Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Prescribed nanoparticle cluster architectures and low-dimensional arrays built using octahedral DNA origami frames

Nature Nanotechnology volume 10, pages 637–644 (2015)Cite this article

Subjects

Abstract

Three-dimensional mesoscale clusters that are formed from nanoparticles spatially arranged in pre-determined positions can be thought of as mesoscale analogues of molecules. These nanoparticle architectures could offer tailored properties due to collective effects, but developing a general platform for fabricating such clusters is a significant challenge. Here, we report a strategy for assembling three-dimensional nanoparticle clusters that uses a molecular frame designed with encoded vertices for particle placement. The frame is a DNA origami octahedron and can be used to fabricate clusters with various symmetries and particle compositions. Cryo-electron microscopy is used to uncover the structure of the DNA frame and to reveal that the nanoparticles are spatially coordinated in the prescribed manner. We show that the DNA frame and one set of nanoparticles can be used to create nanoclusters with different chiroptical activities. We also show that the octahedra can serve as programmable interparticle linkers, allowing one- and two-dimensional arrays to be assembled with designed particle arrangements.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Scheme of three designed clusters assembled from DNA-functionalized gold nanoparticles on correspondingly encoded vertices of octahedral DNA frames.
Figure 2: Structure of the self-assembled DNA origami octahedron, obtained by cryo-EM and 3D reconstruction.
Figure 3: Structure of six-fold P6 and four-fold P4(1234) nanoparticle clusters, as revealed by cryo-EM and 3D reconstruction.
Figure 4: Characterization of heterocluster population and structure of individual heteroclusters, P12(12)P22(34)P32(56).
Figure 5: CD spectra for non-chiral and chiral nanoparticle clusters assembled on an octahedron frame.
Figure 6: Correspondingly encoded octahedra used as programble linkers for assembly into linear and 2D square arrays, respectively.

Similar content being viewed by others

References

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

    Article  Google Scholar 

  2. Zeravcic, Z. & Brenner, M. P. Self-replicating colloidal clusters. Proc. Natl Acad. Sci. USA 111, 1748–1753 (2013).

    Article  Google Scholar 

  3. Maye, M. M., Gang, O. & Cotlet, M. Photoluminescence enhancement in CdSe/ZnS-DNA linked-Au nanoparticle heterodimers probed by single molecule spectroscopy. Chem. Commun. 46, 6111–6113 (2010).

    Article  CAS  Google Scholar 

  4. Yan, W. et al. Self-assembly of chiral nanoparticle pyramids with strong R/S optical activity. J. Am. Chem. Soc. 134, 15114–15121 (2012).

    Article  CAS  Google Scholar 

  5. Fan, J. A. et al. Plasmonic mode engineering with templated self-assembled nanoclusters. Nano Lett. 12, 5318–5324 (2012).

    Article  CAS  Google Scholar 

  6. Hiroi, K., Komatsu, K. & Sato, T. Superspin glass originating from dipolar interaction with controlled interparticle distance among gamma-Fe2O3 nanoparticles with silica shells. Phys. Rev. B 83, 224423 (2011).

    Article  Google Scholar 

  7. Govorov, A. O., Fan, Z., Hernandez, P., Slocik, J. M. & Naik, R. R. Theory of circular dichroism of nanomaterials comprising chiral molecules and nanocrystals: plasmon enhancement, dipole interactions, and dielectric effects. Nano Lett. 10, 1374–1382 (2010).

    Article  CAS  Google Scholar 

  8. Kuzyk, A. et al. DNA-based self-assembly of chiral plasmonic nanostructures with tailored optical response. Nature 483, 311–314 (2012).

    Article  CAS  Google Scholar 

  9. Barrow, S. J., Wei, X., Baldauf, J. S., Funston, A. M. & Mulvaney, P. The surface plasmon modes of self-assembled gold nanocrystals. Nature Commun. 3, 1–9 (2012).

    Article  Google Scholar 

  10. Ruzicka, B. et al. Observation of empty liquids and equilibrium gels in a colloidal clay. Nature Mater. 10, 56–60 (2011).

