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Programmable icosahedral shell system for virus trapping

Abstract

Broad-spectrum antiviral platforms that can decrease or inhibit viral infection would alleviate many threats to global public health. Nonetheless, effective technologies of this kind are still not available. Here, we describe a programmable icosahedral canvas for the self-assembly of icosahedral shells that have viral trapping and antiviral properties. Programmable triangular building blocks constructed from DNA assemble with high yield into various shell objects with user-defined geometries and apertures. We have created shells with molecular masses ranging from 43 to 925 MDa (8 to 180 subunits) and with internal cavity diameters of up to 280 nm. The shell interior can be functionalized with virus-specific moieties in a modular fashion. We demonstrate this virus-trapping concept by engulfing hepatitis B virus core particles and adeno-associated viruses. We demonstrate the inhibition of hepatitis B virus core interactions with surfaces in vitro and the neutralization of infectious adeno-associated viruses exposed to human cells.

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Fig. 1: Design principles for antiviral platform technologies.
Fig. 2: Structures of shells and shell subunits.
Fig. 3: Shell yield and stability.
Fig. 4: Sculpting on an icosahedral canvas.
Fig. 5: Trapping of HBV core particles.
Fig. 6: Neutralization of AAV2 with DNA origami half shells.

Data availability

Source data are provided with this paper. The remaining data supporting the findings of this study are available within the paper and its Supplementary Information files, and are available from the corresponding author upon reasonable request. The cryo-EM data from this study have been deposited in the Electron Microscopy Data Bank with the following accession codes: EMD-12007, EMD-12008, EMD-12009, EMD-12010, EMD-12011, EMD-12012, EMD-12013, EMD-12014, EMD-12015, EMD-12016, EMD-12019, EMD-12020, EMD-12021, EMD-12022, EMD-12023, EMD-12024, EMD-12044, EMD-12045, EMD-12046 and EMD-12049.

References

  1. Lauster, D. et al. Phage capsid nanoparticles with defined ligand arrangement block influenza virus entry. Nat. Nanotechnol. 15, 373–379 (2020).

    CAS  Article  Google Scholar 

  2. Kwon, P. S. et al. Designer DNA architecture offers precise and multivalent spatial pattern-recognition for viral sensing and inhibition. Nat. Chem. 12, 26–35 (2020).

    CAS  Article  Google Scholar 

  3. Cao, L. et al. De novo design of picomolar SARS-CoV-2 miniprotein inhibitors. Science 370, 426–431 (2020).

    CAS  Article  Google Scholar 

  4. Cagno, V., Tseligka, E. D., Jones, S. T. & Tapparel, C. Heparan sulfate proteoglycans and viral attachment: true receptors or adaptation bias? Viruses 11, 596 (2019).

    CAS  Article  Google Scholar 

  5. Legendre, M. et al. Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology. Proc. Natl Acad. Sci. USA 111, 4274–4279 (2014).

    CAS  Article  Google Scholar 

  6. Bale, J. B. et al. Accurate design of megadalton-scale two-component icosahedral protein complexes. Science 353, 389–394 (2016).

    CAS  Article  Google Scholar 

  7. King, N. P. et al. Accurate design of co-assembling multi-component protein nanomaterials. Nature 510, 103–108 (2014).

    CAS  Article  Google Scholar 

  8. Lai, Y. T. et al. Structure of a designed protein cage that self-assembles into a highly porous cube. Nat. Chem. 6, 1065–1071 (2014).

    CAS  Article  Google Scholar 

  9. Butterfield, G. L. et al. Evolution of a designed protein assembly encapsulating its own RNA genome. Nature 552, 415–420 (2017).

    CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

  12. Castro, C. E. et al. A primer to scaffolded DNA origami. Nat. Methods 8, 221–229 (2011).

    CAS  Article  Google Scholar 

  13. Veneziano, R. et al. Designer nanoscale DNA assemblies programmed from the top down. Science 352, 1534 (2016).

    CAS  Article  Google Scholar 

  14. Benson, E. et al. DNA rendering of polyhedral meshes at the nanoscale. Nature 523, 441–444 (2015).

    CAS  Article  Google Scholar 

  15. Dunn, K. E. et al. Guiding the folding pathway of DNA origami. Nature 525, 82–86 (2015).

    CAS  Article  Google Scholar 

  16. Bai, X. C., Martin, T. G., Scheres, S. H. & Dietz, H. Cryo-EM structure of a 3D DNA-origami object. Proc. Natl Acad. Sci. USA 109, 20012–20017 (2012).

    CAS  Article  Google Scholar 

  17. Funke, J. J. & Dietz, H. Placing molecules with Bohr radius resolution using DNA origami. Nat. Nanotechnol. 11, 47–52 (2016).

