{"data":{"id":"10.6084/m9.figshare.3793782.v1","type":"dois","attributes":{"doi":"10.6084/m9.figshare.3793782.v1","prefix":"10.6084","suffix":"m9.figshare.3793782.v1","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":"2016-08-30","dateType":"Created"},{"date":"2016-08-30","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":"IsPreviousVersionOf","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 bisulphate, 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 three 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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","url":"https://tandf.figshare.com/articles/dataset/Dissecting_the_secondary_structure_of_the_circular_RNA_of_a_nuclear_viroid_i_in_vivo_i_a_naked_rod-like_conformation_similar_but_not_identical_to_that_observed_i_in_vitro_i_/3793782/1","contentUrl":null,"metadataVersion":5,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"viewsOverTime":[],"downloadCount":0,"downloadsOverTime":[],"referenceCount":1,"citationCount":0,"citationsOverTime":[],"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2016-08-30T17:26:56.000Z","registered":"2016-08-30T17:26:57.000Z","published":"2016","updated":"2020-09-03T16:24:55.000Z"},"relationships":{"client":{"data":{"id":"figshare.ars","type":"clients"}},"provider":{"data":{"id":"otjm","type":"providers"}},"media":{"data":{"id":"10.6084/m9.figshare.3793782.v1","type":"media"}},"references":{"data":[{"id":"10.1080/15476286.2016.1223005","type":"dois"}]},"citations":{"data":[]},"parts":{"data":[]},"partOf":{"data":[]},"versions":{"data":[]},"versionOf":{"data":[]}}}}