ArticleThe journal of physical chemistry. B2019
Salt Dependence of A-Form RNA Duplexes: Structures and Implications.
Article in The journal of physical chemistry. B, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 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
13 citing papers in PubMed.
- RNA structures and dynamics with Å resolution revealed by x-ray free-electron lasers.Science advances · 2023Article
- On the common pathways of deformation: RNA vs DNA under interrogation.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- RNA structures and dynamics with Å resolution revealed by x-ray free electron lasers.bioRxiv : the preprint server for biology · 2023Article
- Universality in RNA and DNA deformations induced by salt, temperature change, stretching force, and protein binding.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- RNA Captures More Cations than DNA: Insights from Molecular Dynamics Simulations.The journal of physical chemistry. B · 2022Article
- Insights into the structural stability of major groove RNA triplexes by WAXS-guided MD simulations.Cell reports. Physical science · 2022Article
- Graph deep learning locates magnesium ions in RNA.QRB discovery · 2022Article
- Visualizing RNA Structures by SAXS-Driven MD Simulations.Frontiers in bioinformatics · 2022Article
- The structural plasticity of nucleic acid duplexes revealed by WAXS and MD.Science advances · 2021Article
- Machine learning deciphers structural features of RNA duplexes measured with solution X-ray scattering.IUCrJ · 2020Article
- Structural and functional conservation of the programmed -1 ribosomal frameshift signal of SARS coronavirus 2 (SARS-CoV-2).The Journal of biological chemistry · 2020Article
- Structural and functional conservation of the programmed -1 ribosomal frameshift signal of SARS-CoV-2.bioRxiv : the preprint server for biology · 2020Article
- Salt effect on thermodynamics and kinetics of a single RNA base pair.RNA (New York, N.Y.) · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
The biological functions of RNA range from gene regulation through catalysis and depend critically on its structure and flexibility. Conformational variations of flexible, non-base-paired components, including RNA hinges, bulges, or single-stranded tails, are well documented. Recent work has also identified variations in the structure of ubiquitous, base-paired duplexes found in almost all functional RNAs. Duplexes anchor the structures of folded RNAs, and their surface features are recognized by partner molecules. To date, no consistent picture has been obtained that describes the range of conformations assumed by RNA duplexes. Here, we apply wide angle, solution X-ray scattering (WAXS) to quantify these variations, by sampling length scales characteristic of helical geometries under different solution conditions. To identify the radius, helical rise, twist, and length of dsRNA helices, we exploit molecular dynamics generated structures, explicit solvent models, and ensemble optimization methods. Our results quantify the substantial and salt-dependent deviations of double-stranded (ds) RNA duplexes from the assumed canonical A-form conformation. Recent experiments underscore the need to properly describe the structures of RNA duplexes when interpreting the salt dependence of RNA conformations.
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.