Responsive self-assembly of tectoRNAs with loop-receptor interactions from the tetrahydrofolate (THF) riboswitch.

Charles Mitchell,Julio A Polanco,Laura Dewald,Wade W Grabow,Luc Jaeger,Dustin Kress

doi:10.1093/nar/gkz304

Charles Mitchell, Julio A Polanco + Show 4 more

Open Access

https://doi.org/10.1093/nar/gkz304

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Abstract

Naturally occurring RNAs are known to exhibit a high degree of modularity, whereby specific structural modules (or motifs) can be mixed and matched to create new molecular architectures. The modular nature of RNA also affords researchers the ability to characterize individual structural elements in controlled synthetic contexts in order to gain new and critical insights into their particular structural features and overall performance. Here, we characterized the binding affinity of a unique loop–receptor interaction found in the tetrahydrofolate (THF) riboswitch using rationally designed self-assembling tectoRNAs. Our work suggests that the THF loop–receptor interaction has been fine-tuned for its particular role as a riboswitch component. We also demonstrate that the thermodynamic stability of this interaction can be modulated by the presence of folinic acid, which induces a local structural change at the level of the loop–receptor. This corroborates the existence of a THF binding site within this tertiary module and paves the way for its potential use as a THF responsive module for RNA nanotechnology and synthetic biology.

Highlights

Occurring ribonucleic acid (RNA) molecules like the ribosome utilize recurrent structural patterns known as modules or motifs to fold and assemble into specific threedimensional shapes (e.g. [1,2,3,4,5,6,7])
The modular nature by which functional RNAs result from the mixing and matching of structural modules provides a blueprint for the rational design of artificial RNA-based nanostructures
Synthetic RNA nanoparticles built from such structural elements have provided promising tools for synthetic biology, cancer, and genetic diseases [10,12,16,17,18,19]

Summary

Introduction

Occurring ribonucleic acid (RNA) molecules like the ribosome utilize recurrent structural patterns known as modules or motifs to fold and assemble into specific threedimensional shapes (e.g. [1,2,3,4,5,6,7]). Occurring ribonucleic acid (RNA) molecules like the ribosome utilize recurrent structural patterns known as modules or motifs to fold and assemble into specific threedimensional shapes The modular nature by which functional RNAs result from the mixing and matching of structural modules provides a blueprint for the rational design of artificial RNA-based nanostructures RNA modules that facilitate long-range RNA-RNA interactions are known to play especially crucial roles in the initiation and spontaneous folding and/or self-assembly and for this reason have and continue to provide exemplary sources of inspiration for building artificial nanostructures The continued discovery and characterization of RNA modules with distinctive geometrical and functional properties hold potential for various additional applications. A current and rich example of this over the past decade involves the discovery of riboswitches––ncRNA segments that alter gene expression levels through metabolite binding that induces intramolecular transcriptional regulation [23,24]

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