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Henley RY, Carson S, Wanunu M. Studies of RNA Sequence and Structure Using Nanopores. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2016; 139:73-99. [PMID: 26970191 DOI: 10.1016/bs.pmbts.2015.10.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nanopores are powerful single-molecule sensors with nanometer scale dimensions suitable for detection, quantification, and characterization of nucleic acids and proteins. Beyond sequencing applications, both biological and solid-state nanopores hold great promise as tools for studying the biophysical properties of RNA. In this review, we highlight selected landmark nanopore studies with regards to RNA sequencing, microRNA detection, RNA/ligand interactions, and RNA structural/conformational analysis.
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Affiliation(s)
- Robert Y Henley
- Department of Physics, Northeastern University, Boston, Massachusetts, USA
| | - Spencer Carson
- Department of Physics, Northeastern University, Boston, Massachusetts, USA
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts, USA; Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA.
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He J, Zhu J, Gong C, Qi J, Xiao H, Jiang B, Zhao Y. Label-Free Direct Detection of miRNAs with Poly-Silicon Nanowire Biosensors. PLoS One 2015; 10:e0145160. [PMID: 26709827 PMCID: PMC4692481 DOI: 10.1371/journal.pone.0145160] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 12/01/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The diagnostic and prognostic value of microRNAs (miRNAs) in a variety of diseases is promising. The novel silicon nanowire (SiNW) biosensors have advantages in molecular detection because of their high sensitivity and fast response. In this study, poly-crystalline silicon nanowire field-effect transistor (poly-SiNW FET) device was developed to achieve specific and ultrasensitive detection of miRNAs without labeling and amplification. METHODS The poly-SiNW FET was fabricated by a top-down Complementary Metal Oxide Semiconductor (CMOS) wafer fabrication based technique. Single strand DNA (ssDNA) probe was bind to the surface of the poly-SiNW device which was silanated and aldehyde-modified. By comparing the difference of resistance value before and after ssDNA and miRNA hybridization, poly-SiNW device can be used to detect standard and real miRNA samples. RESULTS Poly-SiNW device with different structures (different line width and different pitch) was applied to detect standard Let-7b sample with a detection limitation of 1 fM. One-base mismatched sequence could be distinguished meanwhile. Furthermore, these poly-SiNW arrays can detect snRNA U6 in total RNA samples extracted from HepG2 cells with a detection limitation of 0.2 μg/mL. In general, structures with pitch showed better results than those without pitch in detection of both Let-7b and snRNA U6. Moreover, structures with smaller pitch showed better detection efficacy. CONCLUSION Our findings suggest that poly-SiNW arrays could detect standard and real miRNA sample without labeling or amplification. Poly-SiNW biosensor device is promising for miRNA detection.
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Affiliation(s)
- Jing He
- School of Life Science, East China Normal University, Shanghai, PR China
- Ocean Research Center of Zhoushan, Zhejiang University, Zhejiang Province, PR China
| | - Jianjun Zhu
- Shanghai Integrated Circuit Research & Development Center, Shanghai, PR China
| | - Changguo Gong
- School of Life Science, East China Normal University, Shanghai, PR China
| | - Jiming Qi
- Shanghai Integrated Circuit Research & Development Center, Shanghai, PR China
| | - Han Xiao
- Wuhan Medical and Health Center for Women and Children, Wuhan, Hubei Province, PR China
| | - Bin Jiang
- Shanghai Integrated Circuit Research & Development Center, Shanghai, PR China
- * E-mail: (BJ); (YZ)
| | - Yulan Zhao
- School of Life Science, East China Normal University, Shanghai, PR China
- * E-mail: (BJ); (YZ)
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Zhang YY, Feng QM, Xu JJ, Chen HY. Silver Nanoclusters for High-Efficiency Quenching of CdS Nanocrystal Electrochemiluminescence and Sensitive Detection of microRNA. ACS APPLIED MATERIALS & INTERFACES 2015; 7:26307-14. [PMID: 26561442 DOI: 10.1021/acsami.5b09129] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
In this work, oligonucleotide-encapusulated silver nanoclusters were applied in the electrochemiluminescence (ECL) system of CdS nanocrystals (NCs)/ K2S2O8 based on dual ECL quenching effects. We found that the ECL emission of CdS NCs matched well with the absorption band of oligonucleotide encapsulated Ag nanoclusters, which could act as the energy acceptor of CdS NCs ECL so as to lead to an effective ECL resonance energy transfer (RET). On the other hand, the Ag nanoclusters could also catalyze electrochemical reduction of K2S2O8, resulting in increased consumption of ECL coreactant near the working electrode and decreased ECL intensity from CdS NCs. On the basis of the dual ECL quenching effects, a sensitive ECL biosensor for detection of microRNA was successfully achieved with a wide linear range from 10 fM to 100 pM.