    CAS  Article  Google Scholar 

  18. Iinuma, R. et al. Polyhedra self-assembled from DNA tripods and characterized with 3D DNA-PAINT. Science 344, 65–69 (2014).

    CAS  Article  Google Scholar 

  19. Jungmann, R. et al. DNA origami-based nanoribbons: assembly, length distribution, and twist. Nanotechnology 22, 275301 (2011).

    Article  CAS  Google Scholar 

  20. Liu, W., Zhong, H., Wang, R. & Seeman, N. C. Crystalline two-dimensional DNA-origami arrays. Angew. Chem. Int. Ed. 50, 264–267 (2011).

    CAS  Article  Google Scholar 

  21. Suzuki, Y., Endo, M. & Sugiyama, H. Lipid-bilayer-assisted two-dimensional self-assembly of DNA origami nanostructures. Nat. Commun. 6, 8052 (2015).

    CAS  Article  Google Scholar 

  22. Ke, Y. et al. DNA brick crystals with prescribed depths. Nat. Chem. 6, 994–1002 (2014).

    CAS  Article  Google Scholar 

  23. Wagenbauer, K. F., Sigl, C. & Dietz, H. Gigadalton-scale shape-programmable DNA assemblies. Nature 552, 78–83 (2017).

    CAS  Article  Google Scholar 

  24. Crick, F. H. & Watson, J. D. Structure of small viruses. Nature 177, 473–475 (1956).

    CAS  Article  Google Scholar 

  25. Caspar, D. L. & Klug, A. Physical principles in the construction of regular viruses. Cold Spring Harb. Symp. Quant. Biol. 27, 1–24 (1962).

    CAS  Article  Google Scholar 

  26. Twarock, R. & Luque, A. Structural puzzles in virology solved with an overarching icosahedral design principle. Nat. Commun. 10, 4414 (2019).

    Article  CAS  Google Scholar 

  27. Gerling, T., Wagenbauer, K. F., Neuner, A. M. & Dietz, H. Dynamic DNA devices and assemblies formed by shape-complementary, non-base pairing 3D components. Science 347, 1446–1452 (2015).

    CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

  29. Maffeo, C., Yoo, J. & Aksimentiev, A. De novo reconstruction of DNA origami structures through atomistic molecular dynamics simulation. Nucleic Acids Res. 44, 3013–3019 (2016).

    CAS  Article  Google Scholar 

  30. Wagenbauer, K. F. et al. How we make DNA origami.ChemBioChem 18, 1873–1885 (2017).

    Article  CAS  Google Scholar 

  31. Langecker, M. et al. Synthetic lipid membrane channels formed by designed DNA nanostructures. Science 338, 932–936 (2012).

    CAS  Article  Google Scholar 

  32. Gerling, T., Kube, M., Kick, B. & Dietz, H. Sequence-programmable covalent bonding of designed DNA assemblies. Sci. Adv. 4, eaau1157 (2018).

    CAS  Article  Google Scholar 

  33. Ponnuswamy, N. et al. Oligolysine-based coating protects DNA nanostructures from low-salt denaturation and nuclease degradation. Nat. Commun. 8, 15654 (2017).

    CAS  Article  Google Scholar 

  34. Wang, D., Tai, P. W. L. & Gao, G. Adeno-associated virus vector as a platform for gene therapy delivery. Nat. Rev. Drug Discov. 18, 358–378 (2019).

    CAS  Article  Google Scholar 

  35. Guo, P. et al. Rapid AAV-neutralizing antibody determination with a cell-binding assay. Mol. Ther. Methods Clin. Dev. 13, 40–46 (2019).

    CAS  Article  Google Scholar 

  36. Praetorius, F. et al. Biotechnological mass production of DNA origami. Nature 552, 84–87 (2017).

    CAS  Article  Google Scholar 

  37. Ohto, U. et al. Structural basis of CpG and inhibitory DNA recognition by Toll-like receptor 9. Nature 520, 702–705 (2015).

    CAS  Article  Google Scholar 

  38. Andreeva, L. et al. cGAS senses long and HMGB/TFAM-bound U-turn DNA by forming protein–DNA ladders. Nature 549, 394–398 (2017).

    CAS  Article  Google Scholar 

  39. Engelhardt, F. A. S. et al. Custom-size, functional, and durable DNA origami with design-specific scaffolds. ACS Nano 13, 5015–5027 (2019).

    CAS  Article  Google Scholar 

  40. Kick, B., Praetorius, F., Dietz, H. & Weuster-Botz, D. Efficient production of single-stranded phage DNA as scaffolds for DNA origami. Nano Lett. 15, 4672–4676 (2015).

