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


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 ( or from the corresponding author on reasonable request.


  1. Jones, M. R. et al. DNA-nanoparticle superlattices formed from anisotropic building blocks. Nat. Mater. 9, 913–917 (2010).

    Article  CAS  Google Scholar 

  2. Lu, F., Yager, K. G., Zhang, Y. G., Xin, H. L. & Gang, O. Superlattices assembled through shape-induced directional binding. Nat. Commun. 6, 6912 (2015).

    Article  CAS  Google Scholar 

  3. Agarwal, U. & Escobedo, F. A. Mesophase behaviour of polyhedral particles. Nat. Mater. 10, 230–235 (2011).

    Article  CAS  Google Scholar 

  4. Gantapara, A. P., de Graaf, J., van Roij, R. & Dijkstra, M. Phase diagram and structural diversity of a family of truncated cubes: degenerate close-packed structures and vacancy-rich states. Phys. Rev. Lett. 111, 015501 (2013).

    Article  CAS  Google Scholar 

  5. Talapin, D. V. et al. Quasicrystalline order in self-assembled binary nanoparticle superlattices. Nature 461, 964–967 (2009).

    Article  CAS  Google Scholar 

  6. Damasceno, P. F., Engel, M. & Glotzer, S. C. Predictive self-assembly of polyhedra into complex structures. Science 337, 453–457 (2012).

    Article  CAS  Google Scholar 

  7. Seeman, N. C. Nucleic acid junctions and lattices. J. Theor. Biol. 99, 237–247 (1982).

    Article  CAS  Google Scholar 

  8. Chen, J. & Seeman, N. C. Synthesis from DNA of a molecule with the connectivity of a cube. Nature 350, 631–633 (1991).

    Article  CAS  Google Scholar 

  9. Rothemund, P. W. K. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006).

    Article  CAS  Google Scholar 

  10. He, Y. et al. Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra. Nature 452, 198–201 (2008).

    Article  CAS  Google Scholar 

  11. Seeman, N. C. DNA in a material world. Nature 421, 427–431 (2003).

    Article  CAS  Google Scholar 

  12. Halverson, J. D. & Tkachenko, A. V. DNA-programmed mesoscopic architecture. Phys. Rev. E 87, 062310 (2013).

    Article  CAS  Google Scholar 

  13. Zheng, J. et al. Two-dimensional nanoparticle arrays show the organizational power of robust DNA motifs. Nano Lett. 6, 1502–1504 (2006).

    Article  CAS  Google Scholar 

  14. Nykypanchuk, D., Maye, M. M., van der Lelie, D. & Gang, O. DNA-guided crystallization of colloidal nanoparticles. Nature 451, 549–552 (2008).

    Article  CAS  Google Scholar 

  15. Park, S. Y. et al. DNA-programmable nanoparticle crystallization. Nature 451, 553–556 (2008).

    Article  CAS  Google Scholar 

  16. Vo, T. et al. Stoichiometric control of DNA-grafted colloid self-assembly. Proc. Natl Acad. Sci. USA 112, 4982–4987 (2015).

    Article  CAS  Google Scholar 

  17. Niemeyer, C. M., Koehler, J. & Wuerdemann, C. DNA-directed assembly of bienzymic complexes from in vivo biotinylated NAD(P)H:FMN oxidoreductase and luciferase. ChemBioChem 3, 242–245 (2002).

    Article  CAS  Google Scholar 

  18. Lee, J. B. et al. A mechanical metamaterial made from a DNA hydrogel. Nat. Nanotechnol. 7, 816–820 (2012).

    Article  CAS  Google Scholar 

  19. Church, G. M., Gao, Y. & Kosuri, S. Next-generation digital information storage in DNA. Science 337, 1628 (2012).

    Article  CAS  Google Scholar 

  20. Zheng, J. et al. From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal. Nature 461, 74–77 (2009).

    Article  CAS  Google Scholar 

  21. Wang, X. et al. An organic semiconductor organized into 3D DNA arrays by ‘bottom-up’ rational design. Angew. Chem. Int. Ed. 56, 6445–6448 (2017).

    Article  CAS  Google Scholar 

  22. Hao, Y. et al. A device that operates within within a self-assembled 3D DNA crystal. Nat. Chem. 9, 824–827 (2017).

    Article  CAS  Google Scholar 

  23. Douglas, S. M. et al. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459, 414–418 (2009).

    Article  CAS  Google Scholar 

  24. Zhang, T. et al. 3D DNA origami crystals. Adv. Mater. 30, 1800273 (2018).

    Article  CAS  Google Scholar 

  25. Yager, K. G., Zhang, Y. G., Lu, F. & Gang, O. Periodic lattices of arbitrary nano-objects: modeling and applications for self-assembled systems. J. Appl. Crystallogr. 47, 118–129 (2014).

