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dc.contributor.authorDavlieva, Milya
Donarski, James
Wang, Jiachen
Shamoo, Yousif
Nikonowicz, Edward P.
dc.date.accessioned 2014-09-30T16:31:17Z
dc.date.available 2014-09-30T16:31:17Z
dc.date.issued 2014
dc.identifier.citation Davlieva, 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." Nucleic Acids Research, (2014) Oxford University Press: http://dx.doi.org/10.1093/nar/gku743.
dc.identifier.urihttps://hdl.handle.net/1911/77318
dc.description.abstract Several 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.
dc.language.iso eng
dc.publisher Oxford University Press
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.
dc.rights.urihttp://creativecommons.org/licenses/by/4.0
dc.title Structure analysis of free and bound states of an RNA aptamer against ribosomal protein S8 from Bacillus anthracis
dc.type Journal article
dc.contributor.funder National Institutes of Health, National Institute of Allergy and Infectious Diseases
dc.contributor.funder National Institutes of Health
dc.citation.journalTitle Nucleic Acids Research
dc.type.dcmi Text
dc.identifier.doihttp://dx.doi.org/10.1093/nar/gku743
dc.identifier.pmcid PMC4176348
dc.identifier.pmid 25140011
dc.identifier.grantID U54-AI057156 (National Institutes of Health, National Institute of Allergy and Infectious Diseases)
dc.identifier.grantID GM73969 (National Institutes of Health)
dc.identifier.grantID R01AI080714 (National Institutes of Health)
dc.type.publication publisher version


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This 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.
Except where otherwise noted, this item's license is described as This 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.