{"data":{"id":"10.6084/m9.figshare.3793782.v2","type":"dois","attributes":{"doi":"10.6084/m9.figshare.3793782.v2","prefix":"10.6084","suffix":"m9.figshare.3793782.v2","identifiers":[],"alternateIdentifiers":[],"creators":[{"name":"López-Carrasco, Amparo","nameType":"Personal","givenName":"Amparo","familyName":"López-Carrasco","affiliation":[],"nameIdentifiers":[]},{"name":"Flores, Ricardo","nameType":"Personal","givenName":"Ricardo","familyName":"Flores","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"Dissecting the secondary structure of the circular RNA of a nuclear viroid \u003ci\u003ein vivo\u003c/i\u003e: A “naked” rod-like conformation similar but not identical to that observed \u003ci\u003ein vitro\u003c/i\u003e"}],"publisher":"Taylor \u0026 Francis","container":{},"publicationYear":2016,"subjects":[{"subject":"Biophysics"},{"subject":"Biochemistry"},{"subject":"29999 Physical Sciences not elsewhere classified","subjectScheme":"FOR"},{"subject":"FOS: Physical sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Physical sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Molecular Biology"},{"subject":"39999 Chemical Sciences not elsewhere classified","subjectScheme":"FOR"},{"subject":"FOS: Chemical sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Chemical sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"69999 Biological Sciences not elsewhere classified","subjectScheme":"FOR"},{"subject":"FOS: Biological sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Biological sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Cancer"},{"subject":"110309 Infectious Diseases","subjectScheme":"FOR"},{"subject":"FOS: Health sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Health sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Plant Biology"},{"subject":"60506 Virology","subjectScheme":"FOR"},{"subject":"Computational Biology"}],"contributors":[],"dates":[{"date":"2016-09-21","dateType":"Created"},{"date":"2017-11-09","dateType":"Updated"},{"date":"2016","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[{"relationType":"IsSupplementTo","relatedIdentifier":"10.1080/15476286.2016.1223005","relatedIdentifierType":"DOI"},{"relationType":"IsIdenticalTo","relatedIdentifier":"10.6084/m9.figshare.3793782","relatedIdentifierType":"DOI"}],"relatedItems":[],"sizes":["484047 Bytes"],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[{"description":"With a minimal (250–400 nt), non-protein-coding, circular RNA genome, viroids rely on sequence/structural motifs for replication and colonization of their host plants. These motifs are embedded in a compact secondary structure whose elucidation is crucial to understand how they function. Viroid RNA structure has been tackled \u003ci\u003ein silico\u003c/i\u003e with algorithms searching for the conformation of minimal free energy, and \u003ci\u003ein vitro\u003c/i\u003e by probing in solution with RNases, dimethyl sulphate and bisulphite, and with selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE), which interrogates the RNA backbone at single-nucleotide resolution. However, \u003ci\u003ein vivo\u003c/i\u003e approaches at that resolution have not been assayed. Here, after confirming by 3 termodynamics-based predictions and by \u003ci\u003ein vitro\u003c/i\u003e SHAPE that the secondary structure adopted by the infectious monomeric circular (+) RNA of potato spindle tuber viroid (PSTVd) is a rod-like conformation with double-stranded segments flanked by loops, we have probed it \u003ci\u003ein vivo\u003c/i\u003e with a SHAPE modification. We provide direct evidence that a similar, but not identical, rod-like conformation exists in PSTVd-infected leaves of \u003ci\u003eNicotiana benthamiana\u003c/i\u003e, verifying the long-standing view that this RNA accumulates \u003ci\u003ein planta\u003c/i\u003e as a “naked” form rather than tightly associated with protecting host proteins. However, certain nucleotides of the central conserved region, including some of the loop E involved in key functions such as replication, are more SHAPE-reactive \u003ci\u003ein vitro\u003c/i\u003e than \u003ci\u003ein vivo\u003c/i\u003e. This difference is most likely due to interactions with proteins mediating some of these functions, or to structural changes promoted by other factors of the \u003ci\u003ein vivo\u003c/i\u003e habitat.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"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