A review: MicroRNA detection methods

Organic and Biomolecular Chemistry

Volumn 13, Issue 8, 2015, Pages 2226-2238

  Tian, Tian ^a   Wang, Jiaqi ^a   Zhou, Xiang ^a  

^a WUHAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DIAGNOSIS;

CURRENT DEMANDS; DISEASE DIAGNOSIS; MICRORNA (MIRNA); MICRORNA DETECTIONS; MIRNA DETECTIONS; NOVEL METHODS; REGULATORY FUNCTIONS; SENSITIVITY AND SPECIFICITY;

RNA;

MICRORNA;

CHEMICAL ANALYSIS; CHEMISTRY; METABOLISM; PROCEDURES;

CHEMISTRY TECHNIQUES, ANALYTICAL; CHEMISTRY, ANALYTIC; MICRORNAS;

EID: 84922781307     PISSN: 14770520     EISSN: None     Source Type: Journal    
DOI: 10.1039/c4ob02104e     Document Type: Article

References (70)

1. V. Ambros The functions of animal microRNAs Nature 2004 431 7006 350 355
2. T. M. Rana Illuminating the silence: understanding the structure and function of small RNAs, Nature reviews Mol. Cell. Biol. 2007 8 1 23 36
3. J. Krol K. Sobczak U. Wilczynska M. Drath A. Jasinska D. Kaczynska W. J. Krzyzosiak Structural features of microRNA (miRNA) precursors and their relevance to miRNA biogenesis and small interfering RNA/short hairpin RNA design J. Biol. Chem. 2004 279 40 42230 42239
4. M. Tatsuguchi H. Y. Seok T. E. Callis J. M. Thomson J. F. Chen M. Newman M. Rojas S. M. Hammond D. Z. Wang Expression of microRNAs is dynamically regulated during cardiomyocyte hypertrophy J. Mol. Cell. Cardiol. 2007 42 6 1137 1141
5. D. Leshkowitz S. Horn-Saban Y. Parmet E. Feldmesser Differences in microRNA detection levels are technology and sequence dependent Rna 2013 19 4 527 538
6. A. Valoczi C. Hornyik N. Varga J. Burgyan S. Kauppinen Z. Havelda Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes Nucleic Acids Res. 2004 32 22 e175
7. C. Chen D. A. Ridzon A. J. Broomer Z. Zhou D. H. Lee J. T. Nguyen M. Barbisin N. L. Xu V. R. Mahuvakar M. R. Andersen K. Q. Lao K. J. Livak K. J. Guegler Real-time quantification of microRNAs by stem-loop RT-PCR Nucleic Acids Res. 2005 33 20 e179
8. W. Li K. Ruan MicroRNA detection by microarray Anal. Bioanal. Chem. 2009 394 4 1117 1124
9. E. Koscianska J. Starega-Roslan K. Czubala W. J. Krzyzosiak High-resolution northern blot for a reliable analysis of microRNAs and their precursors Sci. World J. 2011 11 102 117
10. X. Zhang Y. Zeng Performing custom microRNA microarray experiments J. Visualized Exp. 2011 56 e3250
11. W. Hwang do I. C. Song D. S. Lee S. Kim Smart magnetic fluorescent nanoparticle imaging probes to monitor microRNAs Small 2010 6 1 81 88
12. C. Li Z. Li H. Jia J. Yan One-step ultrasensitive detection of microRNAs with loop-mediated isothermal amplification (LAMP) Chem. Commun. 2011 47 9 2595 2597
13. F. Li J. Peng J. Wang H. Tang L. Tan Q. Xie S. Yao Carbon nanotube-based label-free electrochemical biosensor for sensitive detection of miRNA-24 Biosens. Bioelectron. 2014 54 158 164
14. X. Zhu X. Zhou D. Xing Label-free detection of microRNA: two-step signal enhancement with a hairpin-probe-based graphene fluorescence switch and isothermal amplification Chemistry 2013 19 17 5487 5494
15. K. A. Cissell S. K. Deo Trends in microRNA detection Anal. Bioanal. Chem. 2009 394 4 1109 1116
16. A. Git H. Dvinge M. Salmon-Divon M. Osborne C. Kutter J. Hadfield P. Bertone C. Caldas Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression Rna 2010 16 5 991 1006
