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Digital triplex DNA assay based on plasmonic nanocrystals

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Abstract

A new analytical method has been developed to detect three kinds of DNA simultaneously based on magnetic beads and color-encoded plasmonic nanocrystals. Magnetic beads modified with capture DNA are employed to collect the specific target DNA, and color-encoded plasmonic nanocrystals are applied to signal the target through DNA hybridization. As a proof of concept, three types of representative metal nanocrystals of gold nanoparticle (AuNP), gold nanorod (AuNR), and gold/silver nanoparticle (Au/AgNP) were employed to signal three dissimilar virus-related protective antigen genes, Ebola virus (EV), Variola virus (VV), and Bacillus anthracis (BA), respectively. Detection limits of 0.5–3 fM were obtained showing the high sensitivity for DNA detection. The microscopic discrimination of the encoded nanoparticles allows simple, rapid, accurate, and cost-effective detection of multiple DNA molecules, indicative of the potential in practical applications.

Development of a novel digital triplex DNA assay based on single-countable color-encoded plasmonic nanocrystals

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References

  1. Lockhart DJ, Winzeler EA, Lockhart DJ, Winzeleer EA. Genomics, gene expression and DNA arrays. Nature. 2000;405(6788):827–36.

    Article  CAS  Google Scholar 

  2. Qavi AJ, Bailey RC. Multiplexed detection and label-free quantitation of microRNAs using arrays of silicon photonic microring resonators. Angew Chem. 2010;49(27):4712–5.

    Article  Google Scholar 

  3. Zhang M, Liu YQ, Yu CY, Yin BC, Ye BC. Multiplexed detection of microRNAs by tuning DNA-scaffolded silver nanoclusters. Analyst. 2013;138(17):4812–7.

    Article  CAS  Google Scholar 

  4. Zheng W, He L. Label-free, real-time multiplexed DNA detection using fluorescent conjugated polymers. J Am Chem Soc. 2009;131(10):3432–3.

    Article  CAS  Google Scholar 

  5. Yang Y. Sensitive fluorescent sensing for DNA assay. TrAC Trends Anal Chem. 2010;29(9):980–1003.

    Article  CAS  Google Scholar 

  6. Cao YWC, Jin R, Mirkin CA. Nanoparticles with Raman spectroscopic fingerprints for DNA and RNA detection. Science. 2002;297(5586):1536–40.

    Article  CAS  Google Scholar 

  7. Zhang Z, Wen Y, Ma Y, Luo J, Jiang L, Song Y. Mixed DNA-functionalized nanoparticle probes for surface-enhanced Raman scattering-based multiplex DNA detection. Chem Commun. 2011;47(26):7407–9.

    Article  CAS  Google Scholar 

  8. Zhang CY, Hu J. Single quantum dot-based nanosensor for multiple DNA detection. Anal Chem. 2010;82(5):1921–7.

    Article  CAS  Google Scholar 

  9. Li L, Wang X, Zhang X, Wang J, Jin W. Single-cell multiple gene expression analysis based on single-molecule-detection microarray assay for multi-DNA determination. Anal Chim Acta. 2015;854C:122–8.

    Article  Google Scholar 

  10. Mancuso M, Jiang L, Cesarman E, Erickson D. Multiplexed colorimetric detection of Kaposi’s sarcoma associated herpes virus and Bartonella DNA using gold and silver nanoparticles. Nano. 2013;5(4):1678–86.

    CAS  Google Scholar 

  11. Wang C, Irudayaraj J. Gold nanorod probes for the detection of multiple pathogens. Small. 2008;4(12):2204–8.

    Article  CAS  Google Scholar 

  12. Guo Y, Wang Z, Qu W, Shao H, Jiang X. Colorimetric detection of mercury, lead and copper ions simultaneously using protein-functionalized gold nanoparticles. Biosens Bioelectron. 2011;26(10):4064–9.

    Article  CAS  Google Scholar 

  13. Han G, Zhang S, Xing Z, Zhang X. Absolute and relative quantification of multiplex DNA assays based on an elemental labeling strategy. Angew Chem Int Ed. 2013;52(5):1466–71.

    Article  CAS  Google Scholar 

  14. Zhang S, Han G, Xing Z, Zhang S, Zhang X. Multiplex DNA assay based on nanoparticle probes by single particle inductively coupled plasma mass spectrometry. Anal Chem. 2014;86(7):3541–7.

    Article  CAS  Google Scholar 

  15. Sepúlveda B, Angelomé PC, Lechuga LM, Liz-Marzán LM. LSPR-based nanobiosensors. Nano Today. 2009;4(3):244–51.

    Article  Google Scholar 

  16. Khlebtsov NG, Dykman LA. Optical properties and biomedical applications of plasmonic nanoparticles. J Quant Spectrosc Radiat Transf. 2010;111(111):1–35.

    Article  CAS  Google Scholar 

  17. Sönnichsen C, Alivisatos AP. Gold nanorods as novel nonbleaching plasmon-based orientation sensors for polarized single-particle microscopy. Nano Lett. 2005;5(2):301–4.

    Article  Google Scholar 

  18. Hao J, Xiong B, Cheng XD, He Y, Yeung ES. High-throughput sulfide sensing with colorimetric analysis of single Au-Ag core-shell nanoparticles. Anal Chem. 2014;86(10):4663–7.

    Article  CAS  Google Scholar 

  19. Saha K, Agasti SS, Kim C, Li X, Rotello VM. Gold nanoparticles in chemical and biological sensing. Chem Rev. 2012;112(5):2739–79.

