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A device that operates within a self-assembled 3D DNA crystal

Nature Chemistry volume 9, pages 824–827 (2017)Cite this article

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Abstract

Structural DNA nanotechnology finds applications in numerous areas, but the construction of objects, 2D and 3D crystalline lattices and devices is prominent among them. Each of these components has been developed individually, and most of them have been combined in pairs. However, to date there are no reports of independent devices contained within 3D crystals. Here we report a three-state 3D device whereby we change the colour of the crystals by diffusing strands that contain dyes in or out of the crystals through the mother-liquor component of the system. Each colouring strand is designed to pair with an extended triangle strand by Watson–Crick base pairing. The arm that contains the dyes is quite flexible, but it is possible to establish the presence of the duplex proximal to the triangle by X-ray crystallography. We modelled the transition between the red and blue states through a simple kinetic model.

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Figure 1: Operation of the three-state colour device.
Figure 2: Gel evidence for forming the triangle motif in each state.
Figure 3: A time-course experiment on the transition from state B to state C.
Figure 4: Electron-density maps of the system in states A, B and C.

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Acknowledgements

We thank P. Chaikin for the use of his confocal microscope. This research was supported by the following grants to N.C.S.: GM-29554 from National Institute of General Medical Sciences, grants CMMI-1120890, EFRI-1332411, CCF-1117210 and CCF-1526650 from the National Science Foundation, MURI W911NF-11-1-0024 from the Army Research Office, MURI N000140911118 from Office of Naval Research, DE-SC0007991 from the US Department of Energy (DOE) for DNA synthesis and partial salary support, and grant GBMF3849 from the Gordon and Betty Moore Foundation. Beam line X29 of the BNL-NSLS, which is supported principally from the Offices of Biological and Environmental Research and of Basic Energy Sciences of the US DOE and from the National Center for Research Resources of the National Institutes of Health.

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Authors and Affiliations

  1. Department of Chemistry, New York University, New York, 10003, USA

    Yudong Hao, Martin Kristiansen, Ruojie Sha, Jens J. Birktoft, Carina Hernandez & Nadrian C. Seeman

  2. Department of Chemistry, Purdue University, West Lafayette, 47907, Indiana, USA

    Chengde Mao

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  1. Yudong Hao
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  2. Martin Kristiansen
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  7. Nadrian C. Seeman
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Contributions

Y.H., M.K., C.H., J.J.B. and R.S. performed the experiments, and all of the authors analysed data and wrote the manuscript.

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Correspondence to Nadrian C. Seeman.

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Hao, Y., Kristiansen, M., Sha, R. et al. A device that operates within a self-assembled 3D DNA crystal. Nature Chem 9, 824–827 (2017). https://doi.org/10.1038/nchem.2745

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