ArticleNucleic acids research2008
A rugged free energy landscape separates multiple functional RNA folds throughout denaturation.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
54 citing papers in PubMed.
- PlanarFold: a coarse-grained molecular dynamics model of RNA in two-dimensional space.Nature communications · 2026Article
- Single-molecule analysis reveals low-temperature misfolding in HIV-1 TAR RNA.Scientific reports · 2026Article
- In silico conversion of ssRNA aptamers to ssDNA: molecular dynamics assessment of structural stability and conformational preservation.Journal of computer-aided molecular design · 2026Article
- Computational De Novo Design of Group II Introns Yields Highly Active Ribozymes.Chembiochem : a European journal of chemical biology · 2025Article
- Structural flexibility in the ordered domain of the dengue virus strain 2 capsid protein is critical for chaperoning viral RNA replication.Cellular and molecular life sciences : CMLS · 2025Article
- Regulation of bacterial gene expression by non-coding RNA: It is all about time!Cell chemical biology · 2024Review
- Measurement of the specific and non-specific binding energies of MgBiophysical journal · 2022Article
- Peptides before and during the nucleotide world: an origins story emphasizing cooperation between proteins and nucleic acids.Journal of the Royal Society, Interface · 2022Review
- Can DyeCycling break the photobleaching limit in single-molecule FRET?Nano research · 2022Article
- Structural basis of rotavirus RNA chaperone displacement and RNA annealing.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- mRNA structural dynamics shape Argonaute-target interactions.Nature structural & molecular biology · 2020Article
- Local-to-global signal transduction at the core of a MnNature communications · 2019Article
- Disordered RNA chaperones can enhance nucleic acid folding via local charge screening.Nature communications · 2019Article
- The Story of RNA Folding, as Told in Epochs.Cold Spring Harbor perspectives in biology · 2018Review
- Life under the Microscope: Single-Molecule Fluorescence Highlights the RNA World.Chemical reviews · 2018Review
- Differential Assembly of Catalytic Interactions within the Conserved Active Sites of Two Ribozymes.PloS one · 2016Article
- Cation-induced kinetic heterogeneity of the intron-exon recognition in single group II introns.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Native purification and labeling of RNA for single molecule fluorescence studies.Methods in molecular biology (Clifton, N.J.) · 2015Article
- Molecular crowding accelerates ribozyme docking and catalysis.Journal of the American Chemical Society · 2014Article
- Single-molecule tools for enzymology, structural biology, systems biology and nanotechnology: an update.Archives of toxicology · 2014Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
The dynamic mechanisms by which RNAs acquire biologically functional structures are of increasing importance to the rapidly expanding fields of RNA therapeutics and biotechnology. Large energy barriers separating misfolded and functional states arising from alternate base pairing are a well-appreciated characteristic of RNA. In contrast, it is typically assumed that functionally folded RNA occupies a single native basin of attraction that is free of deeply dividing energy barriers (ergodic hypothesis). This assumption is widely used as an implicit basis to interpret experimental ensemble-averaged data. Here, we develop an experimental approach to isolate persistent sub-populations of a small RNA enzyme and show by single molecule fluorescence resonance energy transfer (smFRET), biochemical probing and high-resolution mass spectrometry that commitment to one of several catalytically active folds occurs unexpectedly high on the RNA folding energy landscape, resulting in partially irreversible folding. Our experiments reveal the retention of molecular heterogeneity following the complete loss of all native secondary and tertiary structure. Our results demonstrate a surprising longevity of molecular heterogeneity and advance our current understanding beyond that of non-functional misfolds of RNA kinetically trapped on a rugged folding-free energy landscape.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.