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Single-molecule chemical denaturation of riboswitches
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dc.contributor.author | Dalgarno, Paul Allan | |
dc.contributor.author | Bordello, J | |
dc.contributor.author | Morris, Rhodri | |
dc.contributor.author | St-Pierre, P | |
dc.contributor.author | Dubé, A. | |
dc.contributor.author | Samuel, Ifor David William | |
dc.contributor.author | Lafontaine, Daniel | |
dc.contributor.author | Penedo, Carlos | |
dc.date.accessioned | 2013-03-26T14:31:03Z | |
dc.date.available | 2013-03-26T14:31:03Z | |
dc.date.issued | 2013-02 | |
dc.identifier.citation | Dalgarno , P A , Bordello , J , Morris , R , St-Pierre , P , Dubé , A , Samuel , I D W , Lafontaine , D & Penedo , C 2013 , ' Single-molecule chemical denaturation of riboswitches ' , Nucleic Acids Research , vol. 41 , no. 7 , pp. 4253-4265 . https://doi.org/10.1093/nar/gkt128 | en |
dc.identifier.issn | 0305-1048 | |
dc.identifier.other | PURE: 3449073 | |
dc.identifier.other | PURE UUID: 352d0725-5f9c-41f1-b601-edbf8c420332 | |
dc.identifier.other | WOS: 000318167900041 | |
dc.identifier.other | Scopus: 84876559777 | |
dc.identifier.other | ORCID: /0000-0002-5807-5385/work/74872776 | |
dc.identifier.uri | https://hdl.handle.net/10023/3427 | |
dc.description.abstract | To date, single-molecule RNA science has been developed almost exclusively around the effect of metal ions as folding promoters and stabilizers of the RNA structure. Here, we introduce a novel strategy that combines single-molecule Förster resonance energy transfer (FRET) and chemical denaturation to observe and manipulate RNA dynamics. We demonstrate that the competing interplay between metal ions and denaturant agents provides a platform to extract information that otherwise will remain hidden with current methods. Using the adenine-sensing riboswitch aptamer as a model, we provide strong evidence for a rate-limiting folding step of the aptamer domain being modulated through ligand binding, a feature that is important for regulation of the controlled gene. In the absence of ligand, the rate-determining step is dominated by the formation of long-range key tertiary contacts between peripheral stem-loop elements. In contrast, when the adenine ligand interacts with partially folded messenger RNAs, the aptamer requires specifically bound Mg2+ ions, as those observed in the crystal structure, to progress further towards the native form. Moreover, despite that the ligand-free and ligand-bound states are indistinguishable by FRET, their different stability against urea-induced denaturation allowed us to discriminate them, even when they coexist within a single FRET trajectory; a feature not accessible by existing methods. | |
dc.language.iso | eng | |
dc.relation.ispartof | Nucleic Acids Research | en |
dc.rights | © The Author(s) 2013. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. | en |
dc.subject | QC Physics | en |
dc.subject.lcc | QC | en |
dc.title | Single-molecule chemical denaturation of riboswitches | en |
dc.type | Journal article | en |
dc.contributor.sponsor | EPSRC | en |
dc.description.version | Publisher PDF | en |
dc.contributor.institution | University of St Andrews. School of Physics and Astronomy | en |
dc.contributor.institution | University of St Andrews. Biomedical Sciences Research Complex | en |
dc.contributor.institution | University of St Andrews. Condensed Matter Physics | en |
dc.identifier.doi | https://doi.org/10.1093/nar/gkt128 | |
dc.description.status | Peer reviewed | en |
dc.identifier.url | http://www.scopus.com/inward/record.url?scp=84876559777&partnerID=8YFLogxK | en |
dc.identifier.grantnumber | EP/G061688/1 | en |
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