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Affiliation(s)
- Yan-Yan Zhang
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, China
| | - Qiu-Mei Feng
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, China
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Liu H, Bei X, Xia Q, Fu Y, Zhang S, Liu M, Fan K, Zhang M, Yang Y. Enzyme-free electrochemical detection of microRNA-21 using immobilized hairpin probes and a target-triggered hybridization chain reaction amplification strategy. Mikrochim Acta 2015. [DOI: 10.1007/s00604-015-1636-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Chen Y, Xiang Y, Yuan R, Chai Y. Intercalation of quantum dots as the new signal acquisition and amplification platform for sensitive electrochemiluminescent detection of microRNA. Anal Chim Acta 2015; 891:130-5. [DOI: 10.1016/j.aca.2015.07.059] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 07/16/2015] [Accepted: 07/19/2015] [Indexed: 11/17/2022]
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Suppressing RNA silencing with small molecules and the viral suppressor of RNA silencing protein p19. Biochem Biophys Res Commun 2015; 463:1135-40. [PMID: 26079891 DOI: 10.1016/j.bbrc.2015.06.071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 06/09/2015] [Indexed: 11/22/2022]
Abstract
RNA silencing is a gene regulatory and host defense mechanism whereby small RNA molecules are engaged by Argonaute (AGO) proteins, which facilitate gene knockdown of complementary mRNA targets. Small molecule inhibitors of AGO represent a convenient method for reversing this effect and have applications in human therapy and biotechnology. Viral suppressors of RNA silencing, such as p19, can also be used to suppress the pathway. Here we assess the compatibility of these two approaches, by examining whether synthetic inhibitors of AGO would inhibit p19-siRNA interactions. We observe that aurintricarboxylic acid (ATA) is a potent inhibitor of p19's ability to bind siRNA (IC50 = 0.43 μM), oxidopamine does not inhibit p19:siRNA interactions, and suramin is a mild inhibitor of p19:siRNA interactions (IC50 = 430 μM). We observe that p19 and suramin are compatible inhibitors of RNA silencing in human hepatoma cells. Our data suggests that at least some inhibitors of AGO may be used in combination with p19 to inhibit RNA silencing at different points in the pathway.
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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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Simultaneous detection of two breast cancer-related miRNAs in tumor tissues using p19-based disposable amperometric magnetobiosensing platforms. Biosens Bioelectron 2015; 66:385-91. [DOI: 10.1016/j.bios.2014.11.047] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 11/17/2014] [Accepted: 11/25/2014] [Indexed: 11/21/2022]
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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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62
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Electrochemical sensing of microRNAs: avenues and paradigms. Biosens Bioelectron 2014; 68:83-94. [PMID: 25562735 DOI: 10.1016/j.bios.2014.12.026] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 11/24/2014] [Accepted: 12/09/2014] [Indexed: 01/24/2023]
Abstract
Twenty years has passed since the first discovery of microRNA (miRNA) lin-4 in Caenorhabditis elegans. Over the last two decades, the study of miRNAs has attracted tremendous attention. These new stars of biomarkers are naturally occurring non-coding RNAs that regulate gene expression posttranscriptionally and have been demonstrated to be dysregulated in many diseases. Since their profiles reflect pathological conditions, miRNAs have recently been proposed as biomarkers of the onset, prognosis and risk of diseases, as well as in the classification of different types of cancer. The establishment of miRNA profiles for diseases and the detection of different types and levels of miRNAs in biological samples are therefore critical milestones in diagnostics. This provides powerful impetus and a growing demand for researchers to develop simple analytical techniques to allow for an accurate, sensitive, selective, and cost effective miRNA analysis at point-of-care settings. Among several methods proposed for miRNA detection, electrochemical nucleic acid biosensors exhibit many attractive features and could play a leading role in future miRNA detection and quantification. This review gives an overview of recent advances in the rapidly growing area of electrochemical detection of miRNAs. The fundamentals of the different strategies adopted for miRNA detection are discussed and some examples of relevant approaches are highlighted, along with future prospects and challenges.
