Current progress in quantitative detection of microRNA

ZHU Shenrong; WU Xuri; CHEN Yijun

doi:10.11665/j.issn.1000-5048.20150104

Journal of China Pharmaceutical University > 2015 > 46(1): 40-49. > DOI: 10.11665/j.issn.1000-5048.20150104

ZHU Shenrong, WU Xuri, CHEN Yijun. Current progress in quantitative detection of microRNA[J]. Journal of China Pharmaceutical University, 2015, 46(1): 40-49. DOI: 10.11665/j.issn.1000-5048.20150104

Citation:

ZHU Shenrong, WU Xuri, CHEN Yijun. Current progress in quantitative detection of microRNA[J]. Journal of China Pharmaceutical University, 2015, 46(1): 40-49. DOI: 10.11665/j.issn.1000-5048.20150104

Citation:

ZHU Shenrong, WU Xuri, CHEN Yijun. Current progress in quantitative detection of microRNA[J]. Journal of China Pharmaceutical University, 2015, 46(1): 40-49. DOI: 10.11665/j.issn.1000-5048.20150104

PDF (1715 KB)

Current progress in quantitative detection of microRNA

More Information

Graphical Abstract

Abstract

Abstract

With the recent development of investigating biological functions of microRNA(miRNA), the importance of miRNA in the biological processes including developmental biology, metabolic regulation, disease progression and treatment has been well recognized. Due to its the instability, low level of expression and minor difference in sequence, more sophisticated analytical methods for rapid and easy quantitative detection of miRNA with strong specificity and high sensitivity play an important role in the study of the biological functions of miRNA. This review analyzes and compares recent quantitative methods to detect miRNA, with an attempt to provide a foundation for choosing an appropriate method to quantitatively analyze miRNA.

FullText(HTML)

References (60)

