3D RNA-scaffolded wireframe origami

Abstract

Hybrid RNA:DNA origami, in which a long RNA scaffold strand is folded 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 wireframe RNA-scaffolded origami in three dimensions rendered as polyhedra composed of dual-duplex edges. We computationally designed, fabricated, and characterized 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 characterized secondary and tertiary structures using dimethyl sulfate mutational profiling and cryo-electron microscopy, revealing for the first time 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.