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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| Format: | Article |
| Language: | English |
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Nature Portfolio
2018-05-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-018-25270-6 |
| _version_ | 1818851093237465088 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-19T06:59:32Z |
| format | Article |
| id | doaj.art-eb93bb9c43814661800342a4e751c809 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-19T06:59:32Z |
| publishDate | 2018-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-eb93bb9c43814661800342a4e751c8092022-12-21T20:31:27ZengNature PortfolioScientific Reports2045-23222018-05-018111210.1038/s41598-018-25270-6Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbonEmanuela Torelli0Jerzy Wieslaw Kozyra1Jing-Ying Gu2Ulrich Stimming3Luca Piantanida4Kislon Voïtchovsky5Natalio Krasnogor6Interdisciplinary Computing and Complex BioSystems (ICOS), School of Computing Science, Centre for Synthetic Biology and Bioeconomy (CSBB), Centre for Bacterial Cell Biology (CBCB), Newcastle UniversityInterdisciplinary Computing and Complex BioSystems (ICOS), School of Computing Science, Centre for Synthetic Biology and Bioeconomy (CSBB), Centre for Bacterial Cell Biology (CBCB), Newcastle UniversitySchool of Chemistry, Newcastle UniversitySchool of Chemistry, Newcastle UniversityDepartment of Physics, Durham UniversityDepartment of Physics, Durham UniversityInterdisciplinary Computing and Complex BioSystems (ICOS), School of Computing Science, Centre for Synthetic Biology and Bioeconomy (CSBB), Centre for Bacterial Cell Biology (CBCB), Newcastle UniversityAbstract 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.https://doi.org/10.1038/s41598-018-25270-6 |
| spellingShingle | 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 Scientific Reports |
| title | 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_short | Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon |
| title_sort | isothermal folding of a light up bio orthogonal rna origami nanoribbon |
| url | https://doi.org/10.1038/s41598-018-25270-6 |
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