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Biointerphases

Journal for Biophysical Chemistry

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Study of nucleic acid—gold nanorod interactions and detecting nucleic acid hybridization using gold nanorod solutions in the presence of sodium citrate

Biointerphases volume 5, pages FA98–FA104 (2010)Cite this article

Abstract

In this study, the authors report that sodium citrate can aggregate hexadecyl-trimethyl-ammonium ion+-coated gold nanorods (AuNRs), and nucleic acids of different charge and structure properties, i.e., single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), single-stranded peptide nucleic acid (PNA), and PNA-DNA complex, can bind to the AuNRs and therefore retard the sodium citrate-induced aggregation to different extents. The discovery that hybridized dsDNA (and the PNA-DNA complex) has a more pronounced protection effect than ssDNA (and PNA) allows the authors to develop a homogeneous phase AuNRs-based UV-visible (UV-vis) spectral assay for detecting specific sequences of oligonucleotides (20 mer) with a single-base-mismatch selectivity and a limit of detection of 5 nM. This assay involves no tedious bioconjugation and on-particle hybridization. The simple “set and test” format allows for a highly efficient hybridization in a homogeneous phase and a rapid display of the results in less than a minute. By measuring the degree of reduction in AuNR aggregation in the presence of different nucleic acid samples, one can assess how different nucleic acids interact with the AuNRs to complement the knowledge of spherical gold nanoparticles. Besides UV-vis characterization, transmission electron microscopy and zeta potential measurements were conduced to provide visual evidence of the particle aggregation and to support the discussion of the assay principle.

Reference

  1. W. A. Murray and W. L. Barnes, Adv. Mater. 19, 3771 (2007).

    Article  CAS  Google Scholar 

  2. M. E. Stewart, C. R. Anderton, L. B. Thompson, J. Maria, S. K. Gray, J. A. Rogers, and R. G. Nuzzo, Chem. Rev. (Washington, D.C.) 108, 494 (2008).

    CAS  Google Scholar 

  3. C. S. Thaxton, D. G. Georganopoulou, and C. A. Mirkin, Clin. Chim. Acta 363, 120 (2006).

    Article  CAS  Google Scholar 

  4. P. Baptista, E. Pereira, P. Eaton, G. Doria, A. Miranda, I. Gomes, P. Quaresma, and R. Franc, Anal. Bioanal. Chem. 391, 943 (2008).

    Article  CAS  Google Scholar 

  5. W. A. Zhao, M. A. Brook, and Y. Li, ChemBioChem 9, 2363 (2008).

    Article  CAS  Google Scholar 

  6. E. Dujardin, L. B. Hsin, C. R. C. Wang, and S. Mann, Chem. Commun. (Cambridge) 2001, pp1264.

  7. B. F. Pan, L. M. Ao, F. Gao, H. Y. Tian, R. He, and D. X. Cui, Nanotechnology 16, 1776 (2005).

    Article  CAS  Google Scholar 

  8. C. Wang, Y. Chen, T. Wang, Z. Ma, and Z. Su, Chem. Mater. 19, 5809 (2007).

    Article  CAS  Google Scholar 

  9. H. Nakashima, K. Furukawa, Y. Kashimura, and K. Torimitsu, Chem. Commun. (Cambridge) 2007, 1080.

  10. X. Li, J. Qian, and S. He, Nanotechnology 19, 355501 (2008).

    Article  Google Scholar 

  11. P. K. Sudeep, S. S. T. Joseph, and G. K. Thomas, J. Am. Chem. Soc. 127, 6516 (2005).

    Article  CAS  Google Scholar 

  12. W. He, Z. C. Huang, Y. F. Li, J. P. Xie, R. G. Yang, P. F. Zhou, and J. Wang, Anal. Chem. 80, 8424 (2008).

    Article  CAS  Google Scholar 

  13. Y. F. Huang, Y. W. Lin, and H. T. Chang, Langmuir 23, 12777 (2007).

    Article  CAS  Google Scholar 

  14. J. Pérez-Juste, J. I. Pastoriza-Santos, L. M. Liz-Marzán, and P. Mulvaney, Coord. Chem. Rev. 249, 1870 (2005).

    Article  Google Scholar 

  15. N. Varghese, S. R. C. Vivekchand, and C. N. R. Rao, Chem. Phys. Lett. 450, 340 (2008).

    Article  CAS  Google Scholar 

  16. S. J. Zhen, C. Z. Huang, J. Wang, and F. Li, J. Phys. Chem. C 113, 21543 (dy2009).

    Article  Google Scholar 

  17. M. Sethi, G. E. Joung, and M. R. Knecht, Langmuir 25, 1572 (2009).

    Article  CAS  Google Scholar 

  18. B. Pan et al., J. Phys. Chem. C 111, 12572 (2007).

    Article  CAS  Google Scholar 

  19. G. Kawamura, Y. Yang, and M. Nogami, J. Phys. Chem. C 112, 10632 (2008).

    Article  CAS  Google Scholar 

  20. P. K. Jain, S. Eustis, and M. A. Ei-Sayed, J. Phys. Chem. B 110, 18243 (2006).

    Article  CAS  Google Scholar 

  21. M. Sethi, G. Joung, and M. R. Knecht, Langmuir 25, 317 (2009).

    Article  CAS  Google Scholar 

  22. X. D. Su and R. Kanjanawarut, ACS Nano 3, 2751 (2009).

    Article  CAS  Google Scholar 

  23. R. Kanjanawarut and X. D. Su, Anal. Chem. 81, 6122 (2009).

    Article  CAS  Google Scholar 

  24. H. Li and L. Rothberg, Proc. Natl. Acad. Sci. U.S.A. 101, 14036 (2004).

    Article  CAS  Google Scholar 

  25. See EPAPS supplementary material at E-BJIOBN-5-013003 for UV-vis spectra of AuNRs coated with nucleic acids but without adding sodium citrate, sequence analysis of the nc target, and the reproducibility of UVvis measurement.

  26. K. Sato, K. Hosokawa, and M. Maeda, J. Am. Chem. Soc. 125, 8102 (2003).

    Article  CAS  Google Scholar 

  27. P. Weroński, Y. Jiang, and S. Rasmussen, Biophys. J. 92, 3081 (2007).

    Article  Google Scholar 

  28. A. Gourishankar, S. Shukla, K. N. Ganesh, and M. Sastry, J. Am. Chem. Soc. 126, 13186 (2004).

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 3 Research Link, 117602, Singapore, Singapore

    Roejarek Kanjanawarut & Xiaodi Su

Authors
  1. Roejarek Kanjanawarut
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  2. Xiaodi Su
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Correspondence to Xiaodi Su.

Additional information

This article is part of an In Focus section on Biointerface Science in Singapore, sponsored by Bruker Optik Southeast Asia, IMRE, the Provost's Office and School of Materials Science and Engineering of Nanyang Technological University, and Analytical Technologies Pte. Ltd.

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Kanjanawarut, R., Su, X. Study of nucleic acid—gold nanorod interactions and detecting nucleic acid hybridization using gold nanorod solutions in the presence of sodium citrate. Biointerphases 5, FA98–FA104 (2010). https://doi.org/10.1116/1.3496962

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  • DOI: https://doi.org/10.1116/1.3496962