Placing molecules with Bohr radius resolution using DNA origami (original) (raw)

Abstract

Molecular self-assembly with nucleic acids can be used to fabricate discrete objects with defined sizes and arbitrary shapes1,2. It relies on building blocks that are commensurate to those of biological macromolecular machines and should therefore be capable of delivering the atomic-scale placement accuracy known today only from natural and designed proteins3,4. However, research in the field has predominantly focused on producing increasingly large and complex, but more coarsely defined, objects5,6,7,8,9,10 and placing them in an orderly manner on solid substrates11,12. So far, few objects afford a design accuracy better than 5 nm13,14,15,16, and the subnanometre scale has been reached only within the unit cells of designed DNA crystals17. Here, we report a molecular positioning device made from a hinged DNA origami object in which the angle between the two structural units can be controlled with adjuster helices. To test the positioning capabilities of the device, we used photophysical and crosslinking assays that report the coordinate of interest directly with atomic resolution. Using this combination of placement and analysis, we rationally adjusted the average distance between fluorescent molecules and reactive groups from 1.5 to 9 nm in 123 discrete displacement steps. The smallest displacement step possible was 0.04 nm, which is slightly less than the Bohr radius. The fluctuation amplitudes in the distance coordinate were also small (±0.5 nm), and within a factor of two to three of the amplitudes found in protein structures18.

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Acknowledgements

The authors thank C. Castro for preliminary work on this project and F. Praetorius for scaffold DNA preparations. The authors also thank S. Niekamp for technical assistance. This work was supported by a European Research Council starting grant to H.D. (GA no. 256270) and by the Deutsche Forschungsgemeinschaft through grants provided within the Sonderforschungsbereich SFB863, and the Excellence Clusters CIPSM (Center for Integrated Protein Science Munich) and NIM (Nanosystems Initiative Munich).

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Authors and Affiliations

  1. Physik Department, Walter Schottky Institute, Technische Universität München, Am Coulombwall 4a, Garching near Munich, 85748, Germany
    Jonas J. Funke & Hendrik Dietz

Authors

  1. Jonas J. Funke
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  2. Hendrik Dietz
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Contributions

J.J.F. performed the research. H.D. designed the research. J.J.F and H.D. analysed and discussed the data. J.J.F. and H.D. prepared the figures and wrote the manuscript.

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Correspondence toHendrik Dietz.

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The authors declare no competing financial interests.

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Funke, J., Dietz, H. Placing molecules with Bohr radius resolution using DNA origami.Nature Nanotech 11, 47–52 (2016). https://doi.org/10.1038/nnano.2015.240

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