ArticleRNA (New York, N.Y.)2022
Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments.
Article in RNA (New York, N.Y.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- The Distinct Structural Propensities of Poly-C, A, and U Single-Stranded RNA.Biomacromolecules · 2026Article
- ARNy plotter: A comprehensive web server for RNA ensemble structural analysis and visualization.PLoS computational biology · 2026Article
- Destabilization of Structured RNAs by OPC and TIP4PD Water Models.Journal of chemical theory and computation · 2026Article
- The Kink-Turn 7 Motif: An Additional Test for RNA Force Field Performance.Journal of chemical theory and computation · 2025Article
- Integrated NMR and MD structure and dynamics of the stem-loop-II motif (s2m) from the Omicron variant of SARS-CoV-2.RNA (New York, N.Y.) · 2025Article
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- Can We Ever Develop an Ideal RNA Force Field? Lessons Learned from Simulations of the UUCG RNA Tetraloop and Other Systems.Journal of chemical theory and computation · 2025Article
- Sequence-dependent conformational preferences of disordered single-stranded RNA.Cell reports. Physical science · 2024Article
- mRNA Fragmentation Pattern Detected by SHAPE.Current issues in molecular biology · 2024Article
- Sampling globally and locally correct RNA 3D structures using Ernwin, SPQR and experimental SAXS data.Nucleic acids research · 2024Article
- Prediction of 3D RNA Structures from Sequence Using Energy Landscapes of RNA Dimers: Application to RNA Tetraloops.Journal of chemical theory and computation · 2024Article
- Hierarchical Assembly of Single-Stranded RNA.Journal of chemical theory and computation · 2024Article
- Simple Adjustment of Intranucleotide Base-Phosphate Interaction in the OL3 AMBER Force Field Improves RNA Simulations.Journal of chemical theory and computation · 2023Article
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3 authors.
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Abstract
We describe the conformational ensemble of the single-stranded r(UCAAUC) oligonucleotide obtained using extensive molecular dynamics (MD) simulations and Rosetta's FARFAR2 algorithm. The conformations observed in MD consist of A-form-like structures and variations thereof. These structures are not present in the pool generated using FARFAR2. By comparing with available nuclear magnetic resonance (NMR) measurements, we show that the presence of both A-form-like and other extended conformations is necessary to quantitatively explain experimental data. To further validate our results, we measure solution X-ray scattering (SAXS) data on the RNA hexamer and find that simulations result in more compact structures than observed from these experiments. The integration of simulations with NMR via a maximum entropy approach shows that small modifications to the MD ensemble lead to an improved description of the conformational ensemble. Nevertheless, we identify persisting discrepancies in matching experimental SAXS data.
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