Structure analysis of free and bound states of an RNA aptamer against ribosomal protein S8 from Bacillus anthracis

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dc.citation.journalTitleNucleic Acids Researchen_US
dc.contributor.authorDavlieva, Milyaen_US
dc.contributor.authorDonarski, Jamesen_US
dc.contributor.authorWang, Jiachenen_US
dc.contributor.authorShamoo, Yousifen_US
dc.contributor.authorNikonowicz, Edward P.en_US
dc.date.accessioned2014-09-30T16:31:17Zen_US
dc.date.available2014-09-30T16:31:17Zen_US
dc.date.issued2014en_US
dc.description.abstractSeveral protein-targeted RNA aptamers have been identified for a variety of applications and although the affinities of numerous protein-aptamer complexes have been determined, the structural details of these complexes have not been widely explored. We examined the structural accommodation of an RNA aptamer that binds bacterial r-protein S8. The core of the primary binding site for S8 on helix 21 of 16S rRNA contains a pair of conserved base triples that mold the sugar-phosphate backbone to S8. The aptamer, which does not contain the conserved sequence motif, is specific for the rRNA binding site of S8. The protein-free RNA aptamer adopts a helical structure with multiple non-canonical base pairs. Surprisingly, binding of S8 leads to a dramatic change in the RNA conformation that restores the signature S8 recognition fold through a novel combination of nucleobase interactions. Nucleotides within the non-canonical core rearrange to create a G-(G-C) triple and a U-(A-U)-U quartet. Although native-like S8-RNA interactions are present in the aptamer-S8 complex, the topology of the aptamer RNA differs from that of the helix 21-S8 complex. This is the first example of an RNA aptamer that adopts substantially different secondary structures in the free and protein-bound states and highlights the remarkable plasticity of RNA secondary structure.en_US
dc.identifier.citationDavlieva, Milya, Donarski, James, Wang, Jiachen, et al.. "Structure analysis of free and bound states of an RNA aptamer against ribosomal protein S8 from Bacillus anthracis." <i>Nucleic Acids Research,</i> (2014) Oxford University Press: http://dx.doi.org/10.1093/nar/gku743.en_US
dc.identifier.doihttp://dx.doi.org/10.1093/nar/gku743en_US
dc.identifier.urihttps://hdl.handle.net/1911/77318en_US
dc.language.isoengen_US
dc.publisherOxford University Pressen_US
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.en_US
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en_US
dc.titleStructure analysis of free and bound states of an RNA aptamer against ribosomal protein S8 from Bacillus anthracisen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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