    Article  CAS  Google Scholar 

  11. Wang, Y. et al. Colloids with valence and specific directional bonding. Nature 491, 51–56 (2012).

    Article  CAS  Google Scholar 

  12. Chen, Q. et al. Supracolloidal reaction kinetics of janus spheres. Science 331, 199–202 (2011).

    Article  CAS  Google Scholar 

  13. Mastroianni, A. J., Claridge, S. A. & Alivisatos, A. P. Pyramidal and chiral groupings of gold nanocrystals assembled using DNA scaffolds. J. Am. Chem. Soc. 131, 8455–8459 (2009).

    Article  CAS  Google Scholar 

  14. Klinkova, A., Thérien-Aubin, H., Choueiri, R. M., Rubinstein, M. & Kumacheva, E. Colloidal analogs of molecular chain stoppers. Proc. Natl Acad. Sci. USA 110, 18775–18779 (2013).

    Article  CAS  Google Scholar 

  15. Kim, J-W., Kim, J-H. & Deaton, R. DNA-linked nanoparticle building blocks for programmable matter. Angew. Chem. Int. Ed. 50, 9185–9190 (2011).

    Article  CAS  Google Scholar 

  16. Alivisatos, A. P. et al. Organization of ‘nanocrystal molecules’ using DNA. Nature 382, 609–611 (1996).

    Article  CAS  Google Scholar 

  17. Maye, M. M., Nykypanchuk, D., Cuisinier, M., van der Lelie, D. & Gang, O. Stepwise surface encoding for high-throughput assembly of nanoclusters. Nature Mater. 8, 388–391 (2009).

    Article  CAS  Google Scholar 

  18. Pal, S., Deng, Z., Ding, B., Yan, H. & Liu, Y. DNA-origami-directed self-assembly of discrete silver-nanoparticle architectures. Angew. Chem. Int. Ed. 49, 2700–2704 (2010).

    Article  CAS  Google Scholar 

  19. Lee, J., Hernandez, P., Govorov, A. O. & Kotov, N. A. Exciton–plasmon interactions in molecular spring assemblies of nanowires and wavelength-based protein detection. Nature Mater. 6, 291–295 (2007).

    Article  CAS  Google Scholar 

  20. Sun, D. et al. Heterogeneous nanoclusters assembled by PNA-templated double-stranded DNA. Nanoscale 4, 6722–6725 (2012).

    Article  CAS  Google Scholar 

  21. Zhang, Y., Lu, F., Yager, K. G., van der Lelie, D. & Gang, O. A general strategy for the DNA-mediated self-assembly of functional nanoparticles into heterogeneous systems. Nature Nanotech. 8, 865–872 (2013).

    Article  CAS  Google Scholar 

  22. Zhang, C. et al. A general approach to DNA-programmable atom equivalents. Nature Mater. 12, 741–746 (2013).

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  24. Shih, W. M., Quispe, J. D. & Joyce, G. F. A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron. Nature 427, 618–621 (2004).

    Article  CAS  Google Scholar 

  25. 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 

  26. 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 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  29. Dietz, H., Douglas, S. M. & Shih, W. M. Folding DNA into twisted and curved nanoscale shapes. Science 325, 725–730 (2009).

    Article  CAS  Google Scholar 

  30. Zhang, C. et al. DNA nanocages swallow gold nanoparticles (AuNPs) to form AuNP@DNA cage core–shell structures. ACS Nano 8, 1130–1135 (2014).

    Article  CAS  Google Scholar 

  31. Sharma, J. et al. Control of self-assembly of DNA tubules through integration of gold nanoparticles. Science 323, 112–116 (2009).

    Article  CAS  Google Scholar 

  32. Andersen, E. S. et al. Self-assembly of a nanoscale DNA box with a controllable lid. Nature 459, 73–76 (2009).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  34. Bai, X., Martin, T. G., Scheres, S. H. W. & Dietz, H. Cryo-EM structure of a 3D DNA-origami object. Proc. Natl Acad. Sci. USA 149, 20012–20017 (2012).

    Article  Google Scholar 

  35. Midgley, P. A. & Dunin-Borkowski, R. E. Electron tomography and holography in materials science. Nature Mater. 8, 271–280 (2009).