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63
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A G-quadruplex DNA-based, label-free and ultrasensitive strategy for microRNA detection. Sci Rep 2014; 4:7400. [PMID: 25492390 PMCID: PMC4261168 DOI: 10.1038/srep07400] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 11/18/2014] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) have been considered to be potent biomarkers for early disease diagnosis and for cancer therapy. The rapid and selective detection of miRNAs without reverse transcription and labelling is highly desired. Herein, we report a simple and label-free miRNA detection method that is based on the Duplex-Specific Nuclease (DSN)-Assisted simple target miRNA recycling procedure. The interaction of the G-quadruplex DNA structure with N-methyl mesoporphyrin IX (NMM) led to a label-free signal output. Under the optimised conditions, this method allowed for simple, rapid, and sequence-specific detection of miR-141 over a dynamic range from 1 fM to 100 nM with a linear range from 1 pM to 100 nM. Moreover, our method offered an excellent capacity to discriminate between miRNA family members with just one mismatched nucleotide. This simple and label-free strategy holds great potential in applications in biomedical research and in early clinical diagnostics.
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64
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Joshi G, Deitz-McElyea S, Johnson M, Mali S, Korc M, Sardar R. Highly specific plasmonic biosensors for ultrasensitive microRNA detection in plasma from pancreatic cancer patients. NANO LETTERS 2014; 14:6955-63. [PMID: 25379951 PMCID: PMC4264854 DOI: 10.1021/nl503220s] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/07/2014] [Indexed: 05/20/2023]
Abstract
MicroRNAs (miRs) are small noncoding RNAs that regulate mRNA stability and/or translation. Because of their release into the circulation and their remarkable stability, miR levels in plasma and other biological fluids can serve as diagnostic and prognostic disease biomarkers. However, quantifying miRs in the circulation is challenging due to issues with sensitivity and specificity. This Letter describes for the first time the design and characterization of a regenerative, solid-state localized surface plasmon resonance (LSPR) sensor based on highly sensitive nanostructures (gold nanoprisms) that obviates the need for labels or amplification of the miRs. Our direct hybridization approach has enabled the detection of subfemtomolar concentration of miR-X (X = 21 and 10b) in human plasma in pancreatic cancer patients. Our LSPR-based measurements showed that the miR levels measured directly in patient plasma were at least 2-fold higher than following RNA extraction and quantification by reverse transcriptase-polymerase chain reaction. Through LSPR-based measurements we have shown nearly 4-fold higher concentrations of miR-10b than miR-21 in plasma of pancreatic cancer patients. We propose that our highly sensitive and selective detection approach for assaying miRs in plasma can be applied to many cancer types and disease states and should allow a rational approach for testing the utility of miRs as markers for early disease diagnosis and prognosis, which could allow for the design of effective individualized therapeutic approaches.
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Affiliation(s)
- Gayatri
K. Joshi
- Department
of Chemistry and Chemical Biology, Indiana
University-Purdue University Indianapolis, 402 N. Blackford Street, LD 326, Indianapolis, Indiana 46202, United States
| | - Samantha Deitz-McElyea
- Department of Medicine, Department of Biochemistry and Molecular Biology, and the Center for
Pancreatic Cancer Research at the IU Simon Cancer Center, Indiana University School of Medicine, 980 W. Walnut Street, C549, Indianapolis, Indiana 46202, United States
| | - Merrell Johnson
- Department
of Physics, Indiana University-Purdue University
Indianapolis, 402 N.
Blackford Street, LD 326, Indianapolis, Indiana 46202, United States
| | - Sonali Mali
- Department
of Chemistry and Chemical Biology, Indiana
University-Purdue University Indianapolis, 402 N. Blackford Street, LD 326, Indianapolis, Indiana 46202, United States
| | - Murray Korc
- Department of Medicine, Department of Biochemistry and Molecular Biology, and the Center for
Pancreatic Cancer Research at the IU Simon Cancer Center, Indiana University School of Medicine, 980 W. Walnut Street, C549, Indianapolis, Indiana 46202, United States
- E-mail: (M.K.)
| | - Rajesh Sardar
- Department
of Chemistry and Chemical Biology, Indiana
University-Purdue University Indianapolis, 402 N. Blackford Street, LD 326, Indianapolis, Indiana 46202, United States
- Integrated
Nanosystems Development Institute, Indiana
University-Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, United States
- E-mail: (R.S.)
