ArticleNucleic acids research2019
Thermodynamic characterization and nearest neighbor parameters for RNA duplexes under molecular crowding conditions.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Conjugation of hydrophobic drugs to motile pRNA 4WJ nanoparticles for spontaneous tumor targeting and undetectable toxicity.Nature protocols · 2026Review
- Densities, Viscosities, and Self-Diffusion Coefficients of Sodium Chloride in Mixed Water-Polyethylene Glycol Solvents.Journal of chemical and engineering data · 2026Article
- Article
- Stability of non-canonical nucleic acid structure as a potential modulator of cell fate.Nucleic acids research · 2026Review
- Twisting tetraplex DNA: A strand dynamics regulating i-motif function in diverse molecular crowding environments.Nucleic acids research · 2025Article
- Effects of Molecular Crowding on the Structure, Folding, Stability, and Catalysis of RNA.Sub-cellular biochemistry · 2025Review
- Competitive Influence of Alkali Metals in the Ion Atmosphere on Nucleic Acid Duplex Stability.ACS omega · 2024Article
- In vivo-like nearest neighbor parameters improve prediction of fractional RNA base-pairing in cells.Nucleic acids research · 2023Article
- MeltR software provides facile determination of nucleic acid thermodynamics.Biophysical reports · 2023Article
- Nearest-neighbor parameters for the prediction of RNA duplex stability in diverse in vitro and cellular-like crowding conditions.Nucleic acids research · 2023Article
- The Metabolome Weakens RNA Thermodynamic Stability and Strengthens RNA Chemical Stability.Biochemistry · 2022Article
- A Structural Potential of Rare Trinucleotide Repeat Tracts in RNA.International journal of molecular sciences · 2022Article
- In vitro characterisation of the MS2 RNA polymerase complex reveals host factors that modulate emesviral replicase activity.Communications biology · 2022Article
- Atomistic Simulation of Lysozyme in Solutions Crowded by Tetraethylene Glycol: Force Field Dependence.Molecules (Basel, Switzerland) · 2022Article
- Dielectricity of a molecularly crowded solution accelerates NTP misincorporation during RNA-dependent RNA polymerization by T7 RNA polymerase.Scientific reports · 2022Article
- New Insights into the Functions of Nucleic Acids Controlled by Cellular Microenvironments.Topics in current chemistry (Cham) · 2021Review
- Molecular crowding induces primer extension by RNA polymerase through base stacking beyond Watson-Crick rules.RSC advances · 2020Article
- Nearest-neighbor parameters for predicting DNA duplex stability in diverse molecular crowding conditions.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
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2 authors.
Funding
Abstract
It is essential to study RNA under molecular crowding conditions to better predict secondary structures of RNAs in vivo. No systematic study has been completed to determine the effects of molecular crowding on RNA duplexes of varying lengths and sequence composition. Here, optical melting, circular dichroism, and osmometry data were collected for RNA duplexes in a 20% polyethylene glycol (with an average molecular weight of 200 g/mol) solution (PEG 200), and nearest neighbor parameters were derived using this data. RNA duplexes are destabilized, on average, 1.02 kcal/mol in the presence of 20% PEG 200. The ΔG°37 values predicted by the nearest neighbor parameters for RNA duplexes in 20% PEG 200 were ∼0.65 kcal/mol closer to experimental ΔG°37 values than those predicted by the standard nearest neighbor model. For one DNA sequence in solution with small crowders, the ΔG°37 values predicted by the 20% PEG 200 RNA nearest neighbor parameters were closer to the experimental values than ΔG°37 values predicted by either the RNA or DNA standard nearest neighbor models. This indicates that the nearest neighbor parameters for RNA duplexes in 20% PEG 200 may be generalizable to RNA and DNA duplexes in solutions with small crowding agents.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.