed: 12/19/2022]
Abstract
MicroRNAs have been identified as promising biomarkers for human diseases. The development of a point-of-care (POC) test for the disease-associated miRNAs would be especially beneficial, since miRNAs are unexpectedly well preserved in various human specimens, including urine. Here, we present the Mach-Zehnder interferometer-miRNA detection system capable of detecting multiple miRNAs in clinical urine samples rapidly and simultaneously in a label-free and real-time manner. Through measurement of the light phase change, the MZI sensor provides an optical platform for fast profiling of small molecules with improved accuracy. We demonstrate that this system could specifically detect target miRNAs (miR-21, and let-7a), and even identify the single nucleotide polymorphism of the let-7 family of miRNAs from synthetic and cell line samples. The clinical applicability of this system is confirmed by simultaneously detecting two types of miRNAs in urine samples of bladder cancer patients in a single reaction, with a detection time of 15 min. The POC system can be expanded to detect a number of miRNAs of different species and should be useful for a variety of clinical applications requiring at or near the site of patient care.
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Affiliation(s)
- Qing Liu
- Institute of Microelectronics, A⁎STAR (Agency for Science, Technology and Research), 11 Science Park Road, Singapore Science Park II, 117685, Singapore
| | - Yong Shin
- Institute of Microelectronics, A⁎STAR (Agency for Science, Technology and Research), 11 Science Park Road, Singapore Science Park II, 117685, Singapore
| | - Jack Sheng Kee
- Institute of Microelectronics, A⁎STAR (Agency for Science, Technology and Research), 11 Science Park Road, Singapore Science Park II, 117685, Singapore
| | - Kyung Woo Kim
- Institute of Microelectronics, A⁎STAR (Agency for Science, Technology and Research), 11 Science Park Road, Singapore Science Park II, 117685, Singapore
| | - Siti Rafeah Mohamed Rafei
- Institute of Microelectronics, A⁎STAR (Agency for Science, Technology and Research), 11 Science Park Road, Singapore Science Park II, 117685, Singapore
| | - Agampodi Promoda Perera
- Institute of Microelectronics, A⁎STAR (Agency for Science, Technology and Research), 11 Science Park Road, Singapore Science Park II, 117685, Singapore
| | - Xiaoguang Tu
- Institute of Microelectronics, A⁎STAR (Agency for Science, Technology and Research), 11 Science Park Road, Singapore Science Park II, 117685, Singapore
| | - Guo-Qiang Lo
- Institute of Microelectronics, A⁎STAR (Agency for Science, Technology and Research), 11 Science Park Road, Singapore Science Park II, 117685, Singapore
| | - Estelle Ricci
- Service d'Urologie et Chirurgie de la Transplantation, Hôpital Edouard Herriot, 5 Place d'Arsonval, 69437 Lyon Cedex 03, France
| | - Marc Colombel
- Service d'Urologie et Chirurgie de la Transplantation, Hôpital Edouard Herriot, 5 Place d'Arsonval, 69437 Lyon Cedex 03, France
| | - Edmund Chiong
- Department of Urology, National University Health System, Singapore
| | - Jean Paul Thiery
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, 138673, Singapore
| | - Mi Kyoung Park
- Institute of Microelectronics, A⁎STAR (Agency for Science, Technology and Research), 11 Science Park Road, Singapore Science Park II, 117685, Singapore.
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285
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Duplex-specific nuclease-mediated bioanalysis. Trends Biotechnol 2015; 33:180-8. [DOI: 10.1016/j.tibtech.2014.12.008] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 12/22/2014] [Accepted: 12/30/2014] [Indexed: 12/21/2022]
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286
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Causa F, Aliberti A, Cusano AM, Battista E, Netti PA. Supramolecular Spectrally Encoded Microgels with Double Strand Probes for Absolute and Direct miRNA Fluorescence Detection at High Sensitivity. J Am Chem Soc 2015; 137:1758-61. [DOI: 10.1021/ja511644b] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Filippo Causa
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
- Interdisciplinary
Research Centre on Biomaterials (CRIB), University “‘Federico II”’, Piazzale Tecchio 80, 80125 Naples, Italy
- Dipartimento
di Ingegneria Chimica, dei Materiali e della Produzione Industriale
(DICMAPI), University “‘Federico II”’, Piazzale
Tecchio 80, 80125 Naples, Italy
| | - Anna Aliberti
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
| | - Angela M. Cusano
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
| | - Edmondo Battista
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
| | - Paolo A. Netti
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
- Interdisciplinary
Research Centre on Biomaterials (CRIB), University “‘Federico II”’, Piazzale Tecchio 80, 80125 Naples, Italy
- Dipartimento
di Ingegneria Chimica, dei Materiali e della Produzione Industriale
(DICMAPI), University “‘Federico II”’, Piazzale
Tecchio 80, 80125 Naples, Italy
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287
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Zhang J, Wu D, Chen Q, Chen M, Xia Y, Cai S, Zhang X, Wu F, Chen J. Label-free microRNA detection based on terbium and duplex-specific nuclease assisted target recycling. Analyst 2015; 140:5082-9. [DOI: 10.1039/c5an01042j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper, we describe a novel label-free fluorescence method for microRNA-21 (miR-21) detection based on terbium (Tb3+) and duplex-specific nuclease (DSN) assisted target recycling.
