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Label-free and self-assembled fluorescent DNA nanopompom for determination of miRNA-21

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Abstract

A label-free fluorescence method based on self-assembled DNA nanopompom has been developed for miRNA-21 detection. In the presence of miRNA-21, three DNA hairpin probes with split G-quadruplex assemble the DNA nanopompom. Based on the isothermal toehold-mediated DNA strand displacement reaction, the target miRNA can be catalytically recycled and trigger three DNA hairpin probes to self-assemble the DNA nanopompom and release the G-quadruplex. The formation of the G-quadruplex increases the fluorescence emission intensity of thioflavin. For thioflavin-based miRNA-21 detection, the excitation and emission wavelengths are set to 425 nm and 490 nm, respectively. The limit of detection for miRNA-21 is 0.8 pM according to F/F0 = 0.0031 × CmiRNA-21 + 1.0382 (R2 = 0.9978). This sensing system provides a low-cost, effective, and convenient method for miRNA detection, which holds great potential in biochemical diagnosis and clinical practice.

Label-free and self-assembled fluorescent DNA nanopompom for miRNA detection

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References

  1. Seeman NC, Sleiman HF (2017) DNA nanotechnology. Nat Rev Mater 3(1):1–23

    Google Scholar 

  2. Hu QQ, Li H, Wang LH, Gu HZ, Fan CH (2019) DNA nanotechnology-enabled drug delivery systems. Chem Rev 119(10):6459–6506

    CAS  Google Scholar 

  3. Xiao MS, Lai W, Man TT, Chang BB, Li L, Chandrasekaran AR, Pei H (2019) Rationally engineered nucleic acid architectures for biosensing applications. Chem Rev 119(22):11631–11717

    Article  CAS  Google Scholar 

  4. Bae W, Kocabey S, Liedl T (2019) DNA nanostructures in vitro, in vivo and on membranes. Nano Today 26:98–107

    Article  CAS  Google Scholar 

  5. McConnell EM, Cozma I, Morrison D, Li YF (2020) Biosensors made of synthetic functional nucleic acids toward better human health. Anal Chem 92(1):327–344

    Article  CAS  Google Scholar 

  6. Ding X, Mauk MG, Yin K, Kadimisetty K, Liu CC (2019) Interfacing pathogen detection with smartphones for point-of-care applications. Anal Chem 91(1):655–672

    Article  CAS  Google Scholar 

  7. Xiong Y, Zhang JJ, Yang ZL, Mou QB, Ma Y, Xiong YH, Lu Y (2020) Functional DNA regulated CRISPR-Cas12a sensors for point-of-care diagnostics of non-nucleic acid targets. J Am Chem Soc 142(1):207–213

    Article  CAS  Google Scholar 

  8. Dave VP, Ngo TA, Pernestig AK, Tilevik D, Kant K, Nguyen T, Wolff A, Bang DD (2019) MicroRNA amplification and detection technologies: opportunities and challenges for point of care diagnostics. Lab Investig 99:452–469

    Article  CAS  Google Scholar 

  9. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS, Johnson JM (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433(7027):769–773

    Article  CAS  Google Scholar 

  10. Masud MK, Umer M, Hossain MSA, Yamauchi Y, Nguyen NT, Shiddiky MJ (2019) Nanoarchitecture frameworks for electrochemical miRNA detection. Trends Biochem Sci 44(5):433–452

    Article  CAS  Google Scholar 

  11. Goryacheva OA, Novikova AS, Drozd DD, Pidenko PS, Ponomaryeva TS, Bakal AA, Mishra PK, Beloglazova NV, Goryacheva IY (2019) Water-dispersed luminescent quantum dots for miRNA detection. TrAC Trend Anal Chem 111:197–205

    Article  CAS  Google Scholar 

  12. Fiammengo R (2017) Can nanotechnology improve cancer diagnosis through miRNA detection? Biomark Med 11(1):69–86

    Article  CAS  Google Scholar 

  13. Bi S, Yue SZ, Zhang SS (2017) Hybridization chain reaction: a versatile molecular tool for biosensing, bioimaging, and biomedicine. Chem Soc Rev 46:4281–4298

    Article  CAS  Google Scholar 

  14. Dirks RM, Pierce NA (2004) Triggered amplification by hybridization chain reaction. Proc Natl Acad Sci 101(43):15275–15278

    Article  CAS  Google Scholar 

  15. Ding X, Cheng W, Li Y, Wu J, Li X, Cheng Q, Ding S (2017) An enzyme-free surface plasmon resonance biosensing strategy for detection of DNA and small molecule based on nonlinear hybridization chain reaction. Biosens Bioelectron 87:345–351

    Article  CAS  Google Scholar 

  16. Xie X, Chai Y, Yuan Y, Yuan R (2018) Dual triggers induced disassembly of DNA polymer decorated silver nanoparticle for ultrasensitive electrochemical Pb2+ detection. Anal Chim Acta 1034:56–62

    Article  CAS  Google Scholar 

  17. Li Y, Huang CZ, Li YF (2019) Ultrasensitive electrochemiluminescence detection of microRNA via one-step introduction of target-triggered branched hybridization chain reaction circuit. Anal Chem 91(14):9308–9314

