ArticleJournal of molecular biology2009
Structural rearrangements linked to global folding pathways of the Azoarcus group I ribozyme.
Article in Journal of molecular biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 38 citations in OpenAlex.
- Watching ion-driven kinetics of ribozyme folding and misfolding caused by energetic and topological frustration one molecule at a time.Nucleic acids research · 2023Article
- Graph deep learning locates magnesium ions in RNA.QRB discovery · 2022Article
- 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
- 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
- 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
- Mg2+-dependent conformational changes and product release during DNA-catalyzed RNA ligation monitored by Bimane fluorescence.Nucleic acids research · 2015Article
- Ribosome assembly factors Pwp1 and Nop12 are important for folding of 5.8S rRNA during ribosome biogenesis in Saccharomyces cerevisiae.Molecular and cellular biology · 2014Article
- Understanding the role of three-dimensional topology in determining the folding intermediates of group I introns.Biophysical journal · 2013Article
- The brace for a growing scaffold: Mss116 protein promotes RNA folding by stabilizing an early assembly intermediate.Journal of molecular biology · 2012Article
- Article
- The Azoarcus group I intron ribozyme misfolds and is accelerated for refolding by ATP-dependent RNA chaperone proteins.The Journal of biological chemistry · 2011Article
- RNA molecules with conserved catalytic cores but variable peripheries fold along unique energetically optimized pathways.RNA (New York, N.Y.) · 2011Article
- Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics.Nucleic acids research · 2010Article
- Multistage collapse of a bacterial ribozyme observed by time-resolved small-angle X-ray scattering.Journal of the American Chemical Society · 2010Article
- Site-specific fluorescent probing of RNA molecules by unnatural base-pair transcription for local structural conformation analysis.Nature protocols · 2010Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Stable RNAs must fold into specific three-dimensional structures to be biologically active, yet many RNAs form metastable structures that compete with the native state. Our previous time-resolved footprinting experiments showed that Azoarcus group I ribozyme forms its tertiary structure rapidly (tau < 30 ms) without becoming significantly trapped in kinetic intermediates. Here, we use stopped-flow fluorescence spectroscopy to probe the global folding kinetics of a ribozyme containing 2-aminopurine in the loop of P9. The modified ribozyme was catalytically active and exhibited two equilibrium folding transitions centered at 0.3 and 1.6 mM Mg2+, consistent with previous results. Stopped-flow fluorescence revealed four kinetic folding transitions with observed rate constants of 100, 34, 1, and 0.1 s-1 at 37 degrees C. From comparison with time-resolved Fe(II)-ethylenediaminetetraacetic acid footprinting of the modified ribozyme under the same conditions, these folding transitions were assigned to formation of the IC intermediate, tertiary folding and docking of the nicked P9 tetraloop, reorganization of the P3 pseudoknot, and refolding of nonnative conformers, respectively. The footprinting results show that 50-60% of the modified ribozyme folds in less than 30 ms, while the rest of the RNA population undergoes slow structural rearrangements that control the global folding rate. The results show how small perturbations to the structure of the RNA, such as a nick in P9, populate kinetic folding intermediates that are not observed in the natural ribozyme.
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