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Affiliation(s)
- Jing Zhang
- The Ministry of Education Key Laboratory of Biopesticide and Chemical Biology
- and College of Life Sciences
- Fujian Agriculture and Forestry University
- Fuzhou
- China
| | - Dongzhi Wu
- Department of Pharmaceutical Analysis
- The School of Pharmacy
- Fujian Medical University
- Fuzhou
- China
| | - QiuXiang Chen
- Department of Pharmaceutical Analysis
- The School of Pharmacy
- Fujian Medical University
- Fuzhou
- China
| | - Mei Chen
- Department of Pharmaceutical Analysis
- The School of Pharmacy
- Fujian Medical University
- Fuzhou
- China
| | - Yaokun Xia
- Department of Pharmaceutical Analysis
- The School of Pharmacy
- Fujian Medical University
- Fuzhou
- China
| | - Shuxian Cai
- Department of Pharmaceutical Analysis
- The School of Pharmacy
- Fujian Medical University
- Fuzhou
- China
| | - Xi Zhang
- Department of Pharmaceutical Analysis
- The School of Pharmacy
- Fujian Medical University
- Fuzhou
- China
| | - Fang Wu
- Department of Pharmaceutical Analysis
- The School of Pharmacy
- Fujian Medical University
- Fuzhou
- China
| | - Jinghua Chen
- Department of Pharmaceutical Analysis
- The School of Pharmacy
- Fujian Medical University
- Fuzhou
- China
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288
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Zhang L, Zhang Y, Hu Y, Fan Q, Yang W, Li A, Li S, Huang W, Wang L. Refractive index dependent real-time plasmonic nanoprobes on a single silver nanocube for ultrasensitive detection of the lung cancer-associated miRNAs. Chem Commun (Camb) 2015; 51:294-7. [DOI: 10.1039/c4cc06663d] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We developed a novel method for the real-time monitoring of the delicate change in refractive index (RI) when DNA or RNA hybridize near a DNA-capped silver nanocube (AgNC) surface.
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Affiliation(s)
- Lei Zhang
- Key Laboratory for Organic Electronics and Information Displays & Institute of Advanced Materials (IAM)
- National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts & Telecommunications
- Nanjing 210023
- China
| | - Ying Zhang
- Key Laboratory for Organic Electronics and Information Displays & Institute of Advanced Materials (IAM)
- National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts & Telecommunications
- Nanjing 210023
- China
| | - Yanling Hu
- Key Laboratory for Organic Electronics and Information Displays & Institute of Advanced Materials (IAM)
- National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts & Telecommunications
- Nanjing 210023
- China
| | - Quli Fan
- Key Laboratory for Organic Electronics and Information Displays & Institute of Advanced Materials (IAM)
- National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts & Telecommunications
- Nanjing 210023
- China
| | - Wenjing Yang
- Key Laboratory for Organic Electronics and Information Displays & Institute of Advanced Materials (IAM)
- National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts & Telecommunications
- Nanjing 210023
- China
| | - Anran Li
- Division of Materials Science
- School of Materials Science and Engineering
- Singapore
| | - Shuzhou Li
- Division of Materials Science
- School of Materials Science and Engineering
- Singapore
| | - Wei Huang
- Key Laboratory for Organic Electronics and Information Displays & Institute of Advanced Materials (IAM)
- National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts & Telecommunications
- Nanjing 210023
- China
| | - Lianhui Wang
- Key Laboratory for Organic Electronics and Information Displays & Institute of Advanced Materials (IAM)
- National Synergistic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts & Telecommunications
- Nanjing 210023
- China
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289
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Hunt EA, Broyles D, Head T, Deo SK. MicroRNA Detection: Current Technology and Research Strategies. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2015; 8:217-37. [PMID: 25973944 DOI: 10.1146/annurev-anchem-071114-040343] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The relatively new field of microRNA (miR) has experienced rapid growth in methodology associated with its detection and bioanalysis as well as with its role in -omics research, clinical diagnostics, and new therapeutic strategies. The breadth of this area of research and the seemingly exponential increase in number of publications on the subject can present scientists new to the field with a daunting amount of information to evaluate. This review aims to provide a collective overview of miR detection methods by relating conventional, established techniques [such as quantitative reverse transcription polymerase chain reaction (RT-qPCR), microarray, and Northern blotting (NB)] and relatively recent advancements [such as next-generation sequencing (NGS), highly sensitive biosensors, and computational prediction of microRNA/targets] to common miR research strategies. This should guide interested readers toward a more focused study of miR research and the surrounding technology.