17. C. K. Raymond B. S. Roberts P. Garrett-Engele L. P. Lim J. M. Johnson Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs Rna 2005 11 11 1737 1744
18. H. Liu L. Li L. Duan X. Wang Y. Xie L. Tong Q. Wang B. Tang High specific and ultrasensitive isothermal detection of microRNA by padlock probe-based exponential rolling circle amplification Anal. Chem. 2013 85 16 7941 7947
19. S. P. Jonstrup J. Koch J. Kjems A microRNA detection system based on padlock probes and rolling circle amplification Rna 2006 12 9 1747 1752
20. J. Van Ness L. K. Van Ness D. J. Galas Isothermal reactions for the amplification of oligonucleotides Proc. Natl. Acad. Sci. U. S. A. 2003 100 8 4504 4509
21. E. Tan B. Erwin S. Dames K. Voelkerding A. Niemz Isothermal DNA amplification with gold nanosphere-based visual colorimetric readout for herpes simplex virus detection Clin. Chem. 2007 53 11 2017 2020
22. T. Murakami J. Sumaoka M. Komiyama Sensitive isothermal detection of nucleic-acid sequence by primer generation-rolling circle amplification Nucleic Acids Res. 2009 37 3 e19
23. K. Dhama K. Karthik S. Chakraborty R. Tiwari S. Kapoor A. Kumar P. Thomas Loop-mediated isothermal amplification of DNA (LAMP): a new diagnostic tool lights the world of diagnosis of animal and human pathogens: a review Pakistan J. Biol. Sci. 2014 17 2 151 166
24. F. D. Mairinger R. F. Walter C. Vollbrecht T. Hager K. Worm S. Ting J. Wohlschlager P. Zarogoulidis K. Zarogoulidis K. W. Schmid Isothermal multiple displacement amplification: a methodical approach enhancing molecular routine diagnostics of microcarcinomas and small biopsies OncoTargets Ther. 2014 7 1441 1447
25. H. Jia Z. Li C. Liu Y. Cheng Ultrasensitive detection of microRNAs by exponential isothermal amplification Angew. Chem., Int. Ed. 2010 49 32 5498 5501
26. R. Duan X. Zuo S. Wang X. Quan D. Chen Z. Chen L. Jiang C. Fan F. Xia Lab in a tube: ultrasensitive detection of microRNAs at the single-cell level and in breast cancer patients using quadratic isothermal amplification J. Am. Chem. Soc. 2013 135 12 4604 4607
27. M. M. Ali F. Li Z. Zhang K. Zhang D. K. Kang J. A. Ankrum X. C. Le W. Zhao Rolling circle amplification: a versatile tool for chemical biology, materials science and medicine Chem. Soc. Rev. 2014 43 10 3324 3341
28. F. B. Dean J. R. Nelson T. L. Giesler R. S. Lasken Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification Genome Res. 2001 11 6 1095 1099
29. B. Yao J. Li H. Huang C. Sun Z. Wang Y. Fan Q. Chang S. Li J. Xi Quantitative analysis of zeptomole microRNAs based on isothermal ramification amplification Rna 2009 15 9 1787 1794
30. G. Zhao T. Hu J. Li H. Wei H. Shang Y. Guan A RCA-based assay for analyzing individual strand break in DNA heteroduplex cleavage by restriction endonucleases Chem. Commun. 2014 50 11930 11933
31. A. Lagunavicius E. Merkiene Z. Kiveryte A. Savaneviciute V. Zimbaite-Ruskuliene T. Radzvilavicius A. Janulaitis Novel application of Phi29 DNA polymerase: RNA detection and analysis in vitro and in situ by target RNA-primed RCA Rna 2009 15 5 765 771
32. K. Sato R. Ishii N. Sasaki K. Sato M. Nilsson Bead-based padlock rolling circle amplification for single DNA molecule counting Anal. Biochem. 2013 437 1 43 45