References

[1]	Dong H,Lei J,Ding L,et al.MicroRNA:function,detection,and bioanalysis[J].Chem Rev,2013,113(8):6207-6233.
[2]	Lewis BP,Burge CB,Bartel DP.Conserved seed pairing,often flanked by adenosines,indicates that thousands of human genes are microRNA targets[J].Cell,2005,120(1):15-20.
[3]	Lee YS,Dutta A.MicroRNA in cancer[J].Annu Rev Pathol,2009,4:199-227.
[4]	Chen JF,Murchison EP,Tang R,et al.Targeted deletion of Dicer in the heart leads to dilated cardiomyopathy and heart failure[J].Proc Natl Acad Sci U S A,2008,105(6):2111-2116.
[5]	Lukiw WJ,Zhao Y,Cui JG.An NF-kappaB-sensitive microRNA-146a-mediated inflammatory circuit in Alzheimer disease and in stressed human brain cells[J].J Biol Chem,2008,283(46):31315-31322.
[6]	de Planell-Saguer M,Rodicio MC.Detection methods for microRNA in clinic practice[J].Clin Biochem,2013,46(10/11):869-878.
[7]	Cissell KA,Shrestha S,Deo SK.MicroRNA detection:challenges for the analytical chemist[J].Anal Chem,2007,79(13):4754-4761.
[8]	Várallyay E, Burgyán J, Havelda Z. MicroRNA detection by northern blotting using locked nucleic acid probes[J].Nat Protoc,2008,3(2):190-196.
[9]	Pall GS,Codony-Servat C,Byrne J,et al.Carbodiimide-mediated cross-linking of RNA to nylon membranes improves the detection of siRNA,miRNA and piRNA by northern blot[J].Nucleic Acids Res,2007,35(8):e60.
[10]	Li W,Ruan K.MicroRNA detection by microarray[J].Anal Bioanal Chem,2009,394(4):1117-1124.
[11]	Wang B,Xi Y.Challenges for MicroRNA Microarray Data Analysis[J].Microarrays,2013,2(2),doi: 10.3390/microarrays2020034.
[12]	Liu CG,Calin GA,Volinia S,et al.MicroRNA expression profiling using microarrays[J].Nat Protoc,2008,3(4):563-578.
[13]	Krichevsky AM,King KS,Donahue CP,et al.A microRNA array reveals extensive regulation of microRNA during brain development[J].RNA,2003,9(10):1274-1281.
[14]	Thomson JM,Parker J,Perou CM,et al.A custom microarray platform for analysis of microRNA gene expression[J].Nat Methods,2004,1(1):47-53.
[15]	Shingara J,Keiger K,Shelton J,et al.An optimized isolation and labeling platform for accurate microRNA expression profiling[J].RNA,2005,11(9):1461-1470.
[16]	Pritchard CC,Cheng HH,Tewari M.MicroRNA profiling:approaches and considerations[J].Nat Rev Genet,2012,13(5):358-369.
[17]	Fang S,Lee HJ,Wark AW,et al.Attomole microarray detection of microRNA by nanoparticle-amplified SPR imaging measurements of surface polyadenylation reactions[J].J Am Chem Soc,2006,128(43):14044-14046.
[18]	Schmittgen TD,Lee EJ,Jiang J,et al.Real-time PCR quantification of precursor and mature microRNA[J].Methods,2008,44(1):31-38.
[19]	Yan J, Zhang N, Qi C, et al. One-step real time RT-PCR for detection of microRNA[J].Talanta,2013,110:190-195.
[20]	Benes V, Castoldi M. Expression profiling of microRNA using real-time quantitative PCR,how to use it and what is available[J].Methods,2010,50(4):244-249.
[21]	Raymond CK,Roberts BS,Garrett-Engele P,et al.Simple,quantitative primer-extension PCR assay for direct monitoring of microRNA and short-interfering RNA[J].RNA,2005,11(11):1737-1744.
[22]	Reichenstein I, Aizenberg N, Goshen M, et al. A novel qPCR assay for viral encoded microRNA[J].J Virol Methods,2010,163(2):323-328.
[23]	Ro S,Park C,Jin J,et al.A PCR-based method for detection and quantification of small RNA[J].Biochem Biophys Res Commun,2006,351(3):756-763.
[24]	Mou G,Wang K,Xu D,et al.Evaluation of three RT-qPCR-based miRNA detection methods using seven rice miRNA[J].Biosci Biotechnol Biochem,2013,77(6):1349-1353.
[25]	Van Ness J,Van Ness LK,Galas DJ.Isothermal reactions for the amplification of oligonucleotides[J].Proc Natl Acad Sci U S A,2003,100(8):4504-4509.
[26]	Asiello PJ,Baeumner AJ.Miniaturized isothermal nucleic acid amplification,a review[J].Lab Chip,2011,11(8):1420-1430.
[27]	Jia H,Li Z,Liu C,et al.Ultrasensitive detection of microRNA by exponential isothermal amplification[J].Angew Chem Int Ed Engl,2010,49(32):5498-5501.
[28]	Zhang Y,Zhang CY.Sensitive detection of microRNA with isothermal amplification and a single-quantum-dot-based nanosensor[J].Anal Chem,2011,84(1):224-231.
[29]	Wang K,Zhang K,Lv Z,et al.Ultrasensitive detection of microRNA with isothermal amplification and a time-resolved fluorescence sensor[J].Biosens Bioelectron,2014,57:91-95.
[30]	Liu YQ,Zhang M,Yin BC,et al.Attomolar ultrasensitive microRNA detection by DNA-scaffolded silver-nanocluster probe based on isothermal amplification[J].Anal Chem,2012,84(12):5165-5169.
[31]	Wang GL,Zhang CY.Sensitive detection of microRNA with hairpin probe-based circular exponential amplification assay[J].Anal Chem,2012,84(16):7037-7042.
[32]	Bi S,Cui Y,Li L.Dumbbell probe-mediated cascade isothermal amplification:a novel strategy for label-free detection of microRNA and its application to real sample assay[J].Anal Chim Acta,2013,760:69-74.
[33]	Wang XP,Yin BC,Wang P,et al.Highly sensitive detection of microRNA based on isothermal exponential amplification-assisted generation of catalytic G-quadruplex DNAzyme[J].Biosens Bioelectron,2013,42:131-135.
[34]	Kobori T,Takahashi H.Expanding possibilities of rolling circle amplification as a biosensing platform[J].Anal Sci,2014,30(1):59-64.