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Affiliation(s)
- Eric A Hunt
- Department of Biochemistry and Molecular Biology, University of Miami, Miami, Florida 33136;
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290
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Lan J, Wen F, Fu F, Zhang X, Cai S, Liu Z, Wu D, Li C, Chen J, Wang C. A photoluminescent biosensor based on long-range self-assembled DNA cascades and upconversion nanoparticles for the detection of breast cancer-associated circulating microRNA in serum samples. RSC Adv 2015. [DOI: 10.1039/c5ra01288k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A photoluminescent biosensor was developed for the detection of microRNA (miRNA) combined signal amplification of long-range self-assembled DNA cascades with upconversion nanoparticles.
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291
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Shen W, Yeo KH, Gao Z. A simple and highly sensitive fluorescence assay for microRNAs. Analyst 2015; 140:1932-8. [DOI: 10.1039/c4an02146k] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A simple and highly sensitive assay for miRNAs using magnetic bead-carried DNA probes coupled with DSN-facilitated isothermal target cycling is reported.
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Affiliation(s)
- Wei Shen
- Department of Chemistry
- National University of Singapore
- Singapore 117543
| | - Kiat Huei Yeo
- Department of Chemistry
- National University of Singapore
- Singapore 117543
| | - Zhiqiang Gao
- Department of Chemistry
- National University of Singapore
- Singapore 117543
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292
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Huang J, Ye L, Gao X, Li H, Xu J, Li Z. Molybdenum disulfide-based amplified fluorescence DNA detection using hybridization chain reactions. J Mater Chem B 2015; 3:2395-2401. [DOI: 10.1039/c4tb01986e] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A simple, sensitive, and selective amplified fluorescence DNA detection strategyviaenzyme-free molybdenum disulfide-assisted hybridization chain reactions.
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Affiliation(s)
- Jiahao Huang
- Department of Mechanical and Aerospace Engineering
- The Hong Kong University of Science and Technology
- Kowloon
- China
| | - Lei Ye
- Department of Electronic Engineering
- Materials Science and Technology Research Center
- The Chinese University of Hong Kong
- China
| | - Xiang Gao
- Department of Mechanical and Aerospace Engineering
- The Hong Kong University of Science and Technology
- Kowloon
- China
| | - Hao Li
- Department of Electronic Engineering
- Materials Science and Technology Research Center
- The Chinese University of Hong Kong
- China
| | - Jianbin Xu
- Department of Electronic Engineering
- Materials Science and Technology Research Center
- The Chinese University of Hong Kong
- China
| | - Zhigang Li
- Department of Mechanical and Aerospace Engineering
- The Hong Kong University of Science and Technology
- Kowloon
- China
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293
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Yang K, Zeng M, Fu X, Li J, Ma N, Tao L. Establishing biodegradable single-layer MnO2 nanosheets as a platform for live cell microRNA sensing. RSC Adv 2015. [DOI: 10.1039/c5ra21467j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We have established a simple and effective biosensing platform based on the non-covalent assembly of biodegradable single-layer MnO2 nanosheet and target-specific oligonucleotide, and demonstrated its application for sensing miRNA in living cells.
