ArticleRNA (New York, N.Y.)2014
Molecular crowders and cosolutes promote folding cooperativity of RNA under physiological ionic conditions.
Article in RNA (New York, N.Y.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers, 1 of them a synthesis that pooled it.
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Who cites it
47 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Macromolecular Crowding in Cytoplasm and Cellular Organelles.Sub-cellular biochemistry · 2025Pooled it
- Protein crowders remodel RNA electrostatics, hydration, and dynamics: a challenge to steric crowding models.Nucleic acids research · 2026Article
- Structural basis of MALAT1 RNA maturation and mascRNA biogenesis.Nature structural & molecular biology · 2024Article
- Molecular Crowding: The History and Development of a Scientific Paradigm.Chemical reviews · 2024Review
- Collision-Induced Unfolding Reveals Disease-Associated Stability Shifts in Mitochondrial Transfer Ribonucleic Acids.Journal of the American Chemical Society · 2024Article
- Origin of ribonucleotide recognition motifs through ligand mimicry at early earth.RNA biology · 2024Review
- Direct observation of tRNA-chaperoned folding of a dynamic mRNA ensemble.Nature communications · 2023Article
- Molecular Crowding Facilitates Ribozyme-Catalyzed RNA Assembly.ACS central science · 2023Article
- When Phased without Water: Biophysics of Cellular Desiccation, from Biomolecules to Condensates.Chemical reviews · 2023Review
- Dissecting the energetic architecture within an RNA tertiary structural motif via high-throughput thermodynamic measurements.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Structural basis for impaired 5' processing of a mutant tRNA associated with defects in neuronal homeostasis.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Multiplexed assessment of engineered bacterial constructs for intracellular β-galactosidase expression by redox amplification on catechol-chitosan modified nanoporous gold.Mikrochimica acta · 2021Article
- Progress toward SHAPE Constrained Computational Prediction of Tertiary Interactions in RNA Structure.Non-coding RNA · 2021Article
- Protein cofactors and substrate influence Mg2+-dependent structural changes in the catalytic RNA of archaeal RNase P.Nucleic acids research · 2021Article
- Apolar chemical environments compact unfolded RNAs and can promote folding.Biophysical reports · 2021Article
- HIV-1 matrix-tRNA complex structure reveals basis for host control of Gag localization.Cell host & microbe · 2021Article
- Functional Roles of Chelated Magnesium Ions in RNA Folding and Function.Biochemistry · 2021Article
- Magnesium: Biochemistry, Nutrition, Detection, and Social Impact of Diseases Linked to Its Deficiency.Nutrients · 2021Review
- RNA contributions to the form and function of biomolecular condensates.Nature reviews. Molecular cell biology · 2021Review
- Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement.Frontiers in molecular biosciences · 2021Article
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4 authors.
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Abstract
Folding mechanisms of functional RNAs under idealized in vitro conditions of dilute solution and high ionic strength have been well studied. Comparatively little is known, however, about mechanisms for folding of RNA in vivo where Mg(2+) ion concentrations are low, K(+) concentrations are modest, and concentrations of macromolecular crowders and low-molecular-weight cosolutes are high. Herein, we apply a combination of biophysical and structure mapping techniques to tRNA to elucidate thermodynamic and functional principles that govern RNA folding under in vivo-like conditions. We show by thermal denaturation and SHAPE studies that tRNA folding cooperativity increases in physiologically low concentrations of Mg(2+) (0.5-2 mM) and K(+) (140 mM) if the solution is supplemented with physiological amounts (∼ 20%) of a water-soluble neutral macromolecular crowding agent such as PEG or dextran. Low-molecular-weight cosolutes show varying effects on tRNA folding cooperativity, increasing or decreasing it based on the identity of the cosolute. For those additives that increase folding cooperativity, the gain is manifested in sharpened two-state-like folding transitions for full-length tRNA over its secondary structural elements. Temperature-dependent SHAPE experiments in the absence and presence of crowders and cosolutes reveal extent of cooperative folding of tRNA on a nucleotide basis and are consistent with the melting studies. Mechanistically, crowding agents appear to promote cooperativity by stabilizing tertiary structure, while those low molecular cosolutes that promote cooperativity stabilize tertiary structure and/or destabilize secondary structure. Cooperative folding of functional RNA under physiological-like conditions parallels the behavior of many proteins and has implications for cellular RNA folding kinetics and evolution.
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