ArticleBiochemistry2019
Effects of Refolding on Large-Scale RNA Structure.
Article in Biochemistry, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Genome-wide mapping of RNA-protein associations through sequencing.Nature biotechnology · 2026Article
- Solution structure determination and biophysical characterization studies of 7SK RNP and 7SL SRP RNAs.RNA (New York, N.Y.) · 2025Article
- mRNA vaccine sequence and structure design and optimization: Advances and challenges.The Journal of biological chemistry · 2025Review
- RNA ensembles from in vitro to in vivo: Toward predictive models of RNA cellular function.Current opinion in structural biology · 2024Review
- Causes, functions, and therapeutic possibilities of RNA secondary structure ensembles and alternative states.Cell chemical biology · 2024Review
- Fitness functions for RNA structure design.Nucleic acids research · 2023Article
- Structure-first identification of RNA elements that regulate dengue virus genome architecture and replication.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Regulation of Gene Expression Through Effector-dependent Conformational Switching by Cobalamin Riboswitches.Journal of molecular biology · 2022Review
- SHAPE Directed Discovery of New Functions in Large RNAs.Accounts of chemical research · 2021Review
- In vivo structure of the Ty1 retrotransposon RNA genome.Nucleic acids research · 2021Article
- Identifying Structural Domains and Conserved Regions in the Long Non-Coding RNA lncTCF7.International journal of molecular sciences · 2019Article
Corrections and comments
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Authors and funding
2 authors.
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Abstract
Understanding RNA-mediated functions requires a detailed characterization of the underlying RNA structure. In many cases, structure probing experiments are performed on RNA that has been "refolded" in some way, which may cause the conformation to differ from that of the native RNA. We used SHAPE-MaP (selective 2'-hydroxyl acylation analyzed by primer extension, read out by mutational profiling), to probe the structure of the Dengue virus (DENV) RNA genome after gentle extraction of the native RNA from intact virions (ex virion) and after heat denaturation and refolding. Comparison of mutiple SHAPE-informed structural features revealed that refolded RNA is more highly structured and samples fewer conformations than the ex virion RNA. Regions with similar structural features are generally those with low SHAPE reactivity and low Shannon entropy (lowSS regions), which correspond to elements with high levels of well-determined structure. This high-structure and low-entropy analysis framework, previously shown to make possible discovery of functional RNA structures, is thus now shown to allow de novo identification of structural elements in a refolded RNA that are likely to recapitulate RNA structures in the ex virion RNA state. Regions with less well-defined structures, which occurred more frequently in the more native-like ex virion RNA and may contain RNA switches, are challenging to recapitulate using refolded RNA.
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Registered trials
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