    Article  CAS  Google Scholar 

  36. Kourkoutis, L. F., Plitzko, J. M. & Baumeister, W. Electron microscopy of biological materials at the nanometer scale. Annu. Rev. Mater. Res. 42, 33–58 (2012).

    Article  CAS  Google Scholar 

  37. De-Rosier, D. & Klug, A. Reconstruction of three dimensional structures from electron micrographs. Nature 217, 130–134 (1968).

    Article  CAS  Google Scholar 

  38. Douglas, S. M. et al. Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Res. 37, 5001–5006 (2009).

    Article  CAS  Google Scholar 

  39. Mathieu, F. et al. Six-helix bundles designed from DNA. Nano Lett. 5, 661–665 (2005).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  41. Douglas, S. M., Chou, J. J. & Shih, W. M. DNA-nanotube-induced alignment of membrane proteins for NMR structure determination. Proc. Natl Acad. Sci. USA 104, 6644–6648 (2006).

    Article  Google Scholar 

  42. Hill, H. D., Millstone, J. E., Banholzer, M. J. & Mirkin, C. A. The role radius of curvature plays in thiolated oligonucleotide loading on gold nanoparticles. ACS Nano 3, 418–424 (2009).

    Article  CAS  Google Scholar 

  43. King, R. B. Nonhanded chirality in octahedral metal complexes. Chirality 13, 465–473 (2001).

    Article  CAS  Google Scholar 

  44. Chi, C., Vargas-Lara, F., Tkachenko, A. V., Starr, F. W. & Gang, O. Internal structure of nanoparticle dimers linked by DNA. ACS Nano 6, 6793–7802 (2012).

    Article  CAS  Google Scholar 

  45. Kaya, H. Scattering from cylinders with globular end-caps. J. Appl. Crystallogr. 37, 223–230 (2004).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors thank J. Li for help with tomography analysis and D. Chen for assistance with schematic drawing. Research carried out at the Centre for Functional Nanomaterials, Brookhaven National Laboratory, was supported by the US Department of Energy, Office of Basic Energy Sciences (contract no. DE-SC0012704). H.L. was supported by a National Institutes of Health R01 grant (AG029979) and W.M.S. was supported by a National Science Foundation Expeditions grant (1317694) and Designing Materials to Revolutionize and Engineer Our Future grant (1435964).

Author information

Author notes

  1. Yonggang Ke

    Present address: Present address: Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, USA,

  2. Ye Tian and Tong Wang: These authors contributed equally to this work

Authors and Affiliations

  1. Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, 11973, New York, USA

    Ye Tian, Wenyan Liu, Huolin L. Xin & Oleg Gang

  2. Biosciences Department, Brookhaven National Laboratory, Upton, 11973, New York, USA

    Tong Wang & Huilin Li

  3. Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, 11794-5213, New York, USA

    Huilin Li

  4. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, 02115, Massachusetts, USA

    Yonggang Ke & William M. Shih

  5. Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, 02115, Massachusetts, USA

    Yonggang Ke & William M. Shih

  6. Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, 02115, Massachusetts, USA

    Yonggang Ke & William M. Shih

Authors
  1. Ye Tian
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tong Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Wenyan Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Huolin L. Xin
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Huilin Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Yonggang Ke
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. William M. Shih
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Oleg Gang
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Y.T. and O.G. conceived and designed the experiments. Y.T. performed the experiments. W.M.S. and Y.K. contributed to the octahedral design. Y.T., T.W., W.L. and O.G. analysed the data. T.W. and H.L. contributed to the cryo-EM measurement and reconstruction. H.X. contributed to the tomography analysis. Y.T. and O.G. wrote the paper. O.G. supervised the project. All authors discussed the results and commented on the manuscript.

Corresponding author

Correspondence to Oleg Gang.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary information

Supplementary Information (PDF 3194 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Tian, Y., Wang, T., Liu, W. et al. Prescribed nanoparticle cluster architectures and low-dimensional arrays built using octahedral DNA origami frames. Nature Nanotech 10, 637–644 (2015). https://doi.org/10.1038/nnano.2015.105

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nnano.2015.105

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing