Single-molecule force spectroscopy of the add adenine riboswitch relates folding to regulatory mechanism

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DOIResolve DOI: http://doi.org/10.1093/nar/gkr305
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TypeArticle
Journal titleNucleic Acids Research
ISSN0305-1048
Volume39
Issue17
Pages76777687; # of pages: 11
Subjectbacterial RNA; add adenine riboswitch; gene repression; ligand binding; molecular interaction; RNA conformation; RNA stability; RNA translation; single molecule force spectroscopy; structural homology; thermodynamics; Vibrio vulnificus; Adenine; Aptamers, Nucleotide; Nucleic Acid Conformation
AbstractRiboswitches regulate gene expression via ligand binding to an aptamer domain which induces conformational changes in a regulatory expression platform. By unfolding and refolding single add adenine riboswitch molecules in an optical trap, an integrated picture of the folding was developed and related to the regulatory mechanism. Force-extension curves (FECs) and constant-force folding trajectories measured on the aptamer alone revealed multiple partially-folded states, including several misfolded states not on the native folding pathway. All states were correlated to key structural components and interactions within hierarchical folding pathways. FECs of the full-length riboswitch revealed that the thermodynamically stable conformation switches upon ligand binding from a structure repressing translation to one permitting it. Along with rapid equilibration of the two structures in the absence of adenine, these results support a thermodynamically-controlled regulatory mechanism, in contrast with the kinetic control of the closely-related pbuE adenine riboswitch. Comparison of the folding of these riboswitches revealed many similarities arising from shared structural features but also essential differences related to their different regulatory mechanisms. © 2011 The Author(s).
Publication date
LanguageEnglish
AffiliationNational Research Council Canada (NRC-CNRC); National Institute for Nanotechnology
Peer reviewedYes
NPARC number21272026
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Record identifierf8db5122-60d1-4356-adf8-d8ed5c07676f
Record created2014-05-21
Record modified2016-05-09
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