    Article  CAS  Google Scholar 

  20. Dreaden EC, Alkilany AM, Huang X, Murphy CJ, Elsayed MA. The golden age: gold nanoparticles for biomedicine. Chem Soc Rev. 2011;41(7):2740–79.

    Article  Google Scholar 

  21. Tang D, Yu Y, Niessner R, Miró M, Knopp D. Magnetic bead-based fluorescence immunoassay for aflatoxin B1 in food using biofunctionalized rhodamine B-doped silica nanoparticles. Analyst. 2010;135(10):2661–7.

    Article  CAS  Google Scholar 

  22. Xiang DS, Zeng GP, He Z. Magnetic microparticle-based multiplexed DNA detection with biobarcoded quantum dot probes. Biosens Bioelectron. 2011;26(11):4405–10.

    Article  CAS  Google Scholar 

  23. Basilevsky MV, Shamov AG. Topical review: Functionalisation of magnetic nanoparticles for applications in biomedicine. J Phys D Appl Phys. 2003;36(36):R198–R206(9).

    Google Scholar 

  24. Nakagawa T, Seino S, Yamamoto TA, Abe M. Biomedical applications of magnetic beads. Teion Kogaku. 2010;45(10):436–43.

    Article  CAS  Google Scholar 

  25. Nam JM, Thaxton CS, Mirkin CA. Nanoparticle-based bio-bar codes for the ultrasensitive detection of proteins. Science. 2003;301(5641):1884–6.

    Article  CAS  Google Scholar 

  26. Shad Thaxton C, Hill HD, Georganopoulou DG, Stoeva SI, Mirkin CA. A bio-bar-code assay based upon dithiothreitol-induced oligonucleotide release. Anal Chem. 2006;77(24):8174–8.

    Article  Google Scholar 

  27. Duan J, Park K, Maccuspie RI, Vaia RA, Pachter R. Optical properties of rod like metallic nanostructures: insight from theory and experiment. J Phys Chem C. 2009;113(35):15524–32.

    Article  CAS  Google Scholar 

  28. Ziegler C, Eychmüller A. Seeded growth synthesis of uniform gold nanoparticles with diameters of 15−300 nm. J Phys Chem C. 2011;115(11):4502–6.

    Article  CAS  Google Scholar 

  29. Xiao L, Wei L, He Y, Yeung ES. Single molecule biosensing using color coded plasmon resonant metal nanoparticles. Anal Chem. 2010;82(14):6308–14.

    Article  CAS  Google Scholar 

  30. Pekcevik IC, Poon LC, Wang MC, Gates BD. Tunable loading of single-stranded DNA on gold nanorods through the displacement of polyvinylpyrrolidone. Anal Chem. 2013;85(20):9960–7.

    Article  CAS  Google Scholar 

  31. Cheng X, Dai D, Yuan Z, Peng L, He Y, Yeung ES. Color difference amplification between gold nanoparticles in colorimetric analysis with actively controlled multiband illumination. Anal Chem. 2014;86(15):7584–92.

    Article  CAS  Google Scholar 

  32. Nath N, Chilkoti A. A colorimetric gold nanoparticle sensor to interrogate biomolecular interactions in real time on a surface. Anal Chem. 2002;74(3):504–9.

    Article  CAS  Google Scholar 

  33. Mayer KM, Lee S, Liao H, Rostro BC, Fuentes A, Scully PT, et al. A label-free immunoassay based upon localized surface plasmon resonance of gold nanorods. ACS Nano. 2008;2(4):687–92.

    Article  CAS  Google Scholar 

  34. Byun JY, Shin YB, Li T, Park JH, Kim DM, Choi DH, et al. The use of an engineered single chain variable fragment in a localized surface plasmon resonance method for analysis of the C-reactive protein. Chem Commun. 2013;49(82):9497–9.

    Article  CAS  Google Scholar 

  35. Stoeva SI, Lee JS, Thaxton CS, Mirkin CA. Multiplexed DNA detection with biobarcoded nanoparticle probes. Angew Chem. 2006;118(20):3381–4.

    Article  Google Scholar 

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Acknowledgements

This work was supported by the National Science Foundation of China (grants 21273126 and 21573124) and the Fundamental Research Program of Shenzhen (JCYJ20140509172959966, JCYJ20160317152359560). HT thanks the financial support from The Science Technology Innovation Commission of Shenzhen Municipality (GJHZ20160301163644983) and The Health and Family Planning Commission of Shenzhen Municipality (201601019).

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Author notes

  1. Guohua Li and Liang Zhu contributed equally to this work.

Authors and Affiliations

  1. Institute of Optical Imaging and Sensing, Shenzhen Key Laboratory for Minimal Invasive Medical Technologies, Graduate School at Shenzhen, Tsinghua University, Shenzhen, Guangdong, 518055, China

    Guohua Li, Liang Zhu, Yonghong He & Shuqing Sun

  2. Department of Physics, Tsinghua University, School of Sciences Building, Haidian District, Beijing, 100084, China

    Guohua Li, Liang Zhu, Yonghong He & Shuqing Sun

  3. Shenzhen Key Laboratory of Neurosurgery, The First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, 518035, China

    Hui Tan

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  1. Guohua Li
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  2. Liang Zhu
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  3. Yonghong He
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  4. Hui Tan
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  5. Shuqing Sun
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Correspondence to Yonghong He, Hui Tan or Shuqing Sun.

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Li, G., Zhu, L., He, Y. et al. Digital triplex DNA assay based on plasmonic nanocrystals. Anal Bioanal Chem 409, 3657–3666 (2017). https://doi.org/10.1007/s00216-017-0307-9

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  • DOI: https://doi.org/10.1007/s00216-017-0307-9

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