Structure, folding and flexibility of co-transcriptional RNA origami

Ewan K S McRae, Helena Østergaard Rasmussen, Jianfang Liu, Andreas Bøggild, Michael T A Nguyen, Nestor Sampedro Vallina, Thomas Boesen, Jan Skov Pedersen, Gang Ren, Cody Geary, Ebbe Sloth Andersen

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

Abstract

RNA origami is a method for designing RNA nanostructures that can self-assemble through co-transcriptional folding with applications in nanomedicine and synthetic biology. However, to advance the method further, an improved understanding of RNA structural properties and folding principles is required. Here we use cryogenic electron microscopy to study RNA origami sheets and bundles at sub-nanometre resolution revealing structural parameters of kissing-loop and crossover motifs, which are used to improve designs. In RNA bundle designs, we discover a kinetic folding trap that forms during folding and is only released after 10 h. Exploration of the conformational landscape of several RNA designs reveal the flexibility of helices and structural motifs. Finally, sheets and bundles are combined to construct a multidomain satellite shape, which is characterized by individual-particle cryo-electron tomography to reveal the domain flexibility. Together, the study provides a structural basis for future improvements to the design cycle of genetically encoded RNA nanodevices.

Original languageEnglish
JournalNature Nanotechnology
Volume18
Issue7
Pages (from-to)808-817
Number of pages10
ISSN1748-3387
DOIs
Publication statusPublished - Jul 2023

Keywords

  • Molecular Conformation
  • Nanomedicine
  • Nanostructures/chemistry
  • Nanotechnology/methods
  • Nucleic Acid Conformation
  • RNA/chemistry

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