ArticleThe journal of physical chemistry. B2018
Quantitative Understanding of SHAPE Mechanism from RNA Structure and Dynamics Analysis.
Article in The journal of physical chemistry. B, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Markov models of SHAPE data improve secondary structure prediction.bioRxiv : the preprint server for biology · 2026Article
- Molecular Dynamics Simulations with Grand-Canonical Reweighting Suggest Cooperativity Effects in RNA Structure Probing Experiments.Journal of chemical theory and computation · 2023Article
- Role of RNA Domain Structure and Orientation in the Coxsackievirus B3 Virulence Phenotype.Journal of virology · 2023Article
- Review
- Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site.RNA biology · 2022Article
- An overview of structural approaches to study therapeutic RNAs.Frontiers in molecular biosciences · 2022Review
- Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions.Computational and structural biotechnology journal · 2022Review
- The International Society of RNA Nanotechnology and Nanomedicine (ISRNN): The Present and Future of the Burgeoning Field.ACS nano · 2021Article
- IsRNA1:Journal of chemical theory and computation · 2021Article
- Sieving RNA 3D Structures with SHAPE and Evaluating Mechanisms Driving Sequence-Dependent Reactivity Bias.The journal of physical chemistry. B · 2021Article
- SHAPER: A Web Server for Fast and Accurate SHAPE Reactivity Prediction.Frontiers in molecular biosciences · 2021Article
- A Bayes-inspired theory for optimally building an efficient coarse-grained folding force field.Communications in information and systems · 2021Article
- Advances in the Bioinformatics Knowledge of mRNA Polyadenylation in Baculovirus Genes.Viruses · 2020Review
- Quantitative comparison between sub-millisecond time resolution single-molecule FRET measurements and 10-second molecular simulations of a biosensor protein.PLoS computational biology · 2020Article
- IPANEMAP: integrative probing analysis of nucleic acids empowered by multiple accessibility profiles.Nucleic acids research · 2020Article
- Structural Flexibility of DNA-RNA Hybrid Duplex: Stretching and Twist-Stretch Coupling.Biophysical journal · 2019Article
- Article
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Authors and funding
4 authors.
Funding
Abstract
The selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) method probes RNA local structural and dynamic information at single nucleotide resolution. To gain quantitative insights into the relationship between nucleotide flexibility, RNA 3D structure, and SHAPE reactivity, we develop a 3D Structure-SHAPE Relationship model (3DSSR) to rebuild SHAPE profiles from 3D structures. The model starts from RNA structures and combines nucleotide interaction strength and conformational propensity, ligand (SHAPE reagent) accessibility, and base-pairing pattern through a composite function to quantify the correlation between SHAPE reactivity and nucleotide conformational stability. The 3DSSR model shows the relationship between SHAPE reactivity and RNA structure and energetics. Comparisons between the 3DSSR-predicted SHAPE profile and the experimental SHAPE data show correlation, suggesting that the extracted analytical function may have captured the key factors that determine the SHAPE reactivity profile. Furthermore, the theory offers an effective method to sieve RNA 3D models and exclude models that are incompatible with experimental SHAPE data.
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