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

Lookup NU author(s): Dr James DonarskiORCiD

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This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).

Abstract

© The Author(s) 2014. 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.

Publication metadata

Author(s): Davlieva M, Donarski J, Wang J, Shamoo Y, Nikonowicz EP

Publication type: Article

Publication status: Published

Journal: Nucleic Acids Research

Year: 2014

Volume: 42

Issue: 16

Pages: 10795-10808

Print publication date: 15/09/2014

Online publication date: 19/08/2014

Acceptance date: 03/08/2014

Date deposited: 13/06/2019

ISSN (print): 0305-1048

ISSN (electronic): 1362-4962

Publisher: Oxford University Press

URL: https://doi.org/10.1093/nar/gku743

DOI: 10.1093/nar/gku743

PubMed id: 25140011

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