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Affiliation(s)
- Ke Yang
- Department of Human Anatomy
- Histology and Embryology
- College of Basic Medical Sciences
- Changsha Medical University
- Changsha 410219
| | - Ming Zeng
- Department of Human Anatomy
- Histology and Embryology
- College of Basic Medical Sciences
- Changsha Medical University
- Changsha 410219
| | - Xinling Fu
- Department of Human Anatomy
- Histology and Embryology
- College of Basic Medical Sciences
- Changsha Medical University
- Changsha 410219
| | - Jianming Li
- Department of Human Anatomy
- Histology and Embryology
- College of Basic Medical Sciences
- Changsha Medical University
- Changsha 410219
| | - Ning Ma
- Department of Human Anatomy
- Histology and Embryology
- College of Basic Medical Sciences
- Changsha Medical University
- Changsha 410219
| | - Lu Tao
- Department of Human Anatomy
- Histology and Embryology
- College of Basic Medical Sciences
- Changsha Medical University
- Changsha 410219
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294
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Zhang H, Liu Y, Gao J, Zhen J. A sensitive SERS detection of miRNA using a label-free multifunctional probe. Chem Commun (Camb) 2015; 51:16836-9. [DOI: 10.1039/c5cc06225j] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A novel surface enhanced Raman scattering (SERS) detection method is fabricated for miRNA based on a smart multifunctional probe for dual cyclical nucleic acid strand-displacement polymerization (CNDP).
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Affiliation(s)
- Hao Zhang
- Department of Chemistry
- Qilu University of Technology
- Jinan 250353
- China
| | - Yu Liu
- Department of Chemistry
- Qilu University of Technology
- Jinan 250353
- China
| | - Jian Gao
- Department of Chemistry
- Qilu University of Technology
- Jinan 250353
- China
| | - Junhui Zhen
- School of Medicine
- Shandong University
- Jinan 250012
- China
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295
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Wang Z, Si L, Bao J, Dai Z. A reusable microRNA sensor based on the electrocatalytic property of heteroduplex-templated copper nanoclusters. Chem Commun (Camb) 2015; 51:6305-7. [DOI: 10.1039/c5cc01081k] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Repeat detection of miRNA is accomplished by reconstruction of DNA–RNA heteroduplexes-templated copper nanoclusters on an electrode surface.
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Affiliation(s)
- Zhaoyin Wang
- Jiangsu Collaborative Innovation Centre of Biomedical Functional Materials and Jiangsu key Laboratory of Biofunctional Materials
- College of Chemistry and Materials Science
- Nanjing Normal University
- Nanjing
- P. R. China
| | - Ling Si
- Jiangsu Collaborative Innovation Centre of Biomedical Functional Materials and Jiangsu key Laboratory of Biofunctional Materials
- College of Chemistry and Materials Science
- Nanjing Normal University
- Nanjing
- P. R. China
| | - Jianchun Bao
- Jiangsu Collaborative Innovation Centre of Biomedical Functional Materials and Jiangsu key Laboratory of Biofunctional Materials
- College of Chemistry and Materials Science
- Nanjing Normal University
- Nanjing
- P. R. China
| | - Zhihui Dai
- Jiangsu Collaborative Innovation Centre of Biomedical Functional Materials and Jiangsu key Laboratory of Biofunctional Materials
- College of Chemistry and Materials Science
- Nanjing Normal University
- Nanjing
- P. R. China
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296
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Kilic T, Erdem A, Erac Y, Seydibeyoglu MO, Okur S, Ozsoz M. Electrochemical Detection of a Cancer Biomarker mir‐21 in Cell Lysates Using Graphene Modified Sensors. ELECTROANAL 2014. [DOI: 10.1002/elan.201400518] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Tugba Kilic
- Izmir Katip Celebi University, Faculty of Engineering and Architecture, Department of Biomedical Engineering, 35620, Cigli, Turkey
| | - Arzum Erdem
- Ege University, Faculty of Pharmacy, Department of Analytical Chemistry, 35100 Bornova, Turkey tel: +90 (232) 311 5131
| | - Yasemin Erac
- Ege University, Faculty of Pharmacy, Department of Pharmacology, 35100 Bornova, Turkey
| | - M. Ozgur Seydibeyoglu
- Izmir Katip Celebi University, Faculty of Engineering and Architecture, Department of Materials Science and Engineering, 35620, Cigli, Turkey
| | - Salih Okur
- Izmir Katip Celebi University, Faculty of Engineering and Architecture, Department of Materials Science and Engineering, 35620, Cigli, Turkey
| | - Mehmet Ozsoz
- Gediz University, Faculty of Engineering and Architecture, Department of Biomedical Engineering, 35665, Seyrek, Turkey tel: +90 (232) 355 23 20
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297
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Chen CD, La M, Zhou BB. Strategies for Designing of Electrochemical MicroRNA Genesensors Based on the Difference in the Structure of RNA and DNA. INT J ELECTROCHEM SC 2014; 9:7228-7238. [DOI: 10.1016/s1452-3981(23)10962-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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298
