ArticleJournal of the American Chemical Society2014
Complex RNA folding kinetics revealed by single-molecule FRET and hidden Markov models.
Article in Journal of the American Chemical Society, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed.
- Simulating Freely Diffusing Single-Molecule FRET Data with Consideration of Protein Conformational Dynamics.The journal of physical chemistry. B · 2026Article
- A DNA Scaffold Approach Facilitates 5' Labeling of the SARS-CoV-2 RNA Pseudoknot for Single-Molecule Förster Resonance Energy Transfer Investigation.Chemphyschem : a European journal of chemical physics and physical chemistry · 2025Article
- Using Bayesian priors to overcome non-identifiablility issues in Hidden Markov models.bioRxiv : the preprint server for biology · 2025Article
- Single-photon smFRET. I: Theory and conceptual basis.Biophysical reports · 2023Article
- A blind benchmark of analysis tools to infer kinetic rate constants from single-molecule FRET trajectories.Nature communications · 2022Article
- Unraveling multi-state molecular dynamics in single-molecule FRET experiments. I. Theory of FRET-lines.The Journal of chemical physics · 2022Article
- Multi-parameter photon-by-photon hidden Markov modeling.Nature communications · 2022Article
- Theory and Analysis of Single-Molecule FRET Experiments.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Extraction of rapid kinetics from smFRET measurements using integrative detectors.Cell reports. Physical science · 2021Article
- Integrating single-molecule FRET and biomolecular simulations to study diverse interactions between nucleic acids and proteins.Essays in biochemistry · 2021Review
- FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices.eLife · 2021Review
- Generalizing HMMs to Continuous Time for Fast Kinetics: Hidden Markov Jump Processes.Biophysical journal · 2021Article
- Dissection of Interaction Kinetics through Single-Molecule Interaction Simulation.Analytical chemistry · 2020Article
- Ligand-bound glutamine binding protein assumes multiple metastable binding sites with different binding affinities.Communications biology · 2020Article
- Dynamic graphical models of molecular kinetics.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- A Bayesian Nonparametric Approach to Single Molecule Förster Resonance Energy Transfer.The journal of physical chemistry. B · 2019Article
- Divalent ions tune the kinetics of a bacterial GTPase center rRNA folding transition from secondary to tertiary structure.RNA (New York, N.Y.) · 2018Article
- Azobenzene as a photoregulator covalently attached to RNA: a quantum mechanics/molecular mechanics-surface hopping dynamics study.Chemical science · 2018Article
- Nanopore electric snapshots of an RNA tertiary folding pathway.Nature communications · 2017Article
- Single-molecule FRET reveals the energy landscape of the full-length SAM-I riboswitch.Nature chemical biology · 2017Article
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5 authors.
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Abstract
We have developed a hidden Markov model and optimization procedure for photon-based single-molecule FRET data, which takes into account the trace-dependent background intensities. This analysis technique reveals an unprecedented amount of detail in the folding kinetics of the Diels-Alderase ribozyme. We find a multitude of extended (low-FRET) and compact (high-FRET) states. Five states were consistently and independently identified in two FRET constructs and at three Mg(2+) concentrations. Structures generally tend to become more compact upon addition of Mg(2+). Some compact structures are observed to significantly depend on Mg(2+) concentration, suggesting a tertiary fold stabilized by Mg(2+) ions. One compact structure was observed to be Mg(2+)-independent, consistent with stabilization by tertiary Watson-Crick base pairing found in the folded Diels-Alderase structure. A hierarchy of time scales was discovered, including dynamics of 10 ms or faster, likely due to tertiary structure fluctuations, and slow dynamics on the seconds time scale, presumably associated with significant changes in secondary structure. The folding pathways proceed through a series of intermediate secondary structures. There exist both compact pathways and more complex ones, which display tertiary unfolding, then secondary refolding, and, subsequently, again tertiary refolding.
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