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Electrostatic readout of DNA microarrays with charged microspheres

Nature Biotechnology volume 26, pages 825–830 (2008)Cite this article

Abstract

DNA microarrays are used for gene-expression profiling, single-nucleotide polymorphism detection and disease diagnosis1,2,3. A persistent challenge in this area is the lack of microarray screening technology suitable for integration into routine clinical care4,5. Here, we describe a method for sensitive and label-free electrostatic readout of DNA or RNA hybridization on microarrays. The electrostatic properties of the microarray are measured from the position and motion of charged microspheres randomly dispersed over the surface. We demonstrate nondestructive electrostatic imaging with 10-μm lateral resolution over centimeter-length scales, which is four-orders of magnitude larger than that achievable with conventional scanning electrostatic force microscopy. Changes in surface charge density as a result of specific hybridization can be detected and quantified with 50-pM sensitivity, single base-pair mismatch selectivity and in the presence of complex background. Because the naked eye is sufficient to read out hybridization, this approach may facilitate broad application of multiplexed assays.

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Figure 1: Electrostatic microarray readout using microparticle probes.
Figure 2: Electrostatic response to DNA surface density.
Figure 3: Simplified readout using charged microparticles.
Figure 4: Label-free expression profiling with primary mRNA.

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Acknowledgements

We thank Lance Kizer and the UC Berkeley Functional Genomics Laboratory for assistance in generating microarrays. This work was supported by the Director, Office of Science, Office of Basic Energy Sciences of the US Department of Energy under Contract No. DE-AC03-76SF00098. N.G.C. also received partial support from the National Science Foundation through The Center on Polymer Interfaces and Macromolecular Assemblies.

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Author notes

  1. Nathan G Clack and Khalid Salaita: These authors contributed equally to this work.

Authors and Affiliations

  1. Biophysics Graduate Group, University of California, Berkeley, California 94720-3220, USA.,

    Nathan G Clack & Jay T Groves

  2. Department of Chemistry, University of California, Berkeley, California 94720-3220, USA.,

    Khalid Salaita & Jay T Groves

Authors
  1. Nathan G Clack
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  2. Khalid Salaita
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Contributions

N.G.C. and K.S. designed and implemented all experiments. N.G.C., K.S. and J.T.G. conceived of ideas and wrote the paper.

Corresponding author

Correspondence to Jay T Groves.

Supplementary information

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Figures 1–4, Table 1, Methods, Note (PDF 948 kb)

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Clack, N., Salaita, K. & Groves, J. Electrostatic readout of DNA microarrays with charged microspheres. Nat Biotechnol 26, 825–830 (2008). https://doi.org/10.1038/nbt1416

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