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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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Hao N, Li XL, Zhang HR, Xu JJ, Chen HY. A highly sensitive ratiometric electrochemiluminescent biosensor for microRNA detection based on cyclic enzyme amplification and resonance energy transfer. Chem Commun (Camb) 2014; 50:14828-30. [DOI: 10.1039/c4cc06801g] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Torrente-Rodríguez RM, Campuzano S, López-Hernández E, Granados R, Sánchez-Puelles JM, Pingarrón JM. Direct Determination of miR-21 in Total RNA Extracted from Breast Cancer Samples Using Magnetosensing Platforms and the p19 Viral Protein as Detector Bioreceptor. ELECTROANAL 2014. [DOI: 10.1002/elan.201400317] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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68
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Xia N, Zhang L. Nanomaterials-Based Sensing Strategies for Electrochemical Detection of MicroRNAs. MATERIALS 2014; 7:5366-5384. [PMID: 28788133 PMCID: PMC5455827 DOI: 10.3390/ma7075366] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 06/10/2014] [Accepted: 07/14/2014] [Indexed: 12/28/2022]
Abstract
MicroRNAs (miRNAs) play important functions in post-transcriptional regulation of gene expression. They have been regarded as reliable molecular biomarkers for many diseases including cancer. However, the content of miRNAs in cells can be low down to a few molecules per cell. Thus, highly sensitive analytical methods for miRNAs detection are desired. Recently, electrochemical biosensors have held great promise as devices suitable for point-of-care diagnostics and multiplexed platforms for fast, simple and low-cost nucleic acid analysis. Signal amplification by nanomaterials is one of the most popular strategies for developing ultrasensitive assay methods. This review surveys the latest achievements in the use of nanomaterials to detect miRNAs with a focus on electrochemical techniques.
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Affiliation(s)
- Ning Xia
- College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang 455000, China.
| | - Liping Zhang
- College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang 455000, China.
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69
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Degliangeli F, Pompa PP, Fiammengo R. Nanotechnology-based strategies for the detection and quantification of microRNA. Chemistry 2014; 20:9476-92. [PMID: 24989446 DOI: 10.1002/chem.201402649] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
MicroRNAs (miRNAs) are important regulators of gene expression, and many pathological conditions, including cancer, are characterized by altered miRNA expression levels. Therefore, accurate and sensitive quantification of miRNAs may result in correct disease diagnosis establishing these small noncoding RNA transcripts as valuable biomarkers. Aiming at overcoming some limitations of conventional quantification strategies, nanotechnology is currently providing numerous significant alternatives to miRNA sensing. In this review an up-to-date account of nanotechnology-based strategies for miRNA detection and quantification is given. The topics covered are: nanoparticle-based approaches in solution, sensing based on nanostructured surfaces, combined nanoparticle/surface sensing approaches, and single-molecule approaches.
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Affiliation(s)
- Federica Degliangeli
- Center for Biomolecular Nanotechnologies@UniLe, Istituto Italiano di Tecnologia (IIT), Via Barsanti, 73010 Arnesano (Lecce) (Italy)
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Tran HV, Piro B, Reisberg S, Huy Nguyen L, Dung Nguyen T, Duc HT, Pham MC. An electrochemical ELISA-like immunosensor for miRNAs detection based on screen-printed gold electrodes modified with reduced graphene oxide and carbon nanotubes. Biosens Bioelectron 2014; 62:25-30. [PMID: 24973539 DOI: 10.1016/j.bios.2014.06.014] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 06/06/2014] [Accepted: 06/10/2014] [Indexed: 11/17/2022]
Abstract
We design an electrochemical immunosensor for miRNA detection, based on screen-printed gold electrodes modified with reduced graphene oxide and carbon nanotubes. An original immunological approach is followed, using antibodies directed to DNA.RNA hybrids. An electrochemical ELISA-like amplification strategy was set up using a secondary antibody conjugated to horseradish peroxidase (HRP). Hydroquinone is oxidized into benzoquinone by the HRP/H2O2 catalytic system. In turn, benzoquinone is electroreduced into hydroquinone at the electrode. The catalytic reduction current is related to HRP amount immobilized on the surface, which itself is related to miRNA.DNA surface density on the electrode. This architecture, compared to classical optical detection, lowers the detection limit down to 10 fM. Two miRNAs were studied: miR-141 (a prostate biomarker) and miR-29b-1 (a lung cancer biomarker).
