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dc.creatorLee, Jung C.en
dc.creatorGutell, Robin R.en
dc.date.accessioned2014-12-15T17:10:37Zen
dc.date.available2014-12-15T17:10:37Zen
dc.date.issued2014-04-01en
dc.identifier.citationLee JC, Gutell RR (2014) Helix Capping in RNA Structure. PLoS ONE 9(4): e93664. doi:10.1371/journal.pone.0093664en
dc.identifier.urihttp://hdl.handle.net/2152/27908en
dc.descriptionJung C. Lee, BioMolecular Engineering Program, Physics and Chemistry Department, Milwaukee School of Engineering, Milwaukee, Wisconsin, United States of Americaen
dc.descriptionRobin R. Gutell, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, and Section of Integrative Biology, the University of Texas at Austin, Austin, Texas, United States of Americaen
dc.description.abstractHelices are an essential element in defining the three-dimensional architecture of structured RNAs. While internal basepairs in a canonical helix stack on both sides, the ends of the helix stack on only one side and are exposed to the loop side, thus susceptible to fraying unless they are protected. While coaxial stacking has long been known to stabilize helix ends by directly stacking two canonical helices coaxially, based on analysis of helix-loop junctions in RNA crystal structures, herein we describe helix capping, topological stacking of a helix end with a basepair or an unpaired nucleotide from the loop side, which in turn protects helix ends. Beyond the topological protection of helix ends against fraying, helix capping should confer greater stability onto the resulting composite helices. Our analysis also reveals that this general motif is associated with the formation of tertiary structure interactions. Greater knowledge about the dynamics at the helix-junctions in the secondary structure should enhance the prediction of RNA secondary structure with a richer set of energetic rules and help better understand the folding of a secondary structure into its three-dimensional structure. These together suggest that helix capping likely play a fundamental role in driving RNA folding.en
dc.description.sponsorshipThis work was supported by grants from the National Institutes of Health(GM067317 and GM085337), Microsoft Research Technical Computing Initiative grant (UTA08-531), and Welch Foundation (F-1427). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.en
dc.language.isoEnglishen
dc.publisherPLOS Oneen
dc.rightsAdministrative deposit of works to UT Digital Repository: This works author(s) is or was a University faculty member, student or staff member; this article is already available through open access at http://www.plosone.org. The public license is specified as CC-BY: http://creativecommons.org/licenses/by/4.0/. The library makes the deposit as a matter of fair use (for scholarly, educational, and research purposes), and to preserve the work and further secure public access to the works of the University.en
dc.subjectcrystal structureen
dc.subjectprotien structure predictionen
dc.subjectRNA foldingen
dc.subjectRNA structureen
dc.subjectRNA synthesisen
dc.subjectRibosomal RNAen
dc.subjectSequence motif analysisen
dc.subjecttopologyen
dc.titleHelix Capping in RNA Structureen
dc.typeArticleen
dc.description.departmentCenter for Computational Biology and Bioinformaticsen
dc.description.departmentInstitute for Cellular and Molecular Biologyen
dc.description.catalogingnoteEmail: lee@msoe.edu (JCL)en
dc.description.catalogingnoteEmail: robin.gutell@mail.utexas.edu (RRG)en
dc.identifier.Filenamejournal.pone.0093664.pdfen
dc.identifier.doiDOI: 10.1371/journal.pone.0093664en


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