33. Y. Zhou Q. Huang J. Gao J. Lu X. Shen C. Fan A dumbbell probe-mediated rolling circle amplification strategy for highly sensitive microRNA detection Nucleic Acids Res. 2010 38 15 e156
34. Y. Cheng X. Zhang Z. Li X. Jiao Y. Wang Y. Zhang Highly sensitive determination of microRNA using target-primed and branched rolling-circle amplification Angew. Chem., Int. Ed. 2009 48 18 3268 3272
35. R. Deng L. Tang Q. Tian Y. Wang L. Lin J. Li Toehold-initiated rolling circle amplification for visualizing individual microRNAs in situ in single cells Angew. Chem., Int. Ed. 2014 53 9 2389 2393
36. B. C. Yin Y. Q. Liu B. C. Ye One-step, multiplexed fluorescence detection of microRNAs based on duplex-specific nuclease signal amplification J. Am. Chem. Soc. 2012 134 11 5064 5067
37. R. R. Breaker DNA enzymes Nat. Biotechnol. 1997 15 5 427 431
38. R. R. Breaker G. F. Joyce A DNA enzyme that cleaves RNA Chem. Biol. 1994 1 4 223 229
39. P. Travascio Y. Li D. Sen DNA-enhanced peroxidase activity of a DNA-aptamer-hemin complex Chem. Biol. 1998 5 9 505 517
40. L. Chen K. Sun P. Li X. Fan J. Sun S. Ai DNA-enhanced peroxidase-like activity of layered double hydroxide nanosheets and applications in H2O2 and glucose sensing Nanoscale 2013 5 22 10982 10988
41. J. S. Hartig I. Grune S. H. Najafi-Shoushtari M. Famulok Sequence-specific detection of MicroRNAs by signal-amplifying ribozymes J. Am. Chem. Soc. 2004 126 3 722 723
42. Y. Zhao L. Zhou Z. Tang Cleavage-based signal amplification of RNA Nat. Commun. 2013 4 1493
43. C. H. Li O. M. van 't Erve J. T. Robinson Y. Liu L. Li B. T. Jonker Electrical detection of charge-current-induced spin polarization due to spin-momentum locking in Bi2Se3 Nat. Nanotechnol. 2014 9 3 218 224
44. P. Xie Q. Xiong Y. Fang Q. Qing C. M. Lieber Local electrical potential detection of DNA by nanowire-nanopore sensors Nat. Nanotechnol. 2012 7 2 119 125
45. H. Bai R. Wang B. Hargis H. Lu Y. Li A SPR aptasensor for detection of avian influenza virus H5N1 Sensors 2012 12 9 12506 12518
46. H. Chen J. Li Nanotechnology: moving from microarrays toward nanoarrays Methods Mol. Biol. 2007 381 411 436
47. S. Pedroso I. A. Guillen Microarray and nanotechnology applications of functional nanoparticles Comb. Chem. High Throughput Screening 2006 9 5 389 397
48. F. Degliangeli P. Kshirsagar V. Brunetti P. P. Pompa R. Fiammengo Absolute and direct microRNA quantification using DNA-gold nanoparticle probes J. Am. Chem. Soc. 2014 136 6 2264 2267
49. P. Shah P. W. Thulstrup S. K. Cho Y. J. Bhang J. C. Ahn S. W. Choi M. J. Bjerrum S. W. Yang In-solution multiplex miRNA detection using DNA-templated silver nanocluster probes Analyst 2014 139 9 2158 2166
50. Y. P. Zeng G. Zhu X. Y. Yang J. Cao Z. L. Jing C. Y. Zhang A quantum dot-based microRNA nanosensor for point mutation assays Chem. Commun. 2014 50 54 7160 7162
51. Z. Lu L. Zhang Y. Deng S. Li N. He Graphene oxide for rapid microRNA detection Nanoscale 2012 4 19 5840 5842
52. H. Dong J. Zhang H. Ju H. Lu S. Wang S. Jin K. Hao H. Du X. Zhang Highly sensitive multiple microRNA detection based on fluorescence quenching of graphene oxide and isothermal strand-displacement polymerase reaction Anal. Chem. 2012 84 10 4587 4593
