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Quantification of the affinities and kinetics of protein interactions using silicon nanowire biosensors

Nature Nanotechnology volume 7, pages 401–407 (2012)Cite this article

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Abstract

Monitoring the binding affinities and kinetics of protein interactions is important in clinical diagnostics and drug development because such information is used to identify new therapeutic candidates. Surface plasmon resonance is at present the standard method used for such analysis, but this is limited by low sensitivity and low-throughput analysis. Here, we show that silicon nanowire field-effect transistors can be used as biosensors to measure protein–ligand binding affinities and kinetics with sensitivities down to femtomolar concentrations. Based on this sensing mechanism, we develop an analytical model to calibrate the sensor response and quantify the molecular binding affinities of two representative protein–ligand binding pairs. The rate constant of the association and dissociation of the protein–ligand pair is determined by monitoring the reaction kinetics, demonstrating that silicon nanowire field-effect transistors can be readily used as high-throughput biosensors to quantify protein interactions.

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Figure 1: Schematic of the Si-NW FET biosensor set-up and binding cycles.
Figure 2: Measurements of HMGB1 and DNA binding using the Si-NW FET.
Figure 3: Sensor response of the binding of biotin and streptavidin as measured by the Si-NW FET.
Figure 4: Competitive dissociation processes of streptavidin from a biotin-functionalized surface.

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Acknowledgements

The authors acknowledge financial support from the Netherlands Organization for Scientific Research (NWO, Rubicon grant), the National Institutes of Health (NIH R01EB008260 and P01GM022778), the Burroughs Welcome Fund (to Y.M.) and DTRA (HDTRA1-10-1-0037). The authors thank A. Vacic, M. Weber and W. Guan for help with the electrical measurement and helpful discussions.

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Authors and Affiliations

  1. Department of Electrical Engineering, Yale University, New Haven, 06520, Connecticut, USA

    Xuexin Duan, David A. Routenberg & Mark A. Reed

  2. Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, 06520, Connecticut, USA

    Yue Li & Yorgo Modis

  3. Department of Applied Physics, Yale University, New Haven, 06520, Connecticut, USA

    Nitin K. Rajan & Mark A. Reed

Authors
  1. Xuexin Duan
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  2. Yue Li
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  4. David A. Routenberg
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  5. Yorgo Modis
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Contributions

X.D. and M.A.R. conceived and designed the experiments. X.D. performed the experiments. X.D. and N.K.R. analysed the data. N.K.R. and D.A.R. fabricated the nanowire devices. Y.L. and Y.M. contributed the DNA and proteins, and X.D. and M.A.R. co-wrote the paper.

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Correspondence to Mark A. Reed.

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The authors declare no competing financial interests.

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Duan, X., Li, Y., Rajan, N. et al. Quantification of the affinities and kinetics of protein interactions using silicon nanowire biosensors. Nature Nanotech 7, 401–407 (2012). https://doi.org/10.1038/nnano.2012.82

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