ArticleJournal of structural biology2012
Determining RNA three-dimensional structures using low-resolution data.
Article in Journal of structural biology, 2012. 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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Who cites it
13 citing papers in PubMed.
- Integrative structural and physicochemical characterization of chalcone synthase enzymes from medicinal plants using AlphaFold, molecular docking, and molecular dynamics.Scientific reports · 2026Article
- Combining Experimental Restraints and RNA 3D Structure Prediction in RNA Nanotechnology.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Quantitative Understanding of SHAPE Mechanism from RNA Structure and Dynamics Analysis.The journal of physical chemistry. B · 2018Article
- Structure modeling of RNA using sparse NMR constraints.Nucleic acids research · 2017Article
- CompAnnotate: a comparative approach to annotate base-pairing interactions in RNA 3D structures.Nucleic acids research · 2017Article
- SAXS studies of RNA: structures, dynamics, and interactions with partners.Wiley interdisciplinary reviews. RNA · 2016Review
- Achievements and challenges in structural bioinformatics and computational biophysics.Bioinformatics (Oxford, England) · 2015Article
- Methods for SAXS-based structure determination of biomolecular complexes.Advanced materials (Deerfield Beach, Fla.) · 2014Article
- Characterizing RNA ensembles from NMR data with kinematic models.Nucleic acids research · 2014Article
- Safer one-pot synthesis of the 'SHAPE' reagent 1-methyl-7-nitroisatoic anhydride (1m7).RNA (New York, N.Y.) · 2013Article
- Ensemble analysis of primary microRNA structure reveals an extensive capacity to deform near the Drosha cleavage site.Biochemistry · 2013Article
- Article
- Coarse-grained prediction of RNA loop structures.PloS one · 2012Article
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Authors and funding
2 authors.
Funding
Abstract
Knowing the 3-D structure of an RNA is fundamental to understand its biological function. Nowadays X-ray crystallography and NMR spectroscopy are systematically applied to newly discovered RNAs. However, the application of these high-resolution techniques is not always possible, and thus scientists must turn to lower resolution alternatives. Here, we introduce a pipeline to systematically generate atomic resolution 3-D structures that are consistent with low-resolution data sets. We compare and evaluate the discriminative power of a number of low-resolution experimental techniques to reproduce the structure of the Escherichia coli tRNA(VAL) and P4-P6 domain of the Tetrahymena thermophila group I intron. We test single and combinations of the most accessible low-resolution techniques, i.e. hydroxyl radical footprinting (OH), methidiumpropyl-EDTA (MPE), multiplexed hydroxyl radical cleavage (MOHCA), and small-angle X-ray scattering (SAXS). We show that OH-derived constraints are accurate to discriminate structures at the atomic level, whereas EDTA-based constraints apply to global shape determination. We provide a guide for choosing which experimental techniques or combination of thereof is best in which context. The pipeline represents an important step towards high-throughput low-resolution RNA structure determination.
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Registered trials
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