ArticleNucleic acids research2023
Nearest-neighbor parameters for the prediction of RNA duplex stability in diverse in vitro and cellular-like crowding conditions.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Article
- Insights into siRNA Duplex Stability by UV Spectrophotometry Absorbance and Melting Temperature Analyses.ACS omega · 2026Article
- High-throughput measurement and prediction of the i-motif DNA stability landscape.Nucleic acids research · 2026Article
- Stability of non-canonical nucleic acid structure as a potential modulator of cell fate.Nucleic acids research · 2026Review
- Leveraging Foundation Models for the Characterization of Small-RNA Properties.Computational and structural biotechnology journal · 2026Article
- Twisting tetraplex DNA: A strand dynamics regulating i-motif function in diverse molecular crowding environments.Nucleic acids research · 2025Article
- Predictability of environment-dependent formation of G-quadruplex DNAs in human mitochondria.Communications chemistry · 2025Article
- Imperfect G-quadruplex as an emerging candidate for transcriptional regulation.Nucleic acids research · 2025Article
- RNA Stability: A Review of the Role of Structural Features and Environmental Conditions.Molecules (Basel, Switzerland) · 2024Review
- Elucidating the Role of Groove Hydration on Stability and Functions of Biased DNA Duplexes in Cell-Like Chemical Environments.Journal of the American Chemical Society · 2024Article
- Competitive Influence of Alkali Metals in the Ion Atmosphere on Nucleic Acid Duplex Stability.ACS omega · 2024Article
- Comparative genomics of the extremophileFrontiers in fungal biology · 2024Article
- In vivo-like nearest neighbor parameters improve prediction of fractional RNA base-pairing in cells.Nucleic acids research · 2023Article
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7 authors.
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Abstract
RNA performs various spatiotemporal functions in living cells. As the solution environments significantly affect the stability of RNA duplexes, a stability prediction of the RNA duplexes in diverse crowded conditions is required to understand and modulate gene expression in heterogeneously crowded intracellular conditions. Herein, we determined the nearest-neighbor (NN) parameters for RNA duplex formation when subjected to crowding conditions with an ionic concentration relevant to that found in cells. Determination of the individual contributions of excluded volume effect and water activity to each of the NN parameters in crowded environments enabled prediction of the thermodynamic parameters and their melting temperatures for plenty of tested RNA duplex formation in vitro and in cell with significant accuracy. The parameters reported herein will help predicting RNA duplex stability in different crowded environments, which will lead to an improved understanding of the stability-function relationship for RNAs in various cellular organelles with different molecular environments.
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