ArticleProceedings of the National Academy of Sciences of the United States of America2008
Structural inference of native and partially folded RNA by high-throughput contact mapping.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed, 85 citations in OpenAlex.
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- Isolation and Characterization of scFv Antibody against Internal Ribosomal Entry Site of Enterovirus A71.International journal of molecular sciences · 2023Article
- Computational tools to study RNA-protein complexes.Frontiers in molecular biosciences · 2022Review
- Developing an Updated Strategy for Estimating the Free-Energy Parameters in RNA Duplexes.International journal of molecular sciences · 2021Article
- Predicting RNA Scaffolds with a Hybrid Method of Vfold3D and VfoldLA.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Accurate inference of the full base-pairing structure of RNA by deep mutational scanning and covariation-induced deviation of activity.Nucleic acids research · 2020Article
- Advances in RNA 3D Structure Modeling Using Experimental Data.Frontiers in genetics · 2020Review
- Inferring protein 3D structure from deep mutation scans.Nature genetics · 2019Article
- Computational modeling of RNA 3D structure based on experimental data.Bioscience reports · 2019Review
- Hierarchical Assembly of RNA Three-Dimensional Structures Based on Loop Templates.The journal of physical chemistry. B · 2018Article
- Classification of RNA structure change by 'gazing' at experimental data.Bioinformatics (Oxford, England) · 2017Article
- Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules.Annual review of biophysics · 2017Review
- Kinetic and thermodynamic framework for P4-P6 RNA reveals tertiary motif modularity and modulation of the folding preferred pathway.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Progress and Current Challenges in Modeling Large RNAs.Journal of molecular biology · 2016Review
- Structure Prediction: New Insights into Decrypting Long Noncoding RNAs.International journal of molecular sciences · 2016Review
- Consistent global structures of complex RNA states through multidimensional chemical mapping.eLife · 2015Article
- Predicting RNA 3D structure using a coarse-grain helix-centered model.RNA (New York, N.Y.) · 2015Article
- Computational analysis of RNA structures with chemical probing data.Methods (San Diego, Calif.) · 2015Review
- GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies.PloS one · 2015Article
Corrections and comments
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Authors and funding
10 authors at 5 institutions in 2 countries.
Funding
Abstract
The biological behaviors of ribozymes, riboswitches, and numerous other functional RNA molecules are critically dependent on their tertiary folding and their ability to sample multiple functional states. The conformational heterogeneity and partially folded nature of most of these states has rendered their characterization by high-resolution structural approaches difficult or even intractable. Here we introduce a method to rapidly infer the tertiary helical arrangements of large RNA molecules in their native and non-native solution states. Multiplexed hydroxyl radical (.OH) cleavage analysis (MOHCA) enables the high-throughput detection of numerous pairs of contacting residues via random incorporation of radical cleavage agents followed by two-dimensional gel electrophoresis. We validated this technology by recapitulating the unfolded and native states of a well studied model RNA, the P4-P6 domain of the Tetrahymena ribozyme, at subhelical resolution. We then applied MOHCA to a recently discovered third state of the P4-P6 RNA that is stabilized by high concentrations of monovalent salt and whose partial order precludes conventional techniques for structure determination. The three-dimensional portrait of a compact, non-native RNA state reveals a well ordered subset of native tertiary contacts, in contrast to the dynamic but otherwise similar molten globule states of proteins. With its applicability to nearly any solution state, we expect MOHCA to be a powerful tool for illuminating the many functional structures of large RNA molecules and RNA/protein complexes.
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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.