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Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon

Torelli, E.; Kozyra, J.W.; J.-y., Gu; Stimming, U.; Piantanida, L.; Voïtchovsky, K.; Krasnogor, N.

Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon Thumbnail


Authors

E. Torelli

J.W. Kozyra

Gu J.-y.

U. Stimming

L. Piantanida

N. Krasnogor



Abstract

RNA presents intringuing roles in many cellular processes and its versatility underpins many different applications in synthetic biology. Nonetheless, RNA origami as a method for nanofabrication is not yet fully explored and the majority of RNA nanostructures are based on natural pre-folded RNA. Here we describe a biologically inert and uniquely addressable RNA origami scaffold that self-assembles into a nanoribbon by seven staple strands. An algorithm is applied to generate a synthetic De Bruijn scaffold sequence that is characterized by the lack of biologically active sites and repetitions larger than a predetermined design parameter. This RNA scaffold and the complementary staples fold in a physiologically compatible isothermal condition. In order to monitor the folding, we designed a new split Broccoli aptamer system. The aptamer is divided into two nonfunctional sequences each of which is integrated into the 5′ or 3′ end of two staple strands complementary to the RNA scaffold. Using fluorescence measurements and in-gel imaging, we demonstrate that once RNA origami assembly occurs, the split aptamer sequences are brought into close proximity forming the aptamer and turning on the fluorescence. This light-up ‘bio-orthogonal’ RNA origami provides a prototype that can have potential for in vivo origami applications.

Citation

Torelli, E., Kozyra, J., J.-y., G., Stimming, U., Piantanida, L., Voïtchovsky, K., & Krasnogor, N. (2018). Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon. Scientific Reports, 8(1), Article 6989. https://doi.org/10.1038/s41598-018-25270-6

Journal Article Type Article
Acceptance Date Apr 12, 2018
Online Publication Date May 3, 2018
Publication Date May 3, 2018
Deposit Date May 4, 2018
Publicly Available Date May 8, 2018
Journal Scientific Reports
Publisher Nature Research
Peer Reviewed Peer Reviewed
Volume 8
Issue 1
Article Number 6989
DOI https://doi.org/10.1038/s41598-018-25270-6

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http://creativecommons.org/licenses/by/4.0/

Copyright Statement
This article is licensed under a Creative Commons Attribution 4.0 International<br /> License, which permits use, sharing, adaptation, distribution and reproduction in any medium or<br /> format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative<br /> Commons license, and indicate if changes were made. Te images or other third party material in this<br /> article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the<br /> material. If material is not included in the article’s Creative Commons license and your intended use is not permitted<br /> by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the<br /> copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.<br /> © The Author(s) 2018







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