Title
Characterization of the Mechanical Unfolding of RNA Pseudoknots
Date Issued
11 January 2008
Access level
open access
Resource Type
journal article
Author(s)
Universidad de California
Publisher(s)
Academic Press
Abstract
The pseudoknot is an important RNA structural element that provides an excellent model system for studying the contributions of tertiary interactions to RNA stability and to folding kinetics. RNA pseudoknots are also of interest because of their key role in the control of ribosomal frameshifting by viral RNAs. Their mechanical properties are directly relevant to their unfolding by ribosomes during translation. We have used optical tweezers to study the kinetics and thermodynamics of mechanical unfolding and refolding of single RNA molecules. Here we describe the unfolding of the frameshifting pseudoknot from infectious bronchitis virus (IBV), three constituent hairpins, and three mutants of the IBV pseudoknot. All four pseudoknots cause -1 programmed ribosomal frameshifting. We have measured the free energies and rates of mechanical unfolding and refolding of the four frameshifting pseudoknots. Our results show that the IBV pseudoknot requires a higher force than its corresponding hairpins to unfold. Furthermore, its rate of unfolding changes little with increasing force, in contrast with the rate of hairpin unfolding. The presence of Mg2+ significantly increases the kinetic barriers to unfolding the IBV pseudoknot, but has only a minor effect on the hairpin unfolding. The greater mechanical stability of pseudoknots compared to hairpins, and their kinetic insensitivity to force supports the hypothesis that -1 frameshifting depends on the difficulty of unfolding the mRNA. © 2007 Elsevier Ltd. All rights reserved.
Start page
511
End page
528
Volume
375
Issue
2
Language
English
OCDE Knowledge area
Bioquímica, Biología molecular
Genética, Herencia
Subjects
Scopus EID
2-s2.0-36749056800
PubMed ID
Source
Journal of Molecular Biology
ISSN of the container
00222836
Sponsor(s)
Funding text
The authors are grateful for the technical help and valuable discussions from Dr Steven B. Smith, Dr Pan Li and Dr Delphine Collin. This work was supported by grants from National Institutes of Health (MBRS-SCORE GM48135) and National Science Foundation (MCB-0417248) (to C.-H. K.) and National Institutes of Health grant GM10840 (to I.T.).
Sources of information:
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