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Microchimica Acta

, 186:715 | Cite as

Fluorometric determination of microRNA using arched probe-mediated isothermal exponential amplification combined with DNA-templated silver nanoclusters

  • Hao WuEmail author
  • Jun Wu
  • Yaling Liu
  • Hongyong Wang
  • Pei ZouEmail author
Original Paper
  • 111 Downloads

Abstract

A highly sensitive fluorometric method is described for the determination of microRNA-141. It is based on the use of arched probe-mediated isothermal exponential amplification reaction (EXPAR) and of DNA-templated silver nanoclusters (DNA-AgNCs). The EXPAR utilizes microRNA-141 as the trigger, polymerases and endonucleases as amplification activators, and two arched probes as exponential amplification templates. This enables the conversion of microRNA to a large number of reporter sequences under isothermal conditions within minutes. The generated reporter sequences act as scaffolds for the synthesis of fluorescent DNA-AgNCs by reduction of Ag (I) with NaBH4. The DNA-AgNCs function as signalling fluorophores with excitation/emission maxima at 540/610 nm. The method exhibits high sensitivity for microRNA-141 with a detection limit as low as 0.87 fM and a dynamic range from 1 fM to 500 fM. The method can distinguish nucleotides in the microRNA-200 family.

Graphical abstract

Schematic representation of a fluorometric method for sensitive detection of microRNA based on arched probe-mediated isothermal exponential amplification combined with DNA-templated silver nanoclusters.

Keywords

MicroRNA-141 Arched probe Silver nanoclusters Isothermal amplification DNA polymerase Nicking endonuclease Human serum 

Notes

Acknowledgments

This work was supported by the Natural Science Foundation of Jiangsu Province (Grant No. BK20171144 and BK20161139) and the Scientific Research Foundation of Jiangsu Provincial Commission of Health and Family Planning, China (Grant No. H2018068).

Compliance with ethical standards

Conflict of interest

The author(s) declare that they have no competing interests.

Supplementary material

604_2019_3836_MOESM1_ESM.docx (655 kb)
ESM 1 (DOCX 655 kb)

References

  1. 1.
    Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Radmark O, Kim S, Kim VN (2003) The nuclear RNase III Drosha initiates microRNA processing. Nature 425:415–419CrossRefGoogle Scholar
  2. 2.
    Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297CrossRefGoogle Scholar
  3. 3.
    Feng J, Xing W, Xie L (2016) Regulatory Roles of MicroRNAs in Diabetes. Int J Mol Sci 17:1729CrossRefGoogle Scholar
  4. 4.
    Karnati HK, Panigrahi MK, Gutti RK, Greig NH, Tamargo IA (2015) miRNAs: Key Players in Neurodegenerative Disorders and Epilepsy. J Alzheimers Dis 48:563–580CrossRefGoogle Scholar
  5. 5.
    Di Leva G, Garofalo M, Croce CM (2014) MicroRNAs in cancer. Annu Rev Pathol 9:287–314CrossRefGoogle Scholar
  6. 6.
    Streit S, Michalski CW, Erkan M, Kleeff J, Friess H (2009) Northern blot analysis for detection and quantification of RNA in pancreatic cancer cells and tissues. Nat Protoc 4:37–43CrossRefGoogle Scholar
  7. 7.
    Liu CG, Calin GA, Volinia S, Croce CM (2008) MicroRNA expression profiling using microarrays. Nat Protoc 3:563–578CrossRefGoogle Scholar
  8. 8.
    Schmittgen TD, Lee EJ, Jiang J, Sarkar A, Yang L, Elton TS, Chen C (2008) Real-time PCR quantification of precursor and mature microRNA. Methods 44:31–38CrossRefGoogle Scholar
  9. 9.
    Bi S, Yue S, Zhang S (2017) Hybridization chain reaction: a versatile molecular tool for biosensing, bioimaging, and biomedicine. Chem Soc Rev 46:4281–4298CrossRefGoogle Scholar
  10. 10.
    Reid MS, Le XC, Zhang H (2018) Exponential Isothermal Amplification of Nucleic Acids and Assays for Proteins, Cells, Small Molecules, and Enzyme Activities: An EXPAR Example. Angew Chem Int Ed Engl 57:11856–11866CrossRefGoogle Scholar
  11. 11.
    Dai W, Zhang J, Meng X, He J, Zhang K, Cao Y, Wang D, Dong H, Zhang X (2018) Catalytic hairpin assembly gel assay for multiple and sensitive microRNA detection. Theranostics 8:2646–2656CrossRefGoogle Scholar
  12. 12.
    Li M, Xu X, Cai Q, Luo X, Zhou Z, Xu G, Xie Y (2019) Graphene oxide-based fluorometric determination of microRNA-141 using rolling circle amplification and exonuclease III-aided recycling amplification. Microchim Acta 186:531CrossRefGoogle Scholar
  13. 13.
    Yu Y, Chen Z, Shi L, Yang F, Pan J, Zhang B, Sun D (2014) Ultrasensitive electrochemical detection of microRNA based on an arched probe mediated isothermal exponential amplification. Anal Chem 86:8200–8205CrossRefGoogle Scholar
  14. 14.
    Liu YQ, Zhang M, Yin BC, Ye BC (2012) Attomolar ultrasensitive microRNA detection by DNA-scaffolded silver-nanocluster probe based on isothermal amplification. Anal Chem 84:5165–5169CrossRefGoogle Scholar
  15. 15.
    Diez I, Ras RH (2011) Fluorescent silver nanoclusters. Nanoscale 3:1963–1970CrossRefGoogle Scholar
  16. 16.
    Obliosca JM, Liu C, Yeh HC (2013) Fluorescent silver nanoclusters as DNA probes. Nanoscale 5:8443–8461CrossRefGoogle Scholar
  17. 17.
    Berlina AN, Zherdev AV, Dzantiev BB (2019) Progress in rapid optical assays for heavy metal ions based on the use of nanoparticles and receptor molecules. Microchim Acta 186:172CrossRefGoogle Scholar
  18. 18.
    Yuan Z, Chen YC, Li HW, Chang HT (2014) Fluorescent silver nanoclusters stabilized by DNA scaffolds. Chem Commun (Camb) 50:9800–9815CrossRefGoogle Scholar
  19. 19.
    New SY, Lee ST, Su XD (2016) DNA-templated silver nanoclusters: structural correlation and fluorescence modulation. Nanoscale 8:17729–17746CrossRefGoogle Scholar
  20. 20.
    Chen Y, Phipps ML, Werner JH, Chakraborty S, Martinez JS (2018) DNA Templated Metal Nanoclusters: From Emergent Properties to Unique Applications. Acc Chem Res 51:2756–2763CrossRefGoogle Scholar
  21. 21.
    Mu WY, Yang R, Robertson A, Chen QY (2018) A near-infrared BSA coated DNA-AgNCs for cellular imaging. Colloids Surf B Biointerfaces 162:427–431CrossRefGoogle Scholar
  22. 22.
    Shamsipur M, Pashabadi A, Molaabasi F, Hosseinkhani S (2017) Impedimetric monitoring of apoptosis using cytochrome-aptamer bioconjugated silver nanocluster. Biosens Bioelectron 90:195–202CrossRefGoogle Scholar
  23. 23.
    Wu J, Li N, Yao Y, Tang D, Yang D, Ong'achwa Machuki J, Li J, Yu Y, Gao F (2018) DNA-Stabilized Silver Nanoclusters for Label-Free Fluorescence Imaging of Cell Surface Glycans and Fluorescence Guided Photothermal Therapy. Anal Chem 90:14368–14375CrossRefGoogle Scholar
  24. 24.
    Zhang Y, Zhu C, Zhang L, Tan C, Yang J, Chen B, Wang L, Zhang H (2015) DNA-templated silver nanoclusters for multiplexed fluorescent DNA detection. Small 11:1385–1389CrossRefGoogle Scholar
  25. 25.
    Borghei YS, Hosseini M, Ganjali MR, Ju H (2018) Colorimetric and energy transfer based fluorometric turn-on method for determination of microRNA using silver nanoclusters and gold nanoparticles. Microchim Acta 185:286CrossRefGoogle Scholar
  26. 26.
    Jie G, Tan L, Zhao Y, Wang X (2017) A novel silver nanocluster in situ synthesized as versatile probe for electrochemiluminescence and electrochemical detection of thrombin by multiple signal amplification strategy. Biosens Bioelectron 94:243–249CrossRefGoogle Scholar
  27. 27.
    Zhang Z, Guo C, Zhang S, He L, Wang M, Peng D, Tian J, Fang S (2017) Carbon-based nanocomposites with aptamer-templated silver nanoclusters for the highly sensitive and selective detection of platelet-derived growth factor. Biosens Bioelectron 89:735–742CrossRefGoogle Scholar
  28. 28.
    Li Z, Ma YY, Wang J, Zeng XF, Li R, Kang W, Hao XK (2016) Exosomal microRNA-141 is upregulated in the serum of prostate cancer patients. Onco Targets Ther 9:139–148PubMedGoogle Scholar
  29. 29.
    Li R-D, Yin B-C, Ye B-C (2016) Ultrasensitive, colorimetric detection of microRNAs based on isothermal exponential amplification reaction-assisted gold nanoparticle amplification. Biosens Bioelectron 86:1011–1016CrossRefGoogle Scholar
  30. 30.
    Tang Y, Liu M, Zhao Z, Li Q, Liang X, Tian J, Zhao S (2019) Fluorometric determination of microRNA-122 by using ExoIII-aided recycling amplification and polythymine induced formation of copper nanoparticles. Microchim Acta 186:133CrossRefGoogle Scholar
  31. 31.
    Chen D, Wen S, Peng R, Gong Q, Fei J, Fu Z, Weng C, Liu M (2019) A triple signal amplification method for chemiluminescent detection of the cancer marker microRNA-21. Microchim Acta 186:410CrossRefGoogle Scholar
  32. 32.
    Han Y, Qiu Z, Nawale GN, Varghese OP, Hilborn J, Tian B, Leifer K (2019) MicroRNA detection based on duplex-specific nuclease-assisted target recycling and gold nanoparticle/graphene oxide nanocomposite-mediated electrocatalytic amplification. Biosens Bioelectron 127:188–193CrossRefGoogle Scholar
  33. 33.
    Wang J, Zhang L, Lu L, Kang T (2019) Molecular beacon immobilized on graphene oxide for enzyme-free signal amplification in electrochemiluminescent determination of microRNA. Microchim Acta 186:142CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiPeople’s Republic of China

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