53. S. Fang H. J. Lee A. W. Wark R. M. Corn Attomole microarray detection of microRNAs by nanoparticle-amplified SPR imaging measurements of surface polyadenylation reactions J. Am. Chem. Soc. 2006 128 43 14044 14046
54. Y. Fan X. Chen A. D. Trigg C. H. Tung J. Kong Z. Gao Detection of MicroRNAs using target-guided formation of conducting polymer nanowires in nanogaps J. Am. Chem. Soc. 2007 129 17 5437 5443
55. S. Campuzano R. M. Torrente-Rodriguez E. Lopez-Hernandez F. Conzuelo R. Granados J. M. Sanchez-Puelles J. M. Pingarron Magnetobiosensors based on viral protein p19 for microRNA determination in cancer cells and tissues Angew. Chem., Int. Ed. 2014 53 24 6168 6171
56. H. Lee J. E. Park J. M. Nam Bio-barcode gel assay for microRNA Nat. Commun. 2014 5 3367
57. H. Q. Yin M. X. Jia S. Yang S. Q. Wang J. G. Zhang A nanoparticle-based bio-barcode assay for ultrasensitive detection of ricin toxin Toxicon 2012 59 1 12 16
58. H. Q. Yin M. X. Jia L. J. Shi S. Yang L. Y. Zhang Q. M. Zhang S. Q. Wang G. Li J. G. Zhang Nanoparticle-based bio-barcode assay for the detection of bluetongue virus J. Virol. Methods 2011 178 1-2 225 228
59. H. Yin Y. Zhou H. Zhang X. Meng S. Ai Electrochemical determination of microRNA-21 based on graphene, LNA integrated molecular beacon, AuNPs and biotin multifunctional bio bar codes and enzymatic assay system Biosens. Bioelectron. 2012 33 1 247 253
60. M. Labib N. Khan S. M. Ghobadloo J. Cheng J. P. Pezacki M. V. Berezovski Three-mode electrochemical sensing of ultralow microRNA levels J. Am. Chem. Soc. 2013 135 8 3027 3038
61. Y. Q. Liu M. Zhang B. C. Yin B. C. Ye Attomolar ultrasensitive microRNA detection by DNA-scaffolded silver-nanocluster probe based on isothermal amplification Anal. Chem. 2012 84 12 5165 5169
62. Y. Zhang C. Y. Zhang Sensitive detection of microRNA with isothermal amplification and a single-quantum-dot-based nanosensor Anal. Chem. 2012 84 1 224 231
63. L. Yan J. Zhou Y. Zheng A. S. Gamson B. T. Roembke S. Nakayama H. O. Sintim Isothermal amplified detection of DNA and RNA Mol. BioSyst. 2014 10 5 970 1003
64. D. W. Wegman S. N. Krylov Direct quantitative analysis of multiple miRNAs (DQAMmiR) Angew. Chem., Int. Ed. 2011 50 44 10335 10339
65. H. Dong J. Lei L. Ding Y. Wen H. Ju X. Zhang MicroRNA: function, detection, and bioanalysis Chem. Rev. 2013 113 8 6207 6233
66. J. Zhang Y. Yuan S. biXie Y. Chai R. Yuan Amplified amperometric aptasensor for selective detection of protein using catalase-functional DNA-PtNPs dendrimer as a synergetic signal amplification label Biosens. Bioelectron. 2014 60 224 230
67. R. M. Jiang Y. S. Chang S. J. Chen J. H. Chen H. C. Chen P. L. Chang Multiplexed microRNA detection by capillary electrophoresis with laser-induced fluorescence J. Chromatogr., A 2011 1218 18 2604 2610
68. J. D. Driskell O. M. Primera-Pedrozo R. A. Dluhy Y. Zhao R. A. Tripp Quantitative surface-enhanced Raman spectroscopy based analysis of microRNA mixtures Appl. Spectrosc. 2009 63 10 1107 1114
69. D. Duan K. X. Zheng Y. Shen R. Cao L. Jiang Z. Lu X. Yan J. Li Label-free high-throughput microRNA expression profiling from total RNA Nucleic Acids Res. 2011 39 22 e154
70. S. Catuogno C. L. Esposito C. Quintavalle L. Cerchia G. Condorelli V. De Franciscis Recent Advance in Biosensors for microRNAs Detection in Cancer Cancers 2011 3 2 1877 1898