    CAS  Article  Google Scholar 

  41. Kremer, J. R., Mastronarde, D. N. & McIntosh, J. R. Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116, 71–76 (1996).

    CAS  Article  Google Scholar 

  42. Kimanius, D., Forsberg, B. O., Scheres, S. H. & Lindahl, E. Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2. Elife 5, e18722 (2016).

    Article  CAS  Google Scholar 

  43. Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. Elife 7, e42166 (2018).

    Article  Google Scholar 

  44. Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).

    CAS  Article  Google Scholar 

  45. Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).

    Article  Google Scholar 

  46. Sominskaya, I. et al. A VLP library of C-terminally truncated hepatitis B core proteins: correlation of RNA encapsidation with a Th1/Th2 switch in the immune responses of mice. PLoS ONE 8, e75938 (2013).

    CAS  Article  Google Scholar 

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Acknowledgements

We thank B. Kick for help with the antibody–DNA conjugation and for scaffold preparation. We also thank the Monoclonal Antibody Facility of Helmholtz Zentrum München (head: R. Feederle) for help with generating and providing anti-HBc 17H7. This work was supported by a European Research Council Consolidator Grant to H.D. (grant no. 724261), the Deutsche Forschungsgemeinschaft through grants provided within the Gottfried-Wilhelm-Leibniz Program and the SFB863 TPA9 (to H.D.), the TRR179 (TP14 to U.P.), the German Ministry for Education and Research (BMBF) through StabVacB and DZIF (project 05.806/907 to U.P.), the European Commission FET Open Grant VIROFIGHT (grant no. 899619 to H.D. and U.P.), the Netherlands Organization for Scientific Research (NWO, Rubicon programme, project no. 019.182EN.037 to W.E.), the USA National Science Foundation through the Brandeis University Materials Research Science and Engineering Center (NSF DMR-1420382 and NSF DMR-2011486 to S.F. and M.F.H.), the National Institute of General Medical Sciences (award no. R01GM108021 to M.F.H.) and the Alexander von Humboldt Foundation (Humboldt Research Fellowship to J.A.K.). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 899619. The views expressed here are the responsibility of the authors only. The EU Commission takes no responsibility for any use made of the information set out.

Author information

Authors and Affiliations

Authors

Contributions

H.D. designed the research. S.F. co-designed the icosahedral shell self-assembly studies (Figs. 1 and 2). C.S. performed shell subunit design, shell assembly and all structural studies (Figs. 1–6). E.M.W. performed shell modification and stabilization, and HBV virus-binding inhibition experiments (Figs. 4–6), supported by A.L. W.E. performed subunit exchange and HBV virus-binding inhibition experiments (Figs. 4 and 5). J.A.K. performed the cell culture AAV neutralization experiments (Fig. 6). K.S. performed auxiliary shell subunit geometry alteration experiments (Supplementary Fig. 18). F.K., F.W. and U.P. contributed HBV samples, and generated and provided anti-HBc (Fig. 5). S.A.A. performed cargo encapsulation (Supplementary Fig. 36). M.F.H. contributed to shell design choices.

Corresponding author

Correspondence to Hendrik Dietz.

Ethics declarations

Competing interests

A provisional patent has been filed by the TUM (PCT/EP2021/054307).

Additional information

Peer review information Nature Materials thanks Xing Wang, Andrew Ward, Hao Yan and Todd Yeates for their contribution to the peer review of this work.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

Supplementary Figs. 1–46, Tables 1–3, Videos 1–8, Note 1 and references.

Reporting Summary

Supplementary Video 1

Cryo-EM reconstruction of the octahedron shell.

Supplementary Video 2

Cryo-EM reconstruction of the T = 1 shell.

Supplementary Video 3

Cryo-EM reconstruction of the T = 3 shell.

Supplementary Video 4

Cryo-EM reconstruction of the T = 4 shell.

Supplementary Video 5

Slices through a negative stain TEM tomogram of the T = 9 shell.

Supplementary Video 6

Cryo-EM reconstruction of two half octahedral shells + HBV core.

Supplementary Video 7

Cryo-EM reconstruction of two half octahedral shells + HBV core.

Supplementary Video 8

Cryo-EM reconstruction of the spiky T = 1 shell.

Supplementary Data

DNA sequences of staple strands.

Source data

Source Data Fig. 3

Uncropped gel scans.

Source Data Supplementary Fig. 11

Uncropped gel scans.

Source Data Supplementary Fig. 22

Uncropped gel scans.

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Sigl, C., Willner, E.M., Engelen, W. et al. Programmable icosahedral shell system for virus trapping. Nat. Mater. 20, 1281–1289 (2021). https://doi.org/10.1038/s41563-021-01020-4

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