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Sensitive colorimetric determination of microRNA let-7a through rolling circle amplification and a peroxidase-mimicking system composed of trimeric G-triplex and hemin DNAzyme

Abstract

The authors have incidentally found that the three tandem repeats of a 13-mer G-rich oligomer (with sequence 5′-TGG GAA GGG AGG G-3′; referred to as G3) can directly fold into a stable G3 trimer. The G3 trimer/hemin DNAzyme exhibits an about 3-fold higher peroxidase-mimicking activity compared to the conventional G3/hemin DNAzyme. Combining this finding with rolling circle amplification (RCA), a colorimetric assay was developed for sensitive and specific determination of microRNA. In this method, each cycle of RCA generates three catalytic units. This leads to a significant signal amplification of the RCA. Using let-7a as a model analyte, the colorimetric method (best performed at 420 nm) exhibits high sensitivity toward microRNA-let-7a with a 37 fM detection limit and an analytical range that covers 3 orders of magnitude. The method was applied to the determination of let-7a in some cell lysates.

This G-triplex trimer-based rolling circle amplification (RCA) method can produce three catalytic units per RCA cycle, which can significantly improve the amplification efficiency of RCA.

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References

  1. 1.

    Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism and function. Cell 116:281–297

  2. 2.

    He L, Thomson JM, Hemann MT, Hernando-Monge E, Mu D, Goodson S, Powers S, Cordon-Cardo C, Lowe SW, Hannon GJ, Hammond SM (2005) A microRNA polycistron as a potential human oncogene. Nature 435:828–833

  3. 3.

    Tricoli JV, Jacobson JW (2007) MicroRNA: potential for cancer detection, diagnosis, and prognosis. Cancer Res 67:4553–4555

  4. 4.

    Schmittgen TD, Jiang J, Liu Q, Yang L (2004) A high-throughput method to monitor the expression of microRNA precursors. Nucleic Acids Res 32:e43

  5. 5.

    Wang X, Wang H, Liu C, Wang H, Li Z (2017) A three-way junction structure-based isothermal exponential amplification strategy for sensitive detection of 3′-terminal 2'-O-methylated plant microRNA. Chem Commun 53:1124–1127

  6. 6.

    Qu X, Jin H, Liu Y, Sun Q (2018) Strand displacement amplification reaction on quantum dot-encoded silica bead for visual detection of multiplex microRNAs. Anal Chem 90:3482–3489

  7. 7.

    Guo J, Mingoes C, Qiu X, Hildebrandt N (2019) Simple, amplified, and multiplexed detection of microRNAs using time-gated FRET and hybridization chain reaction. Anal Chem 91:3101–3109

  8. 8.

    Yu S, Wang Y, Jiang LP, Bi S, Zhu JJ (2018) Cascade amplification-mediated in situ hot-spot assembly for microRNA detection and molecular logic gate operations. Anal Chem 90:4544–4551

  9. 9.

    Zhou F, Meng R, Liu Q, Jin Y, Li B (2016) Photoinduced electron transfer-based fluorescence quenching combined with rolling circle amplification for sensitive detection of microRNA. ChemistrySelect 1:6422–6428

  10. 10.

    Zhou F, Li B, Ma J (2015) A linear DNA probe as an alternative to a molecular beacon for improving the sensitivity of a homogenous fluorescence biosensing platform for DNA detection using target-primed rolling circle amplification. RSC Adv 5:4019–4025

  11. 11.

    Ali MM, Li F, Zhang Z, Zhang K, Kang D-K, Ankrum JA, Le XC, Zhao W (2014) Rolling circle amplification: a versatile tool for chemical biology, materials science and medicine. Chem Soc Rev 43:3324–3341

  12. 12.

    Qu X, Bian F, Guo Q, Ge Q, Sun Q, Huang X (2018) Ligation-rolling circle amplification on quantum dot-encoded microbeads for detection of multiplex G-quadruplex-forming sequences. Anal Chem 90:12051–12058

  13. 13.

    Golub E, Albada HB, Liao W, Biniuri Y, Willner I (2016) Nucleoapzymes: hemin/G-quadruplex DNAzyme-aptamer binding site conjugates with superior enzyme-like catalytic functions. J Am Chem Soc 138:164–172

  14. 14.

    Gao Y, Li B (2014) Exonuclease III-assisted cascade signal amplification strategy for label-free and ultrasensitive chemiluminescence detection of DNA. Anal Chem 86:8881–8887

  15. 15.

    Cheglakov Z, Weizmann Y, Basnar B, Willner I (2007) Diagnosing viruses by the rolling circle amplified synthesis of DNAzymes. Org Biomol Chem 5:223–225

  16. 16.

    Xu L, Jiang Z, Mu Y, Zhang Y, Zhan Q, Cui J, Cheng W, Ding S (2018) Colorimetric assay of rare disseminated tumor cells in real sample by aptamer-induced rolling circle amplification on cell surface. Sens Actuators B Chem 259:596–603

  17. 17.