    Article  CAS  Google Scholar 

  26. Tian, Y. et al. Lattice engineering through nanoparticle–DNA frameworks. Nat. Mater. 15, 654–661 (2016).

    Article  CAS  Google Scholar 

  27. Liu, W. et al. Diamond family of nanoparticle superlattices. Science 351, 582–586 (2016).

    Article  CAS  Google Scholar 

  28. Macfarlane, R. J. et al. Nanoparticle superlattice engineering with DNA. Science 334, 204–208 (2011).

    Article  CAS  Google Scholar 

  29. Rogers, W. B. & Crocker, J. C. Direct measurements of DNA-mediated colloidal interactions and their quantitative modeling. Proc. Natl Acad. Sci. USA 108, 15687–15692 (2011).

    Article  CAS  Google Scholar 

  30. Varilly, P., Angioletti-Uberti, S., Mognetti, B. M. & Frenkel, D. A general theory of DNA-mediated and other valence-limited colloidal interactions. J. Chem. Phys. 137, 094108 (2012).

    Article  CAS  Google Scholar 

  31. Travesset, A. Binary nanoparticle superlattices of softparticle systems. Proc. Natl Acad. Sci. USA 112, 9563–9567 (2015).

    Article  CAS  Google Scholar 

  32. Wertheim, M. S. Fluids with highly directional attractive forces. iii. multiple attraction sites. J. Stat. Phys. 42, 459–476 (1986).

    Article  Google Scholar 

  33. Damasecno, P. F., Engel, M. & Glotzer, S. C. Crystalline assemblies and densest packings of a family of truncated tetrahedra and the role of directional entropic forces. ACS Nano 6, 609–614 (2012).

    Article  CAS  Google Scholar 

  34. Murray, C. B., Kagan, C. R. & Bawendi, M. G. Synthesis and characterization of monodisperse nanocrystals and close-packed nanocrystal assemblies. Annu. Rev. Mater. Sci. 30, 545–610 (2000).

    Article  CAS  Google Scholar 

  35. Oliver, J. Quantum dots: global market growth and future commercial prospects. BCC Res. 5, 1–4 (2016).

    Google Scholar 

  36. Jang, E. et al. White-light-emitting diodes with quantum dot color converters for display backlights. Adv. Mater. 22, 3076–3080 (2010).

    Article  CAS  Google Scholar 

  37. Kim, T.-H. et al. Full-colour quantum dot displays fabricated by transfer printing. Nat. Photonics 5, 176–182 (2011).

    Article  CAS  Google Scholar 

  38. Wood, V. & Bulović, V. Colloidal quantum dot light-emitting devices. Nano Rev. 1, 5202 (2010).

    Article  CAS  Google Scholar 

  39. Chang, T.-W. F. et al. High near-infrared photoluminescence quantum efficiency from PbS nanocrystals in polymer films. Synth. Met. 148, 257–261 (2005).

    Article  CAS  Google Scholar 

  40. Kagan, C. R., Murray, C. B., Nirmal, M. & Bawendi, M. G. Electronic energy transfer in CdSe quantum dot solids. Phys. Rev. Lett. 76, 1517–1520 (1996).

    Article  CAS  Google Scholar 

  41. Baimuratov, A. S., Rukhlenko, I. D., Turkov, V. K., Baranov, A. V. & Fedorov, A. V. Quantum-dot supercrystals for future nanophotonics. Sci. Rep. 3, 1727 (2013).

    Article  CAS  Google Scholar 

  42. Kim, D. et al. Evidence of quantum resonance in periodically-ordered three-dimensional superlattice of CdTe quantum dots. Nano Lett. 15, 4343–4347 (2015).

    Article  CAS  Google Scholar 

  43. Wilner, O. I. et al. Enzyme cascades activated on topologically programmed DNA scaffolds. Nat. Nanotechnol. 4, 249–249 (2009).

    Article  CAS  Google Scholar 

  44. Fu, J., Liu, M., Liu, Y., Woodbury, N. W. & Yan, H. Interenzyme substrate diffusion for an enzyme cascade organized on spatially addressable DNA nanostructures. J. Am. Chem. Soc. 134, 5516–5519 (2012).

    Article  CAS  Google Scholar 

  45. Zhao, Z. et al. Nanocaged enzymes with enhanced catalytic activity and increased stability against protease digestion. Nat. Commun. 7, 10619 (2016).

    Article  CAS  Google Scholar 

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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.

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Authors and Affiliations



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.

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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. 19, 789–796 (2020).

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