[35]	Jonstrup SP,Koch J,Kjems J.A microRNA detection system based on padlock probes and rolling circle amplification[J].RNA,2006,12(9):1747-1752.
[36]	Cheng Y,Zhang X,Li Z,et al.Highly sensitive determination of microRNA using target-primed and branched rolling-circle amplification[J].Angew Chem Int Ed Engl,2009,48(18):3268-3272.
[37]	Mashimo Y,Mie M,Suzuki S,et al.Detection of small RNA molecules by a combination of branched rolling circle amplification and bioluminescent pyrophosphate assay[J].Anal Bioanal Chem,2011,401(1):221-227.
[38]	Zhou Y,Huang Q,Gao J,et al.A dumbbell probe-mediated rolling circle amplification strategy for highly sensitive microRNA detection[J].Nucleic Acids Res,2010,38(15):e156.
[39]	Wen Y,Xu Y,Mao X,et al.DNAzyme-based rolling-circle amplification DNA machine for ultrasensitive analysis of microRNA in Drosophila larva[J].Anal Chem,2012,84(18):7664-7669.
[40]	Liu H,Li L,Duan L,et al.High specific and ultrasensitive isothermal detection of microRNA by padlock probe-based exponential rolling circle amplification[J].Anal Chem,2013,85(16):7941-7947.
[41]	Chapin SC, Doyle PS. Ultrasensitive multiplexed microRNA quantification on encoded gel microparticles using rolling circle amplification[J].Anal Chem,2011,83(18):7179-7185.
[42]	Deng R, Tang L, Tian Q, et al. Toehold-initiated rolling circle amplification for visualizing individual microRNA in situ in single cells[J].Angew Chem Int Ed Engl,2014,53(9):2389-2393.
[43]	Zhang LR,Zhu G,Zhang CY.Homogeneous and label-free detection of microRNA using bifunctional strand displacement amplification-mediated hyperbranched rolling circle amplification[J].Anal Chem,2014,86(13):6703-6709.
[44]	Cui L,Zhu Z,Lin N,et al.A T7 exonuclease-assisted cyclic enzymatic amplification method coupled with rolling circle amplification:a dual-amplification strategy for sensitive and selective microRNA detection[J].Chem Commun,2014,50(13):1576-1578.
[45]	Yao B,Liu Y,Tabata M,et al.Sensitive detection of microRNA by chronocoulometry and rolling circle amplification on a gold electrode[J].Chem Commun,2014,50(68):9704-9706.
[46]	Gerasimova YV,Kolpashchikov DM.Enzyme-assisted target recycling(EATR)for nucleic acid detection[J].Chem Soc Rev,2014,43(17):6405-6438.
[47]	Chan SH,Stoddard BL,Xu SY.Natural and engineered nicking endonucleases-from cleavage mechanism to engineering of strand-specificity[J].Nucleic Acids Res,2011,39(1):1-18.
[48]	Dong H, Hao K, Tian Y, et al. Label-free and ultrasensitive microRNA detection based on novel molecular beacon binding readout and target recycling amplification[J].Biosens Bioelectron,2014,153:377-383.
[49]	Yin BC,Liu YQ,Ye BC.Sensitive detection of microRNA in complex biological samples via enzymatic signal amplification using DNA polymerase coupled with nicking endonuclease[J].Anal Chem,2013,85(23):11487-11493.
[50]	Zou B,Ma Y,Wu H,et al.Ultrasensitive DNA detection by cascade enzymatic signal amplification based on Afu flap endonuclease coupled with nicking endonuclease[J].Angew Chem Int Ed Engl,2011,50(32):7395-7398.
[51]	Yin BC, Liu YQ, Ye BC. One-step, multiplexed fluorescence detection of microRNA based on duplex-specific nuclease signal amplification[J].J Am Chem Soc,2012,134(11):5064-5067.
[52]	Lin X,Zhang C,Huang Y,et al.Backbone-modified molecular beacons for highly sensitive and selective detection of microRNA based on duplex specific nuclease signal amplification[J].Chem Commun,2013,49(65):7243-7245.
[53]	Huang RC,Chiu WJ,Li YJ,et al.Detection of microRNA in tumor cells using exonuclease III and graphene oxide-regulated signal amplification[J].ACS Appl Mater Interfaces,2014,6(24):21780-21787.
[54]	Cui L,Lin X,Lin N,et al.Graphene oxide-protected DNA probes for multiplex microRNA analysis in complex biological samples based on a cyclic enzymatic amplification method[J].Chem Commun,2012,48(2):194-196.
[55]	Wang M,Fu Z,Li B,et al.One-step,ultrasensitive,and electrochemical assay of microRNA based on T7 exonuclease assisted cyclic enzymatic amplification[J].Anal Chem,2014,86(12):5606-5610.
[56]	Crew E,Tessel MA,Rahman S,et al.MicroRNA conjugated gold nanoparticles and cell transfection[J].Anal Chem,2012,84(1):26-29.
[57]	Lee H,Park JE,Nam JM.Bio-barcode gel assay for microRNA[J].Nat Commun,2014,5:3367.
[58]	Fan Y,Chen X,Trigg AD,et al.Detection of microRNA using target-guided formation of conducting polymer nanowires in nanogaps[J].J Am Chem Soc,2007,129(17):5437-5443.
[59]	Yin H,Zhou Y,Zhang H,et al.Electrochemical determination of microRNA-21 based on graphene,LNA integrated molecular beacon,AuNPs and biotin multifunctional bio bar codes and enzymatic assay system[J].Biosens Bioelectron,2012,33(1):247-253.
[60]	Alhasan AH,Kim DY,Daniel WL,et al.Scanometric microRNA array profiling of prostate cancer markers using spherical nucleic acid-gold nanoparticle conjugates[J].Anal Chem,2012,84(9):4153-4160.

Cited By

Get Citation

PDF

XML

Article views (1948) PDF downloads (4170)

Turn off MathJax

Article Contents

Abstract

References

Current progress in quantitative detection of microRNA

Abstract

References

Catalog

Export File

Citation

Format

Content