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Yang C, Dou B, Shi K, Chai Y, Xiang Y, Yuan R. Multiplexed and Amplified Electronic Sensor for the Detection of MicroRNAs from Cancer Cells. Anal Chem 2014; 86:11913-8. [DOI: 10.1021/ac503860d] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Cuiyun Yang
- Key Laboratory of Luminescent and Real-Time
Analytical Chemistry, Ministry of Education, School of Chemistry and
Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Baoting Dou
- Key Laboratory of Luminescent and Real-Time
Analytical Chemistry, Ministry of Education, School of Chemistry and
Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Kai Shi
- Key Laboratory of Luminescent and Real-Time
Analytical Chemistry, Ministry of Education, School of Chemistry and
Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yaqin Chai
- Key Laboratory of Luminescent and Real-Time
Analytical Chemistry, Ministry of Education, School of Chemistry and
Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yun Xiang
- Key Laboratory of Luminescent and Real-Time
Analytical Chemistry, Ministry of Education, School of Chemistry and
Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time
Analytical Chemistry, Ministry of Education, School of Chemistry and
Chemical Engineering, Southwest University, Chongqing 400715, PR China
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299
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Akiyama Y, Shikagawa H, Kanayama N, Takarada T, Maeda M. DNA dangling-end-induced colloidal stabilization of gold nanoparticles for colorimetric single-nucleotide polymorphism genotyping. Chemistry 2014; 20:17420-5. [PMID: 25349129 DOI: 10.1002/chem.201404801] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Indexed: 12/19/2022]
Abstract
A single-nucleotide polymorphism (SNP) detection method was developed by combining single-base primer extension and salt-induced aggregation of gold nanoparticles densely functionalized with double-stranded DNA (dsDNA-AuNP). The dsDNA-AuNPs undergo rapid aggregation in a medium of high ionic strength, whereas particles having a single-base protrusion at the outermost surface disperse stably, allowing detection of a single-base difference in length by color changes. When SNP typing primers are used as analytes to hybridize to the single-stranded DNA on the AuNP surface, the resulting dsDNA-AuNP works as a visual indicator of single-base extension. A set of four extension reaction mixtures is prepared using each of ddNTPs and subsequently subjected to the aggregation assay. Three mixtures involving ddNTP that is not complementary to the SNP site in the target produce the aggregates that exhibit a purple color. In contrast, one mixture with the complementary ddNTP generates the single-base protrusion and appears red. This method could potentially be used in clinical diagnostics for personalized medicine.
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Affiliation(s)
- Yoshitsugu Akiyama
- Bioengineering Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan), Fax: (+81) 4-8462-4658
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300
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Li XM, Wang LL, Luo J, Wei QL. A dual-amplified electrochemical detection of mRNA based on duplex-specific nuclease and bio-bar-code conjugates. Biosens Bioelectron 2014; 65:245-50. [PMID: 25461165 DOI: 10.1016/j.bios.2014.10.051] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 10/17/2014] [Accepted: 10/20/2014] [Indexed: 02/08/2023]
Abstract
On the basis of strong preference for cleaving double-stranded DNA or DNA in DNA:RNA heteroduplexes of duplex-specific nuclease (DSN), a dual-amplified electrochemical detection of mRNA was developed in this article, by coupling the enhancement of DSN and bio-bar-code conjugates. Capture probe was linked with magnetic nanoparticles (MNPs) at its 5' end and bio-bar-code at its 3' end. In the presence of target surviving mRNA, all hybridized S1 strands were cleaved off the biosensor by the DSN, and the bio-bar-code probe with CdS nanoparticles (CdS NPs) was released into the solution. The metal sulfide nanoparticles were measured by anodic stripping voltammetry (ASV) subsequently. This assay exhibited high sensitivity and selectivity with a detection limit of 0.48fM. In addition, we proved that this simple and cost-effective strategy is capable of detecting the target in complicated biological samples and holds great potential application in biomedical research and clinical diagnostics.
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Affiliation(s)
- Xue-Mei Li
- School of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, PR China.
| | - Lin-Lin Wang
- State Key Laboratory Base of Eco-chemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Jie Luo
- State Key Laboratory Base of Eco-chemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Qing-Li Wei
- State Key Laboratory Base of Eco-chemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
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