title: Structure analysis of free and bound states of an RNA aptamer against ribosomal protein S8 from Bacillus anthracis.
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.
authors.affiliation: Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251-1892, USA.
authors.forename: Milya
authors.initials: M
authors.lastname: Davlieva
authors.affiliation: Food and Environment Research Agency, Sand Hutton, York, YO41 1LZ, United Kingdom.
authors.forename: James
authors.initials: J
authors.lastname: Donarski
authors.affiliation: Department of Physics, East China Normal University, 200062 Shanghai, P. R. China.
authors.forename: Jiachen
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251-1892, USA.
authors.forename: Yousif
authors.initials: Y
authors.lastname: Shamoo
authors.affiliation: Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251-1892, USA edn@rice.edu.
authors.forename: Edward P
authors.initials: EP
authors.lastname: Nikonowicz
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry*; D001408:Bacillus anthracis; D001426:Bacterial Proteins / Q000737:chemistry*; D001665:Binding Sites; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012336:RNA, Ribosomal, 16S / Q000737:chemistry; D012269:Ribosomal Proteins / Q000737:chemistry*
chemical_list: D052157:Aptamers, Nucleotide; D001426:Bacterial Proteins; D012336:RNA, Ribosomal, 16S; D012269:Ribosomal Proteins; C030254:ribosomal protein S8