    Article  CAS  Google Scholar 

  18. Wei J, Gong X, Wang Q, Pan M, Liu XQ, Liu J, Xia F, Wang FA (2018) Construction of an autonomously concatenated hybridization chain reaction for signal amplification and intracellular imaging. Chem Sci 9:52–61

    Article  CAS  Google Scholar 

  19. Li XT, Huang N, Zhang LL, Zhao JJ, Zhao SL (2019) A T7 exonuclease assisted dual-cycle signal amplification assay of miRNA using nanospheres-enhanced fluorescence polarization. Talanta 202:297–302

    Article  CAS  Google Scholar 

  20. Hao N, Li XL, Zhang HR, Xu JJ, Chen HY (2014) A highly sensitive ratiometric electrochemiluminescent biosensor for microRNA detection based on cyclic enzyme amplification and resonance energy transfer. Chem Commun 50(94):14828–14830

    Article  CAS  Google Scholar 

  21. Cui L, Zhu Z, Lin NH, Zhang HM, Guan ZC, Yang CY (2014) A T7 exonuclease-assisted cyclic enzymatic amplification method coupled with rolling circle amplification: a dual-amplification strategy for sensitive and selective microRNA detection. Chem Commun 50(13):1576–1578

    Article  CAS  Google Scholar 

  22. Li BL, Ellington AD, Chen X (2011) Rational, modular adaptation of enzyme-free DNA circuits to multiple detection methods. Nucleic Acids Res 39(16):e110–e110

    Article  CAS  Google Scholar 

  23. Li JB, Lei PH, Ding SJ, Zhang Y, Yang JR, Cheng Q, Yan YR (2016) An enzyme-free surface plasmon resonance biosensor for real-time detecting microRNA based on allosteric effect of mismatched catalytic hairpin assembly. Biosens Bioelectron 77:435–441

    Article  Google Scholar 

  24. Jiang Y, Li BL, Milligan JN, Bhadra S, Ellington AD (2013) Real-time detection of isothermal amplification reactions with thermostable catalytic hairpin assembly. J Am Chem Soc 135(20):7430–7433

    Article  CAS  Google Scholar 

  25. Zhou WJ, Liang WB, Li X, Chai YQ, Yuan R, Xiang Y (2015) MicroRNA-triggered, cascaded and catalytic self-assembly of functional “DNAzyme ferris wheel” nanostructures for highly sensitive colorimetric detection of cancer cells. Nanoscale 7(19):9055–9061

    Article  CAS  Google Scholar 

  26. Zhou WJ, Li DX, Chai YQ, Yuan R, Xiang Y (2015) RNA responsive and catalytic self-assembly of DNA nanostructures for highly sensitive fluorescence detection of microRNA from cancer cells. Chem Commun 51(92):16494–16497

    Article  CAS  Google Scholar 

  27. Burge S, Parkinson GN, Hazel P, Todd AK, Neidle S (2006) Quadruplex DNA: sequence, topology and structure. Nucleic Acids Res 34(19):5402–5415

    Article  CAS  Google Scholar 

  28. Mohanty J, Barooah N, Dhamodharan V, Harikrishna S, Pradeepkumar PI, Bhasikuttan AC (2013) Thioflavin T as an efficient inducer and selective fluorescent sensor for the human telomeric G-quadruplex DNA. J Am Chem Soc 135(1):367–376

    Article  CAS  Google Scholar 

  29. Khusbu FY, Zhou X, Chen HC, Ma CB, Wang KM (2018) Thioflavin T as a fluorescence probe for biosensing applications. TrAC Trends Anal Chem 109:1–18

    Article  Google Scholar 

  30. Fan TT, Mao Y, Liu F, Zhang W, Yin JX, Jiang YY (2017) Dual signal amplification strategy for specific detection of circulating microRNAs based on Thioflavin T. Sensors Actuators B Chem 249:1–7

    Article  Google Scholar 

  31. Tan XH, Wang Y, Armitage BA, Bruchez MP (2014) Label-free molecular beacons for biomolecular detection. Anal Chem 86(21):10864–10869

    Article  CAS  Google Scholar 

  32. Liu Y, Shen T, Li J, Gong H, Chen CY, Chen XM, Cai CQ (2017) Ratiometric fluorescence sensor for the microRNA determination by catalyzed hairpin assembly. ACS Sens 2(10):1430–1434

    Article  CAS  Google Scholar 

  33. Sun Y, Shi L, Wang Q, Mi L, Li T (2019) Spherical nucleic acid enzyme (SNAzyme) boosted chemiluminescence miRNA imaging using a smartphone. Anal Chem 91(5):3652–3658

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This research was supported by the National Natural Science Foundation of China (Grant No. 81971637), the Guangdong Basic and Applied Basic Research Foundation (2019A1515110402), and the Technology & Innovation Commission of Shenzhen Municipality (Shenzhen, China; Grant No. JCYJ20190807145011340).

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Correspondence to Cunchuan Wang or Ligang Xia.

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Chen, N., Li, J., Feng, X. et al. Label-free and self-assembled fluorescent DNA nanopompom for determination of miRNA-21. Microchim Acta 187, 432 (2020). https://doi.org/10.1007/s00604-020-04377-6

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