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3D RNA-scaffolded wireframe origami

Author

Listed:
  • Molly F. Parsons

    (Massachusetts Institute of Technology)

  • Matthew F. Allan

    (Massachusetts Institute of Technology
    Harvard Medical School
    Massachusetts Institute of Technology)

  • Shanshan Li

    (Stanford University
    University of Science and Technology of China)

  • Tyson R. Shepherd

    (Massachusetts Institute of Technology
    Inscripta, Inc.)

  • Sakul Ratanalert

    (Massachusetts Institute of Technology
    Massachusetts Institute of Technology
    Johns Hopkins University)

  • Kaiming Zhang

    (Stanford University
    University of Science and Technology of China)

  • Krista M. Pullen

    (Massachusetts Institute of Technology)

  • Wah Chiu

    (Stanford University
    Stanford University)

  • Silvi Rouskin

    (Harvard Medical School)

  • Mark Bathe

    (Massachusetts Institute of Technology)

Abstract

Hybrid RNA:DNA origami, in which a long RNA scaffold strand folds into a target nanostructure via thermal annealing with complementary DNA oligos, has only been explored to a limited extent despite its unique potential for biomedical delivery of mRNA, tertiary structure characterization of long RNAs, and fabrication of artificial ribozymes. Here, we investigate design principles of three-dimensional wireframe RNA-scaffolded origami rendered as polyhedra composed of dual-duplex edges. We computationally design, fabricate, and characterize tetrahedra folded from an EGFP-encoding messenger RNA and de Bruijn sequences, an octahedron folded with M13 transcript RNA, and an octahedron and pentagonal bipyramids folded with 23S ribosomal RNA, demonstrating the ability to make diverse polyhedral shapes with distinct structural and functional RNA scaffolds. We characterize secondary and tertiary structures using dimethyl sulfate mutational profiling and cryo-electron microscopy, revealing insight into both global and local, base-level structures of origami. Our top-down sequence design strategy enables the use of long RNAs as functional scaffolds for complex wireframe origami.

Suggested Citation

  • Molly F. Parsons & Matthew F. Allan & Shanshan Li & Tyson R. Shepherd & Sakul Ratanalert & Kaiming Zhang & Krista M. Pullen & Wah Chiu & Silvi Rouskin & Mark Bathe, 2023. "3D RNA-scaffolded wireframe origami," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-36156-1
    DOI: 10.1038/s41467-023-36156-1
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