Skip to main content
SpringerLink
Log in

Fluorometric determination of ssDNA based on functionalized magnetic microparticles and DNA supersandwich self-assemblies

  • Original Paper
  • Published:
Microchimica Acta Aims and scope Submit manuscript

Abstract

A method is described for the determination of DNA via nucleic acid amplification by using nucleic acid concatemers that result from DNA supersandwich self-assemblies (SSAs). The method employs two auxiliary probes to form self-assembled biotin SSAs. These exhibit strong fluorescence if labeled with intercalator SYBR Green I. In the presence of the target (as exemplified for a 30-mer), streptavidin is released from the surface of the functionalized magnetic microparticles (FMMPs) by competitive hybridization on the surface. However, the SSA products do not conjugate to the FMMPs. This leads to a large amount of SYBR Green I intercalated into the concatemers and eventually results in amplified fluorescence in the supernate. The SSA products can be prepared beforehand, and amplification therefore can be completed within 50 min. The method is more efficient than any other conventional amplification. The detection limit for the 30-mer is 26.4 fM which is better by a factor of 10 compared to other amplification methods. Conceivably, the method can be further extended to the determination of a wide variety of targets simply by replacing the sequences of the probes. Finally, this rapid and highly sensitive method was employed for detection of Ebola virus gene (≈30-mer) and ATP in spiked serum with satisfactory results.

A high sensitivity and efficiency bioassay is described based on functionalized magnetic microparticles and DNA supersandwich self-assemblies.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Scheme 1
Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  1. Wang F, Lu CH, Willner I (2017) From cascaded catalytic nucleic acids to enzyme–DNA nanostructures: controlling reactivity, sensing, logic operations, and assembly of complex structures. Chem Rev 114:2881–2941

    Article  Google Scholar 

  2. Yuan Z, Zhou Y, Gao S, Cheng Y, Li Z (2014) Homogeneous and sensitive detection of microRNA with ligase chain reaction and lambda exonuclease-assisted cationic conjugated polymer biosensing. ACS Appl Mater Interfaces 6:6181–6185

    Article  CAS  Google Scholar 

  3. Yao Q, Wang Y, Wang J, Chen S, Liu H, Jiang Z, Zhang X, Liu SM, Yuan Q, Zhou X (2018) An ultrasensitive diagnostic biochip based on biomimetic periodic nanostructure-assisted rolling circle amplification. ACS Nano 12:6777–6783

    Article  CAS  Google Scholar 

  4. Zuo X, Xia F, Xiao Y, Plaxco KW (2010) Sensitive and selective amplified fluorescence DNA detection based on exonuclease III-aided target recycling. J Am Chem Soc 132:1816–1818

    Article  CAS  Google Scholar 

  5. Fan D, Zhu X, Zhai Q, Wang E, Dong S (2016) Polydopamine nanotubes as an effective fluorescent quencher for highly sensitive and selective detection of biomolecules assisted with exonuclease III amplification. Anal Chem 88:9158–9165

    Article  CAS  Google Scholar 

  6. Peng X, Liang WB, Wen ZB, Xiong CY, Zheng YN, Chai Y, Yuan R (2018) Ultrasensitive fluorescent assay based on a rolling-circle-amplification-assisted multisite-strand-displacement-reaction signal-amplification strategy. Anal Chem 90:7474–7479

    Article  CAS  Google Scholar 

  7. Guo Q, Yang X, Wang K, Tan W, Li W, Tang H, Li H (2009) Sensitive fluorescence detection of nucleic acids based on isothermal circular strand-displacement polymerization reaction. Nucleic Acids Res 37:20–25

    Article  Google Scholar 

  8. Ma F, Liu M, Tang B, Zhang C (2017) Rapid and sensitive quantification of microRNAs by isothermal helicase-dependent amplification. Anal Chem 89:6182–6187

    Article  CAS  Google Scholar 

  9. Barreda-García S, González-Álvarez MJ, Delos Santos-Álvarez N, Palacios-Gutiérrez JJ, Miranda-Ordieres AJ, Lobo-Castañón MJ (2015) Attomolar quantitation of mycobacterium tuberculosis by asymmetric helicase-dependent isothermal DNA-amplification and electrochemical detection. Biosens Bioelectron 68:122–128

    Article  Google Scholar 

  10. Mudiyanselage APKKK, Yu Q, Leon-Duque MA, Zhao B, Wu R, You M (2018) Genetically encoded catalytic hairpin assembly for sensitive RNA imaging in live cells. J Am Chem Soc 140:8739–8745

    Article  Google Scholar 

  11. Liu C, Chen C, Li S, Dong H, Dai W, Xu T, Liu Y, Yang F, Zhang X (2018)Target-triggered catalytic hairpin assembly-induced core−satellite nanostructures for high-sensitive “off-to-on” SERS detection of intracellular microRNA. Anal Chem 90:10591–10599

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  13. Huang J, Wang H, Yang X, Quan K, Yang Y, Ying L, Xie N, Ou M, Wang K (2016) Fluorescence resonance energy transfer-based hybridization chain reaction for in situ visualization of tumor-related mRNA. Chem Sci 7:3829–3835

    Article  CAS  Google Scholar 

  14. Liu N, Jiang Y, Zhou Y, Xia F, Guo W, Jiang L (2013)Two-way nanopore sensing of sequence-specific oligonucleotides and small-molecule targets in complex matrices using integrated DNA supersandwich structures. Angew Chem Int Ed 52:2007–2011

    Article  CAS  Google Scholar 

  15. Jiang Y, Liu N, Guo W, Xia F, Jiang L (2012)Highly-efficient gating of solid-state nanochannels by DNA supersandwich structure containing ATP aptamers: a nanofluidic IMPLICATION logic device. J Am Chem Soc 134:15395–15401

    Article  CAS  Google Scholar 

  16. Xia F, White RJ, Zuo X, Patterson A, Xiao Y, Kang D, Gong X, Plaxco KW, Heeger AJ (2010) An electrochemical supersandwich assay for sensitive and selective DNA detection in complex matrices. J Am Chem Soc 132:14346–14348

    Article  CAS  Google Scholar 

  17. Xu L, Shen X, Li B, Zhu C, Zhou X (2017)G-quadruplex based Exo III-assisted signal amplification aptasensor for the colorimetric detection of adenosine. Anal Chim Acta 980:58–64

    Article  CAS  Google Scholar 

  18. Miao P, Tang Y, Wang B, Yin J, Ning L (2015) Signal amplification by enzymatic tools for nucleic acids. Trends Anal Chem 67:1–15

    Article  CAS  Google Scholar 

  19. Gerasimova YV, Kolpashchikov DM (2014)Enzyme-assisted target recycling (EATR) for nucleic acid detection. Chem Soc Rev 43:6405–6438

    Article  CAS  Google Scholar 

  20. Zhao Y, Chen F, Li Q, Wang L, Fan C (2015) Isothermal amplification of nucleic acids. Chem Rev 115:12491–12545

    Article  CAS  Google Scholar 

  21. Xia Y, Zhang R, Wang Z, Tian J, Chen X (2017) Recent advances in high-performance fluorescent and bioluminescent RNA imaging probes. Chem Soc Rev 46:2824–2843

    Article  CAS  Google Scholar 

  22. Zhu Y, Wang H, Wang L, Zhu J, Jiang W (2016) Cascade signal amplification based on copper nanoparticle-reported rolling circle amplification for ultrasensitive electrochemical detection of the prostate cancer biomarker. ACS Appl Mater Interfaces 8:2573–2581

    Article  CAS  Google Scholar 

  23. Li C, Wang H, Shen J, Tang B (2015) Cyclometalated iridium complex-based label-free photoelectrochemical biosensor for DNA detection by hybridization chain reaction amplification. Anal Chem 87:4283–4291

