ArticleBiochemistry2012
Denaturation of RNA secondary and tertiary structure by urea: simple unfolded state models and free energy parameters account for measured m-values.
Article in Biochemistry, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 63 citations in OpenAlex.
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- Conformational dynamics of the hepatitis C virus 3'X RNA.RNA (New York, N.Y.) · 2024Article
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- Stability-Based Proteomics for Investigation of Structured RNA-Protein Interactions.Analytical chemistry · 2024Article
- In vivo-like nearest neighbor parameters improve prediction of fractional RNA base-pairing in cells.Nucleic acids research · 2023Article
- Single-molecule FRET observes opposing effects of urea and TMAO on structurally similar meso- and thermophilic riboswitch RNAs.Nucleic acids research · 2023Article
- CAG-Repeat RNA Hairpin Folding and Recruitment to Nuclear Speckles with a Pivotal Role of ATP as a Cosolute.Journal of the American Chemical Society · 2023Article
- Formulation, Device, and Clinical Factors Influencing the Targeted Delivery of COVID-19 Vaccines to the Lungs.AAPS PharmSciTech · 2022Review
- The Metabolome Weakens RNA Thermodynamic Stability and Strengthens RNA Chemical Stability.Biochemistry · 2022Article
- Functional Roles of Chelated Magnesium Ions in RNA Folding and Function.Biochemistry · 2021Article
- Application of Nucleic Acid Mimics in Fluorescence In Situ Hybridization.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Deletion of the N-Terminal Domain of Yeast Eukaryotic Initiation Factor 4B Reprograms Translation and Reduces Growth in Urea.Frontiers in molecular biosciences · 2021Article
- Urea-aromatic interactions in biology.Biophysical reviews · 2020Review
- Characterization of FFPE-induced bacterial DNA damage and development of a repair method.Biology methods & protocols · 2020Article
- A Widely Applicable Urea-based Fluorescent/Colorimetric mRNABio-protocol · 2019Article
- Energetic, Structural and Dynamic Properties of Nucleobase-Urea Interactions that Aid in Urea Assisted RNA Unfolding.Scientific reports · 2019Article
- Exploring the effects of cosolutes and crowding on the volumetric and kinetic profile of the conformational dynamics of a poly dA loop DNA hairpin: a single-molecule FRET study.Nucleic acids research · 2019Article
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2 authors at 1 institution in 1 country.
Funding
Abstract
To investigate the mechanism by which urea destabilizes RNA structure, urea-induced unfolding of four different RNA secondary and tertiary structures was quantified in terms of an m-value, the rate at which the free energy of unfolding changes with urea molality. From literature data and our osmometric study of a backbone analogue, we derived average interaction potentials (per square angstrom of solvent accessible surface) between urea and three kinds of RNA surfaces: phosphate, ribose, and base. Estimates of the increases in solvent accessible surface areas upon RNA denaturation were based on a simple model of unfolded RNA as a combination of helical and single-strand segments. These estimates, combined with the three interaction potentials and a term to account for interactions of urea with released ions, yield calculated m-values that are in good agreement with experimental values (200 mm monovalent salt). Agreement was obtained only if single-stranded RNAs were modeled in a highly stacked, A-form conformation. The primary driving force for urea-induced denaturation is the strong interaction of urea with the large surface areas of bases that become exposed upon denaturation of either RNA secondary or tertiary structure, though interactions of urea with backbone and released ions may account for up to a third of the m-value. Urea m-values for all four RNAs are salt-dependent, which we attribute to an increased extension (or decreased charge density) of unfolded RNAs with an increased urea concentration. The sensitivity of the urea m-value to base surface exposure makes it a potentially useful probe of the conformations of RNA unfolded states.
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