Letter | Published:

A nanoplasmonic molecular ruler for measuring nuclease activity and DNA footprinting

Nature Nanotechnology volume 1, pages 4752 (2006) | Download Citation

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Abstract

Interactions between nucleic acids and proteins are essential to genetic information processing. The detection of size changes in nucleic acids is the key to mapping such interactions, and usually requires substrates with fluorescent, electrochemical or radioactive labels1,2,3. Recently, methods have been developed to tether DNA to highly water-soluble Au nanoparticles4,5,6,7,8, and nanoparticle pairs linked by DNA have been used to measure nanoscale distances9. Here we demonstrate a molecular ruler in which double-stranded DNA is attached to a Au nanoparticle. The change in plasmon resonance wavelength of individual Au–DNA conjugates depends on the length of the DNA and can be measured with subnanometre axial resolution. An average wavelength shift of approximately 1.24 nm is observed per DNA base pair. This system allows for a label-free, quantitative, real-time measurement of nuclease activity and also serves as a new DNA footprinting platform, which can accurately detect and map the specific binding of a protein to DNA.

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References

  1. 1.

    , & The effect of nucleobase-specific fluorescence quenching on in situ hybridization with rRNA-targeted oligonucleotide probes. Syst. Appl. Microbiol. 27, 565–572 (2004).

  2. 2.

    & Radioactive end labeling to determine hydrolytic rates of nuclease mimics. Anal. Biochem. 220, 53–57 (1994).

  3. 3.

    et al. An electrochemical study of enzymatic oligonucleotide digestion. Bioelectrochemistry 63, 307–310 (2004).

  4. 4.

    et al. Organization of ‘nanocrystal molecules’ using DNA. Nature 382, 609–611 (1996).

  5. 5.

    , , , & Electrophoretic isolation of discrete Au nanocrystal/DNA conjugates. Nano Lett. 1, 32–35 (2001).

  6. 6.

    , & Scanometric DNA array detection with nanoparticle probes. Science 289, 1757–1760 (2000).

  7. 7.

    , , , & One-pot colorimetric differentiation of polynucleotides with single base imperfections using gold nanoparticle probes. J. Am. Chem. Soc. 120, 1959–1964 (1998).

  8. 8.

    , , & A DNA-based method for rationally assembling nanoparticles into macroscopic materials. Nature 382, 607–609 (1996).

  9. 9.

    , , & A molecular ruler based on plasmon coupling of single gold and silver nanoparticles. Nature Biotechnol. 23, 741–745 (2005).

  10. 10.

    , & Surface plasmon resonance sensors: review. Sensor Actuat. B-Chem. 54, 3–15 (1999).

  11. 11.

    SPR for molecular interaction analysis: a review of emerging application areas. J. Mol. Recognit. 17, 151–161 (2004).

  12. 12.

    Surface plasmon spectroscopy of nanosized metal particles. Langmuir 12, 788–800 (1996).

  13. 13.

    , , , & Selective colorimetric detection of polynucleotides based on the distance-dependent optical properties of gold nanoparticles. Science 277, 1078–1081 (1997).

  14. 14.

    , , & Plasmon resonance measurements of the adsorption and adsorption kinetics of a biopolymer onto gold nanocolloids. Langmuir 17, 957–960 (2001).

  15. 15.

    , & High-throughput screening using the surface plasmon resonance effect of colloidal gold nanoparticles. Analyst 126, 1645–1651 (2001).

  16. 16.

    & A colorimetric gold nanoparticle sensor to interrogate biomolecular interactions in real time on a surface. Anal. Chem. 74, 504–509 (2002).

  17. 17.

    & Increased sensitivity of surface plasmon resonance of gold nanoshells compared to that of gold solid colloids in response to environmental changes. Anal. Chem. 74, 5297–5305 (2002).

  18. 18.

    & Single silver nanoparticles as real-time optical sensors with zeptomole sensitivity. Nano Lett. 3, 1057–1062 (2003).

  19. 19.

    et al. Biomolecular recognition based on single gold nanoparticle light scattering. Nano Lett. 3, 935–938 (2003).

  20. 20.

