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

doi:10.1038/s41565-023-01321-6

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

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avis › Tidsskriftartikel › Forskning › peer 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.

Originalsprog	Engelsk
Tidsskrift	Nature Nanotechnology
Vol/bind	18
Nummer	7
Sider (fra-til)	808-817
Antal sider	10
ISSN	1748-3387
DOI	https://doi.org/10.1038/s41565-023-01321-6
Status	Udgivet - jul. 2023

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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.",

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AU - Rasmussen, Helena Østergaard

AU - Liu, Jianfang

AU - Bøggild, Andreas

AU - Nguyen, Michael T A

AU - Sampedro Vallina, Nestor

AU - Boesen, Thomas

AU - Pedersen, Jan Skov

AU - Ren, Gang

AU - Geary, Cody

AU - Andersen, Ebbe Sloth

PY - 2023/7

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N2 - 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.

AB - 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.

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KW - Nanostructures/chemistry

KW - Nanotechnology/methods

KW - Nucleic Acid Conformation

KW - RNA/chemistry

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DO - 10.1038/s41565-023-01321-6

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VL - 18

SP - 808

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JO - Nature Nanotechnology

JF - Nature Nanotechnology

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Structure, folding and flexibility of co-transcriptional RNA origami

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