ArticleFrontiers in molecular biosciences2021
Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement.
Article in Frontiers in molecular biosciences, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Effects of Molecular Crowding on the Structure, Folding, Stability, and Catalysis of RNA.Sub-cellular biochemistry · 2025Review
- RNA 3D Structure Prediction: Progress and Perspective.Molecules (Basel, Switzerland) · 2023Review
- Predicting 3D structures and stabilities for complex RNA pseudoknots in ion solutions.Biophysical journal · 2023Article
- cgRNASP: coarse-grained statistical potentials with residue separation for RNA structure evaluation.NAR genomics and bioinformatics · 2023Article
- FebRNA: An automated fragment-ensemble-based model for building RNA 3D structures.Biophysical journal · 2022Article
- rsRNASP: A residue-separation-based statistical potential for RNA 3D structure evaluation.Biophysical journal · 2022Article
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Authors and funding
5 authors.
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Abstract
Macromolecules, such as RNAs, reside in crowded cell environments, which could strongly affect the folded structures and stability of RNAs. The emergence of RNA-driven phase separation in biology further stresses the potential functional roles of molecular crowding. In this work, we employed the coarse-grained model that was previously developed by us to predict 3D structures and stability of the mouse mammary tumor virus (MMTV) pseudoknot under different spatial confinements over a wide range of salt concentrations. The results show that spatial confinements can not only enhance the compactness and stability of MMTV pseudoknot structures but also weaken the dependence of the RNA structure compactness and stability on salt concentration. Based on our microscopic analyses, we found that the effect of spatial confinement on the salt-dependent RNA pseudoknot stability mainly comes through the spatial suppression of extended conformations, which are prevalent in the partially/fully unfolded states, especially at low ion concentrations. Furthermore, our comprehensive analyses revealed that the thermally unfolding pathway of the pseudoknot can be significantly modulated by spatial confinements, since the intermediate states with more extended conformations would loss favor when spatial confinements are introduced.
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