    , , & Base pair mismatch recognition using plasmon resonant particle labels. Anal. Biochem. 309, 109–116 (2002).

  21. 21.

    et al. Conformation of oligonucleotides attached to gold nanocrystals probed by gel electrophoresis. Nano Lett. 3, 33–36 (2003).

  22. 22.

    & Absorption and Scattering of Light by Small Particles (Wiley, New York, 1983).

  23. 23.

    & Distance-dependent dielectric-constants and their application to double-helical DNA. Biopolymers 31, 1615–1629 (1991).

  24. 24.

    , & Glu-111 is required for activation of the DNA cleavage center of EcoRI endonuclease. J. Biol. Chem. 264, 11807–11815 (1989).

  25. 25.

    & Elongation by Escherichia coli RNA polymerase is blocked in vitro by a site-specific DNA binding protein. J. Biol. Chem. 265, 9960–9969 (1990).

  26. 26.

    & Snapshot blotting — Transfer of nucleic-acids and nucleoprotein complexes from electrophoresis gels to grids for electron-microscopy. Proc. Natl Acad. Sci. USA 91, 6870–6874 (1994).

  27. 27.

    , & Extracellular nucleases of pseudomonas BAL 31. III. Use of the double-strand deoxyriboexonuclease activity as the basis of a convenient method for the mapping of fragments of DNA produced by cleavage with restriction enzymes. Nucleic Acids Res. 5, 1445–1464 (1978).

  28. 28.

    et al. Sensitivity of transmission surface plasmon resonance (T-SPR) spectroscopy: Self-assembled multilayers on evaporated gold island films. Chem. Eur. J. 11, 5555–5562 (2005).

  29. 29.

    et al. Branched coordination multilayers on gold. J. Am. Chem. Soc. 127, 17877–17887 (2005).

  30. 30.

    , , , & Protection of polynucleotides against nuclease-mediated hydrolysis by complexation with schizophyllan. Biomaterials 25, 3109–3116 (2004).

Download references

Acknowledgements

This work was supported by DARPA, DOD BC045345, NIH R21CA95393, UCSF Prostate Cancer SPORE award (NIH P50 CA89520), and the UCSF Prostate Cancer Center Developmental Research Program, Intel, the Korea Ministry of Science and Technology “21st Century Frontier R&D Program” grant 05K1501-02810. This work was performed under the auspices of the U.S. Dept. of Energy, at the University of California/Lawrence Berkeley National Laboratory under contract no. DE-AC03-76SF00098 and at the University of California/Lawrence Livermore National Laboratory under contract no. W-7405-Eng-48.

Author information

Author notes

    • Yadong Yin

    Present address: Department of Chemistry, University of California at Riverside, Riverside, California 92521, USA

Affiliations

  1. Biomolecular Nanotechnology Center, Department of Bioengineering, University of California at Berkeley, Berkeley, California 94720, USA

    • Gang L. Liu
    •  & Luke P. Lee
  2. Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA

    • Yadong Yin
    • , Siri Kunchakarra
    • , Bipasha Mukherjee
    • , Daniele Gerion
    • , Joe W. Gray
    • , A. Paul Alivisatos
    •  & Fanqing Frank Chen
  3. Department of Chemistry, University of California, Berkeley, California 94720, USA

    • Yadong Yin
    •  & A. Paul Alivisatos
  4. Lawrence Livermore National Laboratory, Livermore, California 94551, USA

    • Daniele Gerion
  5. Department of Cell Biology and Physiology and the Cancer Research and Treatment Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico 87131, USA

    • Stephen D. Jett
    •  & David G. Bear

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Contributions

F.F.C. conceived and designed the experiments, G.L.L., Y.Y., S.K. and B.M. performed the experiments, G.L.L. and D.G. analysed the data, and S.D.J. and D.G.B. synthesized the EcoRI(Q111). Correspondence and requests for material should be addressed to F.F.C. and L.P.L.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Luke P. Lee or Fanqing Frank Chen.

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    Supplementary Information

    Supplementary materials and methods, figures S1-S4, and table S1

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DOI

https://doi.org/10.1038/nnano.2006.51

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