ArticleJournal of the American Chemical Society2013
Quantifying functional group interactions that determine urea effects on nucleic acid helix formