Skip to main content
SpringerLink
Log in

Colorimetric detection of DNA by using target catalyzed DNA nanostructure assembly and unmodified gold nanoparticles

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

Abstract

The authors describe a strategy for colorimetric detection of DNA. It is making use of a target catalyzed DNA nanostructure assembly and gold nanoparticles. The assay comprises the following steps: (a) A programmed DNA nanostructure is assembled from three auxiliary hairpin structure DNAs and the single stranded DNA (ssDNA; the target/analyte); (b) in the presence of target DNA, these three hairpin DNAs are opened, thereby activating a catalytic self-assembly process via a target assisted toe-hold strand displacement reaction; (c) The formed DNA nanostructures are mixed with gold nanoparticles. As the DNA nanostructure is less stabilized without ssDNA sticky ends, it cannot prevent the gold nanoparticles (AuNPs) to undergo salt-induced aggregation which is accompanied by a color change from purple to blue; (d) The color change of the colloid solution can be read out with bare eyes or instrumentally. The detection limit by using UV–vis spectrometry is 0.6 pM of target DNA. This is comparable to previously AuNP-based methods. Thus, this assay provides free modification detection based on DNA nanostructure without sophisticated procedures. Conceivably, the method can be applied to numerous other DNA targets.

Schematic of a method for colorimetric detection of DNA by using target catalyzed DNA nanostructure assembly and unmodified gold nanoparticles. This system is highly specific and sensitive, with a detection limit of 0.6 pM target DNA.

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

Similar content being viewed by others

References

  1. Bell NA, Keyser UF (2016) Digitally encoded DNA nanostructures for multiplexed, single-molecule protein sensing with nanopores. Nat Nanotechnol 11(7):645–651

    Article  CAS  Google Scholar 

  2. Edwardson TG, Lau KL, Bousmail D, Serpell CJ, Sleiman HF (2016) Transfer of molecular recognition information from DNA nanostructures to gold nanoparticles. Nat Chem 8(2):162–170

    CAS  Google Scholar 

  3. Ding X, Wang Y, Cheng W, Mo F, Sang Y, Xu L, Ding S (2017) Aptamer based electrochemical adenosine triphosphate assay based on a target-induced dendritic DNA nanoassembly. Microchimica Acta 184(2):431–438

  4. Kim M-G, Park JY, Shim G, Choi H-G, Oh Y-K (2015) Biomimetic DNA nanoballs for oligonucleotide delivery. Biomaterials 62:155–163

    Article  CAS  Google Scholar 

  5. Yang Y, Goetzfried MA, Hidaka K, You M, Tan W, Sugiyama H, Endo M (2015) Direct visualization of walking motions of a photocontrolled nanomachine on the DNA nanostructure. Nano Lett 15(10):6672–6676

    Article  CAS  Google Scholar 

  6. Lee JB, Roh YH, Um SH, Funabashi H, Cheng W, Cha JJ, Kiatwuthinon P, Muller DA, Luo D (2009) Multifunctional nanoarchitectures from DNA-based ABC monomers. Nat Nanotechnol 4(7):430–436

    Article  CAS  Google Scholar 

  7. Tan SJ, Campolongo MJ, Luo D, Cheng W (2011) Building plasmonic nanostructures with DNA. Nat Nanotechnol 6(5):268–276

    Article  CAS  Google Scholar 

  8. Meng H-M, Liu H, Kuai H, Peng R, Mo L, Zhang X-B (2016) Aptamer-integrated DNA nanostructures for biosensing, bioimaging and cancer therapy. Chem Soc Rev 45(9):2583–2602

    Article  CAS  Google Scholar 

  9. Li Y, Cu YTH, Luo D (2005) Multiplexed detection of pathogen DNA with DNA-based fluorescence nanobarcodes. Nat Biotechnol 23(7):885–889

    Article  CAS  Google Scholar 

  10. Marín AG, García-Mendiola T, Bernabeu CN, Hernández MJ, Piqueras J, Pau JL, Pariente F, Lorenzo E (2016) Gallium plasmonic nanoparticles for label-free DNA and single nucleotide polymorphism sensing. Nanoscale 8(18):9842–9851

    Article  Google Scholar 

  11. Peterson EM, Manhart MW, Harris JM (2016) Competitive assays of label-free DNA hybridization with single-molecule fluorescence imaging detection. Anal Chem 88(12):6410–6417

    Article  CAS  Google Scholar 

  12. Zhao C, Liu L, Ge J, He Y (2017) Ultrasensitive determination for flavin coenzyme by using a ZnO nanorod photoelectrode in a four-electrode system. Microchim Acta 184(7):2333–2339

    Article  CAS  Google Scholar 

  13. Ning Y, Wei K, Cheng L, Hu J, Xiang Q (2017) Fluorometric aptamer based determination of adenosine triphosphate based on deoxyribonuclease I-aided target recycling and signal amplification using graphene oxide as a quencher. Microchim Acta 184(7):1847–1854

    Article  CAS  Google Scholar 

  14. Saha K, Agasti SS, Kim C, Li X, Rotello VM (2012) Gold nanoparticles in chemical and biological sensing. Chem Rev 112(5):2739–2779

    Article  CAS  Google Scholar 

  15. Elghanian R, Storhoff JJ, Mucic RC, Letsinger RL, Mirkin CA (1997) Selective colorimetric detection of polynucleotides based on the distance-dependent optical properties of gold nanoparticles. Science 277(5329):1078–1081

    Article  CAS  Google Scholar 

  16. Chang C-C, Chen C-P, Chen C-Y, Lin C-W (2016) DNA base-stacking assay utilizing catalytic hairpin assembly-induced gold nanoparticle aggregation for colorimetric protein sensing. Chem Commun 52(22):4167–4170

    Article  CAS  Google Scholar 

  17. Ma C, Wu Z, Wang W, Jiang Q, Shi C (2015) Three-dimensional DNA nanostructures for colorimetric assay of nucleic acids. J Mater Chem B 3(14):2853–2857

    Article  CAS  Google Scholar 

  18. Chang C-C, Chen C-Y, Chuang T-L, Wu T-H, Wei S-C, Liao H, Lin C-W (2016) Aptamer-based colorimetric detection of proteins using a branched DNA cascade amplification strategy and unmodified gold nanoparticles. Biosens Bioelectron 78:200–205

    Article  CAS  Google Scholar 

  19. Grabar KC, Smith PC, Musick MD, Davis JA, Walter DG, Jackson MA, Guthrie AP, Natan MJ (1996) Kinetic control of interparticle spacing in Au colloid-based surfaces: rational nanometer-scale architecture. J ACS 118(5):1148–1153

    CAS  Google Scholar 

  20. Yurke B, Turberfield AJ, Mills AP, Simmel FC, Neumann JL (2000) A DNA-fuelled molecular machine made of DNA. Nature 406(6796):605–608

    Article  CAS  Google Scholar 

  21. Zhang Z, Zeng D, Ma H, Feng G, Hu J, He L, Li C, Fan C (2010) A DNA-origami chip platform for label-free SNP genotyping using toehold-mediated strand displacement. Small 6(17):1854–1858

    Article  CAS  Google Scholar 

  22. Li X, Guo J, Zhai Q, Xia J, Yi G (2016) Ultrasensitive electrochemical biosensor for specific detection of DNA based on molecular beacon mediated circular strand displacement polymerization and hyperbranched rolling circle amplification. Anal Chim Acta 934:52–58

    Article  CAS  Google Scholar 

  23. Zhou L, Wang J, Chen Z, Li J, Wang T, Zhang Z, Xie G (2017) A universal electrochemical biosensor for the highly sensitive determination of microRNAs based on isothermal target recycling amplification and a DNA signal transducer triggered reaction. Microchim Acta 184:1–9

    Article  Google Scholar 

  24. Zhou L, Wang J, Chen Z, Li J, Wang T, Zhang Z, Xie G (2017) A universal electrochemical biosensor for the highly sensitive determination of microRNAs based on isothermal target recycling amplification and a DNA signal transducer triggered reaction. Microchim Acta 184(5):1305–1313

    Article  CAS  Google Scholar 

  25. Wen D, Liu W, Herrmann AK, Haubold D, Holzschuh M, Simon F, Eychmüller A (2016) Simple and sensitive colorimetric detection of dopamine based on assembly of Cyclodextrin-modified Au nanoparticles. Small 12(18):2439–2442

    Article  CAS  Google Scholar 

  26. Chen L, Wu N, Sun B, Su H, Ai S (2013) Colorimetric detection of peroxynitrite-induced DNA damage using gold nanoparticles, and on the scavenging effects of antioxidants. Microchim Acta 180(7–8):573–580

    Article  CAS  Google Scholar 

  27. He H, Dai J, Duan Z, Meng Y, Zhou C, Long Y, Zheng B, Du J, Guo Y, Xiao D (2016) Target-catalyzed autonomous assembly of dendrimer-like DNA nanostructures for enzyme-free and signal amplified colorimetric nucleic acids detection. Biosens Bioelectron 86:985–989

    Article  CAS  Google Scholar 

  28. Liu P, Yang X, Sun S, Wang Q, Wang K, Huang J, Liu J, He L (2013) Enzyme-free colorimetric detection of DNA by using gold nanoparticles and hybridization chain reaction amplification. Anal Chem 85(16):7689–7695

    Article  CAS  Google Scholar 

  29. Dai J, He H, Duan Z, Zhou C, Long Y, Zheng B, Du J, Guo Y, Xiao D (2016) Target-triggered autonomous assembly of DNA polymer chains and its application in colorimetric nucleic acid detection. J Mater Chem B 4(19):3191–3194

    Article  CAS  Google Scholar 

  30. Ma C, Wang W, Mulchandani A, Shi C (2014) A simple colorimetric DNA detection by target-induced hybridization chain reaction for isothermal signal amplification. Anal Biochem 457:19–23

    Article  CAS  Google Scholar 

  31. McVey C, Huang F, Elliott C, Cao C (2017) Endonuclease controlled aggregation of gold nanoparticles for the ultrasensitive detection of pathogenic bacterial DNA. Biosens Bioelectron 92:502–508

    Article  CAS  Google Scholar 

  32. Yang Y, Li C, Yin L, Liu M, Wang Z, Shu Y, Li G (2014) Enhanced charge transfer by gold nanoparticle at DNA modified electrode and its application to label-free DNA detection. ACS Appl Mater Interface 6(10):7579–7584

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We gratefully acknowledge support from the National Natural Science Foundation of China (NO. 41506094) and National Key Basic Research Program of China (2014CB643304). Project funded by China Postdoctoral Science Foundation (2016 M602199). AoShan Talent Program Supported by Qingdao National Laboratory for Marine Science and Technology.

Author information

Authors and Affiliations

  1. Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China

    Yan Zeng, Dun Zhang, Peng Qi & Laibao Zheng

  2. University of the Chinese Academy of Science, 19 (Jia) Yuquan Road, Beijing, 100039, China

    Laibao Zheng

Authors
  1. Yan Zeng
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Dun Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Peng Qi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Laibao Zheng
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Dun Zhang.

Ethics declarations

The authors declare no competing financial interest

Electronic supplementary material

ESM 1

(DOC 801 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zeng, Y., Zhang, D., Qi, P. et al. Colorimetric detection of DNA by using target catalyzed DNA nanostructure assembly and unmodified gold nanoparticles. Microchim Acta 184, 4809–4815 (2017). https://doi.org/10.1007/s00604-017-2463-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00604-017-2463-1

Keywords

Search

Navigation