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Toehold integrated molecular beacon system for a versatile non-enzymatic application

  • Zhenping Liu
  • Yiyun Wang
  • Xuchu Wang
  • Weiwei Liu
  • Yibei Dai
  • Pan Yu
  • Zhaoping Liao
  • Ying Ping
  • Zhihua Tao
Paper in Forefront
  • 18 Downloads

Abstract

A molecular beacon (MB) is an oligonucleotide hybridization probe with a hairpin-shaped structure that leads to specific and instantaneous nucleic acid hybridization, enabling a variety of applications. However, integration of additional module sequences interferes with the performance of MBs and increases the complexity of sequence design. Herein, we develop and characterize a toehold integrated molecular beacon (ToMB) strategy for nucleic acid hybridization, where the reaction rate can be flexibly regulated by a target-induced MB conformational switch. Using this basic mechanism, the ToMB is capable of identifying nucleic acids with high specificity and a wider linearity range compared with the conventional molecular beacon system. We further applied the ToMB to the construction of a hybridization chain reaction system and a basic OR logic gate VJHto explore its programmability and versatility. Our results strongly suggest that the novel ToMB can act as a powerful nano-module to construct universal and multifunctional biosensors or molecular computations.

Graphical abstract

Molecular beacon is employed as a flexible and switchable spacer to control the toehold-mediated strand displacement reaction.

Keywords

Molecular beacon Toehold-mediated strand displacement reaction Nucleic acid hybridization 

Notes

Acknowledgments

We thank the Clinical Research Center from the Second Affiliated Hospital of Zhejiang University School of Medicine for essential technical supports. We thank the American Journal Experts (AJE) for English language editing.

Funding

This study was supported by grant from Natural Science Foundation of Zhejiang Province (Grant nos. LY14H200002, LY15H200002, and LY16H160023).

Compliance with ethical standards

Conflicts of interest

The authors declare that they have no conflicts of interest.

Supplementary material

216_2018_1340_MOESM1_ESM.pdf (552 kb)
ESM 1 (PDF 551 kb)

References

  1. 1.
    Tyagi S, Kramer FR. Molecular beacons: probes that fluoresce upon hybridization. Nat Biotechnol. 1996;14(3):303–8.  https://doi.org/10.1038/nbt0396-303.CrossRefPubMedGoogle Scholar
  2. 2.
    Li F, Huang Y, Yang Q, Zhong Z, Li D, Wang L, et al. A graphene-enhanced molecular beacon for homogeneous DNA detection. Nanoscale. 2010;2(6):1021–6.  https://doi.org/10.1039/b9nr00401g.CrossRefPubMedGoogle Scholar
  3. 3.
    Diaz LA Jr, Bardelli A. Liquid biopsies: genotyping circulating tumor DNA. J Clin Oncol. 2014;32(6):579–86.  https://doi.org/10.1200/JCO.2012.45.2011.CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Connolly AR, Trau M. Isothermal detection of DNA by beacon-assisted detection amplification. Angew Chem Int Ed Engl. 2010;49(15):2720–3.  https://doi.org/10.1002/anie.200906992.CrossRefPubMedGoogle Scholar
  5. 5.
    Xu J, Dong H, Shen W, He S, Li H, Lu Y, et al. New molecular beacon for p53 gene point mutation and significant potential in serving as the polymerization primer. Biosens Bioelectron. 2015;66:504–11.  https://doi.org/10.1016/j.bios.2014.12.008.CrossRefPubMedGoogle Scholar
  6. 6.
    Zhang J, Li C, Zhi X, Ramon GA, Liu Y, Zhang C, et al. Hairpin DNA-templated silver nanoclusters as novel beacons in strand displacement amplification for microRNA detection. Anal Chem. 2016;88(2):1294–302.  https://doi.org/10.1021/acs.analchem.5b03729. CrossRefPubMedGoogle Scholar
  7. 7.
    Kong RM, Zhang XB, Zhang LL, Huang Y, Lu DQ, Tan W, et al. Molecular beacon-based junction probes for efficient detection of nucleic acids via a true target-triggered enzymatic recycling amplification. Anal Chem. 2011;83(1):14–7.  https://doi.org/10.1021/ac1025072.CrossRefPubMedGoogle Scholar
  8. 8.
    Huang J, Wu J, Li Z. Molecular beacon-based enzyme-free strategy for amplified DNA detection. Biosens Bioelectron. 2016;79:758–62.  https://doi.org/10.1016/j.bios.2016.01.014.CrossRefPubMedGoogle Scholar
  9. 9.
    Qian Y, Wang C, Gao F. Enzyme-free amplification for sensitive electrochemical detection of DNA via target-catalyzed hairpin assembly assisted current change. Talanta. 2014;130:33–8.  https://doi.org/10.1016/j.talanta.2014.06.051.CrossRefPubMedGoogle Scholar
  10. 10.
    Zheng J, Li N, Li C, Wang X, Liu Y, Mao G, et al. A nonenzymatic DNA nanomachine for biomolecular detection by target recycling of hairpin DNA cascade amplification. Biosens Bioelectron. 2018;107:40–6.  https://doi.org/10.1016/j.bios.2018.01.054.CrossRefPubMedGoogle Scholar
  11. 11.
    Jung C, Allen PB, Ellington AD. A simple, cleated DNA Walker that hangs on to surfaces. ACS Nano. 2017;11(8):8047–54.  https://doi.org/10.1021/acsnano.7b02693.CrossRefPubMedGoogle Scholar
  12. 12.
    Zhang DY, Seelig G. Dynamic DNA nanotechnology using strand-displacement reactions. Nat Chem. 2011;3(2):103–13.  https://doi.org/10.1038/nchem.957.CrossRefGoogle Scholar
  13. 13.
    Jung C, Ellington AD. Diagnostic applications of nucleic acid circuits. Acc Chem Res. 2014;47(6):1825–35.  https://doi.org/10.1021/ar500059c.CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Zhang DY, Turberfield AJ, Yurke B, Winfree E. Engineering entropy-driven reactions and networks catalyzed by DNA. Science. 2007;318(5853):1121–5.  https://doi.org/10.1126/science.1148532.CrossRefPubMedGoogle Scholar
  15. 15.
    Yin P, Choi HM, Calvert CR, Pierce NA. Programming biomolecular self-assembly pathways. Nature. 2008;451(7176):318–22.  https://doi.org/10.1038/nature06451.CrossRefGoogle Scholar
  16. 16.
    Wu C, Cansiz S, Zhang L, Teng IT, Qiu L, Li J, et al. A nonenzymatic hairpin DNA cascade reaction provides high signal gain of mRNA imaging inside live cells. J Am Chem Soc. 2015;137(15):4900–3.  https://doi.org/10.1021/jacs.5b00542. CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Choi HM, Chang JY, Trinh le A, Padilla JE, Fraser SE, Pierce NA. Programmable in situ amplification for multiplexed imaging of mRNA expression. Nat Biotechnol. 2010;28(11):1208–12.  https://doi.org/10.1038/nbt.1692.CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Bi S, Chen M, Jia X, Dong Y, Wang Z. Hyperbranched hybridization chain reaction for triggered signal amplification and concatenated logic circuits. Angew Chem Int Ed Engl. 2015;54(28):8144–8.  https://doi.org/10.1002/anie.201501457.CrossRefPubMedGoogle Scholar
  19. 19.
    Xuan F, Hsing IM. Triggering hairpin-free chain-branching growth of fluorescent DNA dendrimers for nonlinear hybridization chain reaction. J Am Chem Soc. 2014;136(28):9810–3.  https://doi.org/10.1021/ja502904s.CrossRefPubMedGoogle Scholar
  20. 20.
    Qian L, Winfree E. Scaling up digital circuit computation with DNA strand displacement cascades. Science. 2011;332(6034):1196–201.  https://doi.org/10.1126/science.1200520.CrossRefGoogle Scholar
  21. 21.
    Pei R, Matamoros E, Liu M, Stefanovic D, Stojanovic MN. Training a molecular automaton to play a game. Nat Nanotechnol. 2010;5(11):773–7.  https://doi.org/10.1038/nnano.2010.194.CrossRefPubMedGoogle Scholar
  22. 22.
    Zhang DY, Winfree E. Control of DNA strand displacement kinetics using toehold exchange. J Am Chem Soc. 2009;131(47):17303–14.  https://doi.org/10.1021/ja906987s.CrossRefPubMedGoogle Scholar
  23. 23.
    Srinivas N, Ouldridge TE, Sulc P, Schaeffer JM, Yurke B, Louis AA, et al. On the biophysics and kinetics of toehold-mediated DNA strand displacement. Nucleic Acids Res. 2013;41(22):10641–58.  https://doi.org/10.1093/nar/gkt801.CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Genot AJ, Zhang DY, Bath J, Turberfield AJ. Remote toehold: a mechanism for flexible control of DNA hybridization kinetics. J Am Chem Soc. 2011;133(7):2177–82.  https://doi.org/10.1021/ja1073239.CrossRefPubMedGoogle Scholar
  25. 25.
    Li F, Lin Y, Le XC. Binding-induced formation of DNA three-way junctions and its application to protein detection and DNA strand displacement. Anal Chem. 2013;85(22):10835–41.  https://doi.org/10.1021/ac402179a.CrossRefPubMedGoogle Scholar
  26. 26.
    Zadeh JN, Steenberg CD, Bois JS, Wolfe BR, Pierce MB, Khan AR, et al. NUPACK: analysis and design of nucleic acid systems. J Comput Chem. 2011;32(1):170–3.  https://doi.org/10.1002/jcc.21596.CrossRefGoogle Scholar
  27. 27.
    Wang X, Liu W, Yin B, Yu P, Duan X, Liao Z, et al. Colorimetric detection of gene transcript by target-induced three-way junction formation. Talanta. 2016;158:1–5.  https://doi.org/10.1016/j.talanta.2016.05.039. CrossRefPubMedGoogle Scholar
  28. 28.
    Tsourkas A, Behlke MA, Rose SD, Bao G. Hybridization kinetics and thermodynamics of molecular beacons. Nucleic Acids Res. 2003;31(4):1319–30.CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Dirks RM, Pierce NA. Triggered amplification by hybridization chain reaction. Proc Natl Acad Sci U S A. 2004;101(43):15275–8.  https://doi.org/10.1073/pnas.0407024101. CrossRefPubMedPubMedCentralGoogle Scholar
  30. 30.
    Liu X, Yan Z, Sun Y, Ren J, Qu X. A label-free ratiometric electrochemical DNA sensor for monitoring intracellular redox homeostasis. Chem Commun (Camb). 2017;53(46):6215–8.  https://doi.org/10.1039/c7cc03239k.CrossRefGoogle Scholar
  31. 31.
    Wang YM, Wu Z, Liu SJ, Chu X. Structure-switching aptamer triggering hybridization chain reaction on the cell surface for activatable theranostics. Anal Chem. 2015;87(13):6470–4.  https://doi.org/10.1021/acs.analchem.5b01634.CrossRefPubMedGoogle Scholar
  32. 32.
    Huang R, Liao Y, Zhou X, Xing D. Toehold-mediated nonenzymatic amplification circuit on graphene oxide fluorescence switching platform for sensitive and homogeneous microRNA detection. Anal Chim Acta. 2015;888:162–72.  https://doi.org/10.1016/j.aca.2015.07.041.CrossRefPubMedGoogle Scholar
  33. 33.
    Chen HG, Ren W, Jia J, Feng J, Gao ZF, Li NB, et al. Fluorometric detection of mutant DNA oligonucleotide based on toehold strand displacement-driving target recycling strategy and exonuclease III-assisted suppression. Biosens Bioelectron. 2016;77:40–5.  https://doi.org/10.1016/j.bios.2015.09.027.CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Zhenping Liu
    • 1
  • Yiyun Wang
    • 1
  • Xuchu Wang
    • 2
  • Weiwei Liu
    • 2
  • Yibei Dai
    • 2
  • Pan Yu
    • 2
  • Zhaoping Liao
    • 3
  • Ying Ping
    • 2
  • Zhihua Tao
    • 1
    • 2
  1. 1.Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life SciencesWenzhou Medical UniversityWenzhouChina
  2. 2.Department of Laboratory Medicinethe Second Affiliated Hospital of Zhejiang University School of MedicineHangzhouChina
  3. 3.Department of Transfusionthe Second Affiliated Hospital of Zhejiang University School of MedicineHangzhouChina

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