Ordered three-dimensional nanomaterials using DNA-prescribed and valence-controlled material voxels

Abstract

The ability to organize nanoscale objects into well-defined three-dimensional (3D) arrays can translate advances in nanoscale synthesis into targeted material fabrication. Despite successes in nanoparticle assembly, most extant methods are system specific and not fully compatible with biomolecules. Here, we report a platform for creating distinct 3D ordered arrays from different nanomaterials using DNA-prescribed and valence-controlled material voxels. These material voxels consist of 3D DNA frames that integrate nano-objects within their scaffold, thus enabling the object’s valence and coordination to be determined by the frame’s vertices, which can bind to each other through hybridization. Such DNA material voxels define the lattice symmetry through the spatially prescribed valence decoupling the 3D assembly process from the nature of the nanocomponents, such as their intrinsic properties and shapes. We show this by assembling metallic and semiconductor nanoparticles and also protein superlattices. We support the technological potential of such an assembly approach by fabricating light-emitting 3D arrays with diffraction-limited spectral purity and 3D enzymatic arrays with increased activity.

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Fig. 1: Schematic of the DNA material voxels platform for assembly of 3D lattices from inorganic (nanoparticle) and bio-organic (protein) nano-objects with DNA frames.
Fig. 2: Assembly of octahedra frames into DNA lattice.
Fig. 3: SC lattice of AuNP assembled using material voxels based on DNA octahedra.
Fig. 4: Assembly of nanoparticles from different materials and frames of different geometries into SC, BCC and cubic diamond superlattices.
Fig. 5: Structure and enzymatic activity of assembled 3D designed lattices (SC) of material voxels with proteins.
Fig. 6: Optical and enzymatic functions of 3D lattices assembled from DNA material voxels with QDs and enzymes.

Data availability

The data supporting the findings of this study are available within this article and its Supplementary Information, or from the corresponding author on reasonable request.

Code availability

The scripts used in X-ray scattering analysis and modelling are a part of the ScatterSim software package, a Python package available for download through GitHub (https://github.com/CFN-softbio/scattersim) or from the corresponding author on reasonable request.

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Acknowledgements

We thank W. Xia for help with cryo-STEM imaging, M. Ji for help with negative stained TEM imaging, Y. Zhang and A. Fluerasu for help with SAXS measurement at the CHX beamline (NSLS-II at the Brookhaven National Laboratory), M. Cotlet and J. Chen for help with optical characterization, and D. Chen for help with illustrations. Cryo-EM data were collected at the David Van Andel Advanced Cryo-Electron Microscopy Suite in the Van Andel Research Institute. Y.T.’s work at Nanjing University was supported by Jiangsu Youth Fund of China (grant no. BK20180337) and the Fundamental Research Funds for the Central Universities (grant no. 14380151). H.L. was supported by the US National Institutes of Health (grant nos. GM111472 and GM124170) and the Van Andel Research Institute. This research used resources of the Center for Functional Nanomaterials, and the National Synchrotron Light Source II, which are US DOE Office of Science Facilities at Brookhaven National Laboratory under contract no. DE-SC0012704. This work was supported by the US Department of Energy, Office of Basic Energy Sciences, grant no. DE-SC0008772.

Author information

Y.T. and O.G. conceived and designed the experiments. Y.T. performed the assembly experiments. J.R.L. and K.G.Y. contributed to the model fitting of the SAXS data. Y.T., L.B. and H.L. contributed to the cryo-EM imaging and reconstruction. Y.T. and H.L.X. contributed to the electron microscopy imaging of the superlattice. T.V. and S.K.K. performed computational modelling. J.S.K., B.M. and Y.X. prepared optical and enzymatic samples and conducted the experiments. R.L. and M.F. helped with SAXS experiments. Y.T. and O.G. wrote the paper. O.G. supervised the project. All authors discussed the results and commented on the manuscript.

Correspondence to Oleg Gang.

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Supplementary Information

Supplementary Sections 1–8, Figs. 1–61, Tables 1–3 and references.

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Tian, Y., Lhermitte, J.R., Bai, L. et al. Ordered three-dimensional nanomaterials using DNA-prescribed and valence-controlled material voxels. Nat. Mater. (2020). https://doi.org/10.1038/s41563-019-0550-x

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