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Affiliation(s)
- H V Tran
- Université Paris Diderot, Sorbonne Paris Cité, ITODYS, UMR 7086 CNRS, 15 rue J-A de Baïf, 75205 Paris Cedex 13, France; USTH, University of Science and Technology of Hanoi, 18 Hoang Quoc Viet, Hanoi, Vietnam; School of Chemical Engineering, Hanoi University of Science and Technology, 1st Dai Co Viet Road, Hanoi, Vietnam
| | - B Piro
- Université Paris Diderot, Sorbonne Paris Cité, ITODYS, UMR 7086 CNRS, 15 rue J-A de Baïf, 75205 Paris Cedex 13, France
| | - S Reisberg
- Université Paris Diderot, Sorbonne Paris Cité, ITODYS, UMR 7086 CNRS, 15 rue J-A de Baïf, 75205 Paris Cedex 13, France
| | - L Huy Nguyen
- Université Paris Diderot, Sorbonne Paris Cité, ITODYS, UMR 7086 CNRS, 15 rue J-A de Baïf, 75205 Paris Cedex 13, France
| | - T Dung Nguyen
- Université Paris Diderot, Sorbonne Paris Cité, ITODYS, UMR 7086 CNRS, 15 rue J-A de Baïf, 75205 Paris Cedex 13, France
| | - H T Duc
- Université Paris 11, INSERM U-1014, Hôpital Paul Brousse 94800 Villejuif, France
| | - M C Pham
- Université Paris Diderot, Sorbonne Paris Cité, ITODYS, UMR 7086 CNRS, 15 rue J-A de Baïf, 75205 Paris Cedex 13, France.
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Supervised learning classification models for prediction of plant virus encoded RNA silencing suppressors. PLoS One 2014; 9:e97446. [PMID: 24828116 PMCID: PMC4020838 DOI: 10.1371/journal.pone.0097446] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 04/21/2014] [Indexed: 12/21/2022] Open
Abstract
Viral encoded RNA silencing suppressor proteins interfere with the host RNA silencing machinery, facilitating viral infection by evading host immunity. In plant hosts, the viral proteins have several basic science implications and biotechnology applications. However in silico identification of these proteins is limited by their high sequence diversity. In this study we developed supervised learning based classification models for plant viral RNA silencing suppressor proteins in plant viruses. We developed four classifiers based on supervised learning algorithms: J48, Random Forest, LibSVM and Naïve Bayes algorithms, with enriched model learning by correlation based feature selection. Structural and physicochemical features calculated for experimentally verified primary protein sequences were used to train the classifiers. The training features include amino acid composition; auto correlation coefficients; composition, transition, and distribution of various physicochemical properties; and pseudo amino acid composition. Performance analysis of predictive models based on 10 fold cross-validation and independent data testing revealed that the Random Forest based model was the best and achieved 86.11% overall accuracy and 86.22% balanced accuracy with a remarkably high area under the Receivers Operating Characteristic curve of 0.95 to predict viral RNA silencing suppressor proteins. The prediction models for plant viral RNA silencing suppressors can potentially aid identification of novel viral RNA silencing suppressors, which will provide valuable insights into the mechanism of RNA silencing and could be further explored as potential targets for designing novel antiviral therapeutics. Also, the key subset of identified optimal features may help in determining compositional patterns in the viral proteins which are important determinants for RNA silencing suppressor activities. The best prediction model developed in the study is available as a freely accessible web server pVsupPred at http://bioinfo.icgeb.res.in/pvsup/.
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Hong CY, Chen X, Li J, Chen JH, Chen G, Yang HH. Direct detection of circulating microRNAs in serum of cancer patients by coupling protein-facilitated specific enrichment and rolling circle amplification. Chem Commun (Camb) 2014; 50:3292-5. [DOI: 10.1039/c3cc48996e] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A simple method for direct detection of circulating miRNAs in serum by coupling p19 protein-facilitated specific enrichment and RCA.
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Affiliation(s)
- Cheng-Yi Hong
- The Key Lab of Analysis and Detection for Food Safety of MOE and Fujian Provincial
- College of Chemistry and Chemical Engineering
- Fuzhou University
- Fuzhou 350108, China
| | - Xian Chen
- The Key Lab of Analysis and Detection for Food Safety of MOE and Fujian Provincial
- College of Chemistry and Chemical Engineering
- Fuzhou University
- Fuzhou 350108, China
| | - Juan Li
- The Key Lab of Analysis and Detection for Food Safety of MOE and Fujian Provincial
- College of Chemistry and Chemical Engineering
- Fuzhou University
- Fuzhou 350108, China
| | - Jing-Hua Chen
- Department of Pharmaceutical Analysis
- Faculty of Pharmacy
- Fujian Medical University
- Fuzhou 350004, China
| | - Guonan Chen
- The Key Lab of Analysis and Detection for Food Safety of MOE and Fujian Provincial
- College of Chemistry and Chemical Engineering
- Fuzhou University
- Fuzhou 350108, China
| | - Huang-Hao Yang
- The Key Lab of Analysis and Detection for Food Safety of MOE and Fujian Provincial
- College of Chemistry and Chemical Engineering
- Fuzhou University
- Fuzhou 350108, China
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