Protein-driven RNA nanostructured devices that function in vitro and control mammalian cell fate

Karin Hayashi,Shin Yonehara,Kumi Hidaka,Kaoru R Komatsu,Yoshihiko Fujita,Masayuki Endo,Hirohisa Ohno,Tomonori Shibata,Shunsuke Kawasaki,Hiroshi Sugiyama,Hirohide Saito,Yuki Suzuki

doi:10.1038/s41467-017-00459-x

Karin Hayashi, Shin Yonehara + Show 10 more

Open Access

https://doi.org/10.1038/s41467-017-00459-x

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Journal: Nature Communications	Publication Date: Sep 14, 2017
Citations: 43	License type: open-access

Affiliation: Kyoto University, Tohoku University

Abstract

Nucleic acid nanotechnology has great potential for future therapeutic applications. However, the construction of nanostructured devices that control cell fate by detecting and amplifying protein signals has remained a challenge. Here we design and build protein-driven RNA-nanostructured devices that actuate in vitro by RNA-binding-protein-inducible conformational change and regulate mammalian cell fate by RNA–protein interaction-mediated protein assembly. The conformation and function of the RNA nanostructures are dynamically controlled by RNA-binding protein signals. The protein-responsive RNA nanodevices are constructed inside cells using RNA-only delivery, which may provide a safe tool for building functional RNA–protein nanostructures. Moreover, the designed RNA scaffolds that control the assembly and oligomerization of apoptosis-regulatory proteins on a nanometre scale selectively kill target cells via specific RNA–protein interactions. These findings suggest that synthetic RNA nanodevices could function as molecular robots that detect signals and localize target proteins, induce RNA conformational changes, and programme mammalian cellular behaviour.

Highlights

Nucleic acid nanotechnology has great potential for future therapeutic applications
We have previously designed trianglelike RNP nanostructures in vitro using three K-turn-L7Ae motifs inserted into three vertexes of nanostructures composed of double-stranded RNAs31–33
To induce an apparent conformational change via the RNP interaction, we designed two RNA strands (long (L) and short (S) strands) in which Watson–Crick base pairs are formed within the strands but where the two ends of the double-stranded RNA do not interact with each other (Fig. 2a; protein-free double-stranded RNAs should form open, nearly linear structures)

Summary

Introduction

Nucleic acid nanotechnology has great potential for future therapeutic applications. the construction of nanostructured devices that control cell fate by detecting and amplifying protein signals has remained a challenge. We design and build protein-driven RNAnanostructured devices that actuate in vitro by RNA-binding-protein-inducible conformational change and regulate mammalian cell fate by RNA–protein interaction-mediated protein assembly. The designed RNA scaffolds that control the assembly and oligomerization of apoptosis-regulatory proteins on a nanometre scale selectively kill target cells via specific RNA–protein interactions These findings suggest that synthetic RNA nanodevices could function as molecular robots that detect signals and localize target proteins, induce RNA conformational changes, and programme mammalian cellular behaviour. We considered building synthetic RNP nanostructured devices by mimicking natural RNP complexes that have the following properties: (1) RNA-nanostructured devices detect and localize target RNA-binding proteins both in vitro and inside cells; (2) the conformation of the RNA devices is dynamically changed through specific RNP interactions; and (3) the actuation of the RNA devices produces functional outputs dependent on the extracellular and intracellular environment. Synthetic RNA scaffolds formed in mammalian cells can selectively control cell-death pathways by detecting endogenous RNA-binding protein or microRNA (miRNA) signals and regulating the assembly and oligomerization of apoptosis-regulatory proteins on a nanometre scale (Fig. 1d)

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