ArticleBiophysical journal2019
Conformations of an RNA Helix-Junction-Helix Construct Revealed by SAXS Refinement of MD Simulations.
Article in Biophysical journal, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Article
- Advances in microfluidic mixers for time-resolved structural biology with X-rays.Biophysical reviews · 2025Review
- Predicting RNA structure and dynamics with deep learning and solution scattering.Biophysical journal · 2025Article
- Predicting RNA Structure and Dynamics with Deep Learning and Solution Scattering.bioRxiv : the preprint server for biology · 2024Article
- Atomistic structure of the SARS-CoV-2 pseudoknot in solution from SAXS-driven molecular dynamics.Nucleic acids research · 2023Article
- Kinetic Resolution of the Atomic 3D Structures Formed by Ground and Excited Conformational States in an RNA Dynamic Ensemble.Journal of the American Chemical Society · 2023Article
- Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix-Junction-Helix RNA.The journal of physical chemistry letters · 2022Article
- Visualizing RNA Structures by SAXS-Driven MD Simulations.Frontiers in bioinformatics · 2022Article
- Structural analyses of an RNA stability element interacting with poly(A).Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- The structural plasticity of nucleic acid duplexes revealed by WAXS and MD.Science advances · 2021Article
- Elucidating the Role of Microprocessor Protein DGCR8 in Bending RNA Structures.Biophysical journal · 2020Article
- Assembly and Stability of Simian Virus 40 Polymorphs.ACS nano · 2020Article
- Nanoscale Structure Determination of Murray Valley Encephalitis and Powassan Virus Non-Coding RNAs.Viruses · 2020Article
- Visualizing Disordered Single-Stranded RNA: Connecting Sequence, Structure, and Electrostatics.Journal of the American Chemical Society · 2020Article
- Salt Dependence of A-Form RNA Duplexes: Structures and Implications.The journal of physical chemistry. B · 2019Article
- Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway.RNA (New York, N.Y.) · 2019Article
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Authors and funding
4 authors.
Funding
Abstract
RNA is involved in a broad range of biological processes that extend far beyond translation. Many of RNA's recently discovered functions rely on folding to a specific conformation or transitioning between conformations. The RNA structure contains rigid, short basepaired regions connected by more flexible linkers. Studies of model constructs such as small helix-junction-helix (HJH) motifs are useful in understanding how these elements work together to determine RNA conformation. Here, we reveal the full ensemble of solution structures assumed by a model RNA HJH. We apply small-angle x-ray scattering and an ensemble optimization method to selectively refine models generated by all-atom molecular dynamics simulations. The expectation of a broad distribution of helix orientations, at and above physiological ionic strength, is not met. Instead, this analysis shows that the HJH structures are dominated by two distinct conformations at moderate to high ionic strength. Atomic structures, selected from the molecular dynamics simulations, reveal strong base-base interactions in the junction that critically constrain the conformational space available to the HJH molecule and lead to a surprising re-extension at high salt. These results are corroborated by comparison with previous single-molecule fluorescence resonance energy transfer experiments on the same constructs.
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