Multistage collapse of a bacterial ribozyme observed by time-resolved small-angle x-ray scattering

Joon Ho Roh, Liang Guo, J. Duncan Kilburn, Robert M. Briber, Thomas Irving, Sarah A. Woodson

Research output: Contribution to journalArticle

Abstract

Ribozymes must fold into compact, native structures to function properly in the cell. The first step in forming the RNA tertiary structure is the neutralization of the phosphate charge by cations, followed by collapse of the unfolded molecules into more compact structures. The specificity of the collapse transition determines the structures of the folding intermediates and the folding time to the native state. However, the forces that enable specific collapse in RNA are not understood. Using time-resolved SAXS, we report that upon addition of 5 mM Mg 2+ to the Azoarcus group I ribozyme up to 80% of chains form compact structures in less than 1 ms. In 1 mM Mg 2+, the collapse transition produces extended structures that slowly approach the folded state, while ≥1.5 mM Mg 2+ leads to an ensemble of random coils that fold with multistage kinetics. Increased flexibility of molecules in the intermediate ensemble correlates with a Mg 2+-dependent increase in the fast folding population and a previously unobserved crossover in the collapse kinetics. Partial denaturation of the unfolded RNA with urea also increases the fraction of chains following the fast-folding pathway. These results demonstrate that the preferred collapse mechanism depends on the extent of Mg 2+-dependent charge neutralization and that non-native interactions within the unfolded ensemble contribute to the heterogeneity of the ribozyme folding pathways at the very earliest stages of tertiary structure formation.

Original languageEnglish (US)
Pages (from-to)10148-10154
Number of pages7
JournalJournal of the American Chemical Society
Volume132
Issue number29
DOIs
StatePublished - Jul 28 2010

Fingerprint

Catalytic RNA
RNA
Azoarcus
X-Rays
RNA Folding
Scattering
Nucleic Acid Denaturation
X rays
Urea
Cations
Denaturation
Molecules
Kinetics
Phosphates
Positive ions
Population
GIR1 ribozyme

ASJC Scopus subject areas

  • Chemistry(all)
  • Catalysis
  • Biochemistry
  • Colloid and Surface Chemistry

Cite this

Roh, J. H., Guo, L., Kilburn, J. D., Briber, R. M., Irving, T., & Woodson, S. A. (2010). Multistage collapse of a bacterial ribozyme observed by time-resolved small-angle x-ray scattering. Journal of the American Chemical Society, 132(29), 10148-10154. https://doi.org/10.1021/ja103867p

Multistage collapse of a bacterial ribozyme observed by time-resolved small-angle x-ray scattering. / Roh, Joon Ho; Guo, Liang; Kilburn, J. Duncan; Briber, Robert M.; Irving, Thomas; Woodson, Sarah A.

In: Journal of the American Chemical Society, Vol. 132, No. 29, 28.07.2010, p. 10148-10154.

Research output: Contribution to journalArticle

Roh, Joon Ho ; Guo, Liang ; Kilburn, J. Duncan ; Briber, Robert M. ; Irving, Thomas ; Woodson, Sarah A. / Multistage collapse of a bacterial ribozyme observed by time-resolved small-angle x-ray scattering. In: Journal of the American Chemical Society. 2010 ; Vol. 132, No. 29. pp. 10148-10154.
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