    Article  CAS  Google Scholar 

  24. Zheng J, Li N, Li C, Wang X, Liu Y, Mao G, Ji X, He Z (2018) A nonenzymatic DNA nanomachine for biomolecular detection by target recycling of hairpin DNA cascade amplification. Biosens Bioelectron 107:40–46

    Article  CAS  Google Scholar 

  25. Liu S, Cheng C, Gong H, Wang L (2015) Programmable Mg2+-dependent DNAzyme switch by the catalytic hairpin DNA assembly for dual-signal amplification toward homogeneous analysis of protein and DNA. Chem Commun 51:7364–7367

    Article  CAS  Google Scholar 

  26. Yin BC, Ma JL, Le HN, Wang S, Xu Z, Ye BC (2014) A new mode to light up an adjacent DNA-scaffolded silver probe pair and its application for specific DNA detection. Chem Commun 50:15991–15994

    Article  CAS  Google Scholar 

  27. Ren W, Liu H, Yang W, Fan Y, Yang L, Wang Y, Liu C, Li Z (2013) A cytometric bead assay for sensitive DNA detection based on enzyme-free signal amplification of hybridization chain reaction. Biosens Bioelectron 49:380–386

    Article  CAS  Google Scholar 

  28. Wang S, Yang F, Jin D, Dai Q, Tu J, Liu Y, Ning Y, Zhang GJ (2017) Toehold mediated one-step conformation-switchable “signal-on” electrochemical DNA sensing enhanced with homogeneous enzymatic amplification. Anal Chem 89:5349–5356

    Article  CAS  Google Scholar 

  29. Peng Y, Li D, Yuan R, Xiang Y (2018) A catalytic and dual recycling amplification ATP sensor based on target-driven allosteric structure switching of aptamer beacons. Biosens Bioelectron 105:1–5

    Article  CAS  Google Scholar 

  30. Li X, Yang J, Xie J, Jiang B, Yuan R, Xiang Y (2018) Cascaded signal amplification via target-triggered formation of aptazyme for sensitive electrochemical detection of ATP. Biosens Bioelectron 102:296–300

    Article  CAS  Google Scholar 

  31. Li X, Peng Y, Chai Y, Yuan R, Xiang Y (2016) A target responsive aptamer machine for label-free and sensitive non-enzymatic recycling amplification detection of ATP. Chem Commun 52:3673–3676

    Article  CAS  Google Scholar 

  32. Zhang T, Peng Y, Yuan R, Xiang Y (2018)Target-catalyzed assembly formation of metal-ion dependent DNAzymes for non-enzymatic and label-free amplified ATP detection. Sensors Actuators B Chem 273:70–75

    Article  CAS  Google Scholar 

  33. Li W, Sun J, Wang H, Wang L, Jiang W (2018) Multifunctional aptamer probe mediated cascade amplification for label-free detection of adenosine. Sensors Actuators B Chem 260:581–586

    Article  CAS  Google Scholar 

  34. Song W, Zhang Q, Xie X, Zhang S (2014) Fluorescence aptameric sensor for isothermal circular strand-displacement polymerization amplification detection of adenosine triphosphate. Biosens Bioelectron 61:51–56

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by the National Natural Science Foundation of China (21505114) and Xinxiang Innovative Technology Team (CXTD17004).

Author information

Authors and Affiliations

  1. School of Pharmacy, Xinxiang Medical University, Xinxiang, Henan, 453003, People’s Republic of China

    Yufei Liu, Jingfang Shangguan, Ningning He, Haixia Lv, Qianqian Wang & Suping Bai

Authors
  1. Yufei Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jingfang Shangguan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ningning He
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Haixia Lv
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Qianqian Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Suping Bai
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yufei Liu.

Ethics declarations

Conflict of interests

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

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

ESM 1

(DOCX 128 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Liu, Y., Shangguan, J., He, N. et al. Fluorometric determination of ssDNA based on functionalized magnetic microparticles and DNA supersandwich self-assemblies. Microchim Acta 186, 707 (2019). https://doi.org/10.1007/s00604-019-3865-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00604-019-3865-z

Keywords

Search

Navigation