ArticleNucleic acids research2024
Visualizing a two-state conformational ensemble in stem-loop 3 of the transcriptional regulator 7SK RNA.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- PlanarFold: a coarse-grained molecular dynamics model of RNA in two-dimensional space.Nature communications · 2026Article
- Thermodynamic prediction of RNA cellular activity from sequence via conformational ensembles.Cell · 2026Article
- Multi-site DMS probing reveals higher-order structure of RNA-protein complexes in living cells.Molecular cell · 2026Article
- Quantifying MgbioRxiv : the preprint server for biology · 2026Article
- Structural Features Within Precursor microRNA-20a Regulate Dicer-TRBP Processing.Journal of molecular biology · 2025Article
- Solution structure determination and biophysical characterization studies of 7SK RNP and 7SL SRP RNAs.RNA (New York, N.Y.) · 2025Article
- Structural features within precursor microRNA-20a regulate Dicer-TRBP processing.bioRxiv : the preprint server for biology · 2025Article
- Promoted read-through and mutation against pseudouridine-CMC by an evolved reverse transcriptase.Communications biology · 2025Article
- Deciphering ligand and metal ion dependent intricate folding landscape of Vc2 c-di-GMP riboswitch aptamer.Nucleic acids research · 2025Article
- Visualizing RNA structure ensembles by single-molecule correlated chemical probing.Current opinion in structural biology · 2024Review
- Insights into the A-C Mismatch Conformational Ensemble in Duplex DNA and its Role in Genetic Processes through a Structure-based Review.Journal of molecular biology · 2024Review
- Promoted Read-through and Mutation Against Pseudouridine-CMC by an Evolved Reverse Transcriptase.bioRxiv : the preprint server for biology · 2024Article
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4 authors.
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Abstract
Structural plasticity is integral to RNA function; however, there are currently few methods to quantitatively resolve RNAs that have multiple structural states. NMR spectroscopy is a powerful approach for resolving conformational ensembles but is size-limited. Chemical probing is well-suited for large RNAs but provides limited structural and kinetics information. Here, we integrate the two approaches to visualize a two-state conformational ensemble for the central stem-loop 3 (SL3) of 7SK RNA, a critical element for 7SK RNA function in transcription regulation. We find that the SL3 distal end exchanges between two equally populated yet structurally distinct states in both isolated SL3 constructs and full-length 7SK RNA. We rationally designed constructs that lock SL3 into a single state and demonstrate that both chemical probing and NMR data fit to a linear combination of the two states. Comparison of vertebrate 7SK RNA sequences shows either or both states are highly conserved. These results provide new insights into 7SK RNA structural dynamics and demonstrate the utility of integrating chemical probing with NMR spectroscopy to gain quantitative insights into RNA conformational ensembles.
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