    Tian Y, He Y, Mao C (2006) Cascade signal amplification for DNA detection. ChemBioChem 7:1862–1864

  18. 18.

    Wang F, Lu CH, Liu X, Freage L, Willner I (2014) Amplified and multiplexed detection of DNA using the dendritic rolling circle amplified synthesis of DNAzyme reporter units. Anal Chem 86:1614–1621

  19. 19.

    Wen Y, Xu Y, Mao X, Wei Y, Song H, Chen N, Huang Q, Fan C, Li D (2012) DNAzyme-based rolling-circle amplification DNA machine for ultrasensitive analysis of microRNA in Drosophila larva. Anal Chem 84:7664–7669

  20. 20.

    Zhang P, Wu X, Yuan R, Chai Y (2015) An "off−on" electrochemiluminescent biosensor based on DNAzyme-assisted target recycling and rolling circle amplifications for ultrasensitive detection of microRNA. Anal Chem 87:3202–3207

  21. 21.

    Gomez A, Miller NS, Smolina I (2014) Visual detection of bacterial pathogens via PNA-based padlock probe assembly and isothermal amplification of DNAzymes. Anal Chem 86:11992–11998

  22. 22.

    Dong H, Wang C, Xiong Y, Lu H, Ju H, Zhang X (2013) Highly sensitive and selective chemiluminescent imaging for DNA detection by ligation-mediated rolling circle amplified synthesis of DNAzyme. Biosens Bioelectron 41:348–353

  23. 23.

    Rajendran A, Endo M, Hidaka K, Sugiyama H (2014) Direct and single-molecule visualization of the solution-state structures of G-hairpin and G-triplex intermediates. Angew Chem Int Ed 53:4107–4112

  24. 24.

    Wang S, Fu B, Peng S, Zhang X, Tian T, Zhou X (2013) The G-triplex DNA could function as a new variety of DNA peroxidase. Chem Commun 49:7920–7922

  25. 25.

    Wang S, Fu B, Wang J, Long Y, Zhang X, Peng S, Guo P, Tian T, Zhou X (2014) Novel amplex red oxidases based on noncanonical DNA structures: property studies and applications in microRNA detection. Anal Chem 86:2925–2930

  26. 26.

    Ma DL, Lu L, Lin S, He B, Leung CH (2015) A G-triplex luminescent switch-on probe for the detection of mung bean nuclease activity. J Mater Chem B 3:348–352

  27. 27.

    Zhou H, Wu ZF, Han QJ, Zhong HM, Peng JB, Li X, Fan XL (2018) Stable and label-free fluorescent probe based on G-triplex DNA and thioflavin T. Anal Chem 90:3220–3226

  28. 28.

    Li R, Liu Q, Jin Y, Li B (2019) G-triplex/hemin DNAzyme: an ideal signal generator for isothermal exponential amplification reaction-based biosensing platform. Anal Chim Acta 1079:139–145

  29. 29.

    Ma L, Han X, Xia L, Kong RM, Qu F (2018) G-triplex based molecular beacon for label-free fluorescence "turn-on" detection of bleomycin. Analyst 143:5474–5480

  30. 30.

    Kong D-M, Cai L-L, Guo J-H, Wu J, Shen H-X (2009) Characterization of the G-quadruplex structure of a catalytic DNA with peroxidase activity. Biopolymers 91:331–339

  31. 31.

    Xiao CD, Shibata T, Yamamoto Y, Xu Y (2018) An intramolecular antiparallel G-quadruplex form by human telomere RNA. Chem Comm 54:3994–3946

  32. 32.

    Tang L, Li J (2017) Plasmon-based colorimetric nanosensors for ultrasensitive molecular diagnostics. ACS Sens 2:857–875

  33. 33.

    Gao ZQ, Deng HM, Shen W, Ren YQ (2013) A label-free biosensor for electrochemical detection of femtomolar microRNAs. Anal Chem 85:1624–1630

  34. 34.

    Zhang Q, Chen F, Xu F, Zhao YX, Fan CH (2014) Target-triggered three-way junction structure and polymerase/nicking enzyme synergetic isothermal quadratic DNA machine for highly specific, one-step, and rapid microRNA detection at attomolar level. Anal Chem 86:8098–8105

  35. 35.

    Lin Y, Zhao J, Hu X, Wang L, Liang L, Chen W (2016) Transcription factor CCAAT/enhancer binding protein alpha up-regulates microRNA let-7a-1 in lung cancer cells by direct binding. Cancer Cell Int 16:17

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (No. 21775099 and 21974082).

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Correspondence to Baoxin Li.

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The authors declare that they have no competing interests.

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Li, R., Liu, Q., Jin, Y. et al. Sensitive colorimetric determination of microRNA let-7a through rolling circle amplification and a peroxidase-mimicking system composed of trimeric G-triplex and hemin DNAzyme. Microchim Acta 187, 139 (2020). https://doi.org/10.1007/s00604-019-4093-2

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Keywords

  • Multiple G-triplex
  • ABTS
  • H2O2
  • DNAzyme
  • Isothermal amplification