ArticleNucleic acids research2017
Determination of the conformational ensemble of the TAR RNA by X-ray scattering interferometry.
Article in Nucleic acids research, 2017. 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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16 citing papers in PubMed, 21 citations in OpenAlex.
- Molecular insights into the interaction between a disordered protein and a folded RNA.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Molecular insights into the interaction between a disordered protein and a folded RNA.bioRxiv : the preprint server for biology · 2024Article
- Structural and computational studies of HIV-1 RNA.RNA biology · 2024Review
- Capturing heterogeneous conformers of cobalamin riboswitch by cryo-EM.Nucleic acids research · 2023Article
- Pressure pushes tRNAProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Recent advances in RNA structurome.Science China. Life sciences · 2022Review
- Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction.Nature communications · 2020Article
- Site-specific covalent labeling of large RNAs with nanoparticles empowered by expanded genetic alphabet transcription.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- The structural ensemble of a Holliday junction determined by X-ray scattering interference.Nucleic acids research · 2020Article
- Salt Dependence of A-Form RNA Duplexes: Structures and Implications.The journal of physical chemistry. B · 2019Article
- Sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Conformations of an RNA Helix-Junction-Helix Construct Revealed by SAXS Refinement of MD Simulations.Biophysical journal · 2019Article
- Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics.RNA (New York, N.Y.) · 2018Article
- Recording and Analyzing Nucleic Acid Distance Distributions with X-Ray Scattering Interferometry (XSI).Current protocols in nucleic acid chemistry · 2018Article
- Gold nanocrystal labels provide a sequence-to-3D structure map in SAXS reconstructions.Science advances · 2018Article
- Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics.Nucleic acids research · 2017Article
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Authors and funding
4 authors at 1 institution in 1 country.
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Abstract
The conformational ensembles of structured RNA's are crucial for biological function, but they remain difficult to elucidate experimentally. We demonstrate with HIV-1 TAR RNA that X-ray scattering interferometry (XSI) can be used to determine RNA conformational ensembles. X-ray scattering interferometry (XSI) is based on site-specifically labeling RNA with pairs of heavy atom probes, and precisely measuring the distribution of inter-probe distances that arise from a heterogeneous mixture of RNA solution structures. We show that the XSI-based model of the TAR RNA ensemble closely resembles an independent model derived from NMR-RDC data. Further, we show how the TAR RNA ensemble changes shape at different salt concentrations. Finally, we demonstrate that a single hybrid model of the TAR RNA ensemble simultaneously fits both the XSI and NMR-RDC data set and show that XSI can be combined with NMR-RDC to further improve the quality of the determined ensemble. The results suggest that XSI-RNA will be a powerful approach for characterizing the solution conformational ensembles of RNAs and RNA-protein complexes under diverse solution conditions.
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