ArticleNucleic acids research2004
Heat capacity changes in RNA folding: application of perturbation theory to hammerhead ribozyme cold denaturation.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 48 citations in OpenAlex.
- Single-molecule analysis reveals low-temperature misfolding in HIV-1 TAR RNA.Scientific reports · 2026Article
- Interpretation of Short RNA Thermal Unfolding Data Obtained by Circular Dichroism Using ChiraKit.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Fluorescent Dyes for Differential Scanning Fluorimetry of RNA.Chembiochem : a European journal of chemical biology · 2025Article
- Hammerhead ribozymes directed against mRNA of an essential gene inhibitFrontiers in microbiology · 2025Article
- Energy landscapes of homopolymeric RNAs revealed by deep unsupervised learning.Biophysical journal · 2024Article
- An optimized method for high-quality RNA extraction from distinctive intrinsic laryngeal muscles in the rat model.Scientific reports · 2022Article
- Stem-loop formation drives RNA folding in mechanical unzipping experiments.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Thermodynamics and kinetics of RNA tertiary structure formation in the junctionless hairpin ribozyme.Biophysical chemistry · 2017Article
- Entropic stabilization of folded RNA in crowded solutions measured by SAXS.Nucleic acids research · 2016Article
- In vitro evolution of distinct self-cleaving ribozymes in diverse environments.Nucleic acids research · 2015Article
- Tetracycline determines the conformation of its aptamer at physiological magnesium concentrations.Biophysical journal · 2014Article
- Energy parameters and novel algorithms for an extended nearest neighbor energy model of RNA.PloS one · 2014Article
- Enhanced deoxyribozyme-catalyzed RNA ligation in the presence of organic cosolvents.Biopolymers · 2013Article
- Laser-induced temperature jump infrared measurements of RNA folding.Methods in enzymology · 2009Article
- Monitoring of an RNA multistep folding pathway by isothermal titration calorimetry.Biophysical journal · 2009Article
- Charge density of divalent metal cations determines RNA stability.Journal of the American Chemical Society · 2007Article
- Heat capacity changes associated with nucleic acid folding.Biopolymers · 2006Review
- Heat capacity changes associated with DNA duplex formation: salt- and sequence-dependent effects.Biochemistry · 2006Article
- Sequence effects of aminofluorene-modified DNA duplexes: thermodynamic and circular dichroism properties.Nucleic acids research · 2006Article
- Length-dependent energetics of (CTG)n and (CAG)n trinucleotide repeats.Nucleic acids research · 2005Article
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2 authors at 1 institution in 1 country.
Funding
Abstract
In proteins, empirical correlations have shown that changes in heat capacity (DeltaC(P)) scale linearly with the hydrophobic surface area buried upon folding. The influence of DeltaC(P) on RNA folding has been widely overlooked and is poorly understood. In addition to considerations of solvent reorganization, electrostatic effects might contribute to DeltaC(P)s of folding in polyanionic species such as RNAs. Here, we employ a perturbation method based on electrostatic theory to probe the hot and cold denaturation behavior of the hammerhead ribozyme. This treatment avoids much of the error associated with imposing two-state folding models on non-two-state systems. Ribozyme stability is perturbed across a matrix of solvent conditions by varying the concentration of NaCl and methanol co-solvent. Temperature-dependent unfolding is then monitored by circular dichroism spectroscopy. The resulting array of unfolding transitions can be used to calculate a DeltaC(P) of folding that accurately predicts the observed cold denaturation temperature. We confirm the accuracy of the calculated DeltaC(P) by using isothermal titration calorimetry, and also demonstrate a methanol-dependence of the DeltaC(P). We weigh the strengths and limitations of this method for determining DeltaC(P) values. Finally, we discuss the data in light of the physical origins of the DeltaC(P)s for RNA folding and consider their impact on biological function.
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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 OpenQuestion graph.