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

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...

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Autores principales:	Emanuela Torelli, Jerzy Wieslaw Kozyra, Jing-Ying Gu, Ulrich Stimming, Luca Piantanida, Kislon Voïtchovsky, Natalio Krasnogor
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/eb93bb9c43814661800342a4e751c809
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spelling	oai:doaj.org-article:eb93bb9c43814661800342a4e751c8092021-12-02T16:08:16ZIsothermal folding of a light-up bio-orthogonal RNA origami nanoribbon10.1038/s41598-018-25270-62045-2322https://doaj.org/article/eb93bb9c43814661800342a4e751c8092018-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-25270-6https://doaj.org/toc/2045-2322Abstract 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.Emanuela TorelliJerzy Wieslaw KozyraJing-Ying GuUlrich StimmingLuca PiantanidaKislon VoïtchovskyNatalio KrasnogorNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-12 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Emanuela Torelli Jerzy Wieslaw Kozyra Jing-Ying Gu Ulrich Stimming Luca Piantanida Kislon Voïtchovsky Natalio Krasnogor Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon
description	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.
format	article
author	Emanuela Torelli Jerzy Wieslaw Kozyra Jing-Ying Gu Ulrich Stimming Luca Piantanida Kislon Voïtchovsky Natalio Krasnogor
author_facet	Emanuela Torelli Jerzy Wieslaw Kozyra Jing-Ying Gu Ulrich Stimming Luca Piantanida Kislon Voïtchovsky Natalio Krasnogor
author_sort	Emanuela Torelli
title	Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon
title_short	Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon
title_full	Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon
title_fullStr	Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon
title_full_unstemmed	Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon
title_sort	isothermal folding of a light-up bio-orthogonal rna origami nanoribbon
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/eb93bb9c43814661800342a4e751c809
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Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon

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