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Self-assembled DNA nanostructures for distance-dependent multivalent ligand–protein binding

Nature Nanotechnology volume 3, pages 418–422 (2008)Cite this article

Abstract

An important goal of nanotechnology is to assemble multiple molecules while controlling the spacing between them. Of particular interest is the phenomenon of multivalency, which is characterized by simultaneous binding of multiple ligands on one biological entity to multiple receptors on another1. Various approaches have been developed to engineer multivalency by linking multiple ligands together2,3,4. However, the effects of well-controlled inter-ligand distances on multivalency are less well understood. Recent progress in self-assembling DNA nanostructures with spatial and sequence addressability5,6,7,8,9,10,11,12 has made deterministic positioning of different molecular species possible8,11,12,13. Here we show that distance-dependent multivalent binding effects can be systematically investigated by incorporating multiple-affinity ligands into DNA nanostructures with precise nanometre spatial control. Using atomic force microscopy, we demonstrate direct visualization of high-affinity bivalent ligands being used as pincers to capture and display protein molecules on a nanoarray. These results illustrate the potential of using designer DNA nanoscaffolds to engineer more complex and interactive biomolecular networks.

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Figure 1: Schematics of the self-assembled divalent aptamers on a DNA tile for protein binding.
Figure 2: Gel-mobility shift assays.
Figure 3: Evaluation of bivalent binding by AFM.

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Acknowledgements

This work was derived from a discussion of the synthetic antibody project with S.A. Johnston at the Biodesign Institute, Arizona State University. We also thank S. Lindsay, C. Diehnelt and Dong-Kyun Seo for helpful discussions. S.R. was partly supported by the Technology and Research Initiative Fund from Arizona State University to S.A. Johnston. This work was partly supported by grants from the National Science Foundation, the National Institute of Health, the Air Force Office of Scientific Research and the Office of Naval Research to Hao Yan and TRIF funds from Arizona State University to Hao Yan and Yan Liu.

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  1. Sherri Rinker and Yonggang Ke: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Chemistry and Biochemistry, and Centre for Single Molecule Biophysics at the Biodesign Institute, Arizona State University, Tempe, 85287, Arizona, USA

    Sherri Rinker, Yonggang Ke, Yan Liu, Rahul Chhabra & Hao Yan

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  1. Sherri Rinker
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  2. Yonggang Ke
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  3. Yan Liu
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Contributions

H.Y. and Y.L conceived the project. H.Y., Y.L, S.R. and Y.K. designed the experiments. S.R., Y.K. and R.C. performed the experiments. H.Y., Y.L., S.R. and Y.K. analysed the data. H.Y., Y.L. and S.R. co-wrote the paper. All authors discussed the results and commented on the manuscript.

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Correspondence to Yan Liu or Hao Yan.

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Rinker, S., Ke, Y., Liu, Y. et al. Self-assembled DNA nanostructures for distance-dependent multivalent ligand–protein binding. Nature Nanotech 3, 418–422 (2008). https://doi.org/10.1038/nnano.2008.164

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