ArticleJournal of the American Chemical Society2010
Multistage collapse of a bacterial ribozyme observed by time-resolved small-angle X-ray scattering.
Article in Journal of the American Chemical Society, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Watching ion-driven kinetics of ribozyme folding and misfolding caused by energetic and topological frustration one molecule at a time.Nucleic acids research · 2023Article
- Shear-free mixing to achieve accurate temporospatial nanoscale kinetics through scanning-SAXS: ion-induced phase transition of dispersed cellulose nanocrystals.Lab on a chip · 2021Article
- Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Evolving SAXS versatility: solution X-ray scattering for macromolecular architecture, functional landscapes, and integrative structural biology.Current opinion in structural biology · 2019Review
- Divalent ions tune the kinetics of a bacterial GTPase center rRNA folding transition from secondary to tertiary structure.RNA (New York, N.Y.) · 2018Article
- Effects of Preferential Counterion Interactions on the Specificity of RNA Folding.The journal of physical chemistry letters · 2018Article
- Revealing the distinct folding phases of an RNA three-helix junction.Nucleic acids research · 2018Article
- Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo.Biophysical journal · 2017Article
- Nucleobases Undergo Dynamic Rearrangements during RNA Tertiary Folding.Journal of molecular biology · 2016Article
- Entropic stabilization of folded RNA in crowded solutions measured by SAXS.Nucleic acids research · 2016Article
- Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme.Nucleic acids research · 2016Article
- Bridging the gap between in vitro and in vivo RNA folding.Quarterly reviews of biophysics · 2016Article
- How do metal ions direct ribozyme folding?Nature chemistry · 2015Article
- Formation of Tertiary Interactions during rRNA GTPase Center Folding.Journal of molecular biology · 2015Article
- Molecular crowding overcomes the destabilizing effects of mutations in a bacterial ribozyme.Nucleic acids research · 2015Article
- Methods for SAXS-based structure determination of biomolecular complexes.Advanced materials (Deerfield Beach, Fla.) · 2014Article
- Sub-millisecond time-resolved SAXS using a continuous-flow mixer and X-ray microbeam.Journal of synchrotron radiation · 2013Article
- Crowders perturb the entropy of RNA energy landscapes to favor folding.Journal of the American Chemical Society · 2013Article
- Kinetics of structural reorganizations in multilamellar photosynthetic membranes monitored by small-angle neutron scattering.The European physical journal. E, Soft matter · 2013Article
- Understanding the role of three-dimensional topology in determining the folding intermediates of group I introns.Biophysical journal · 2013Article
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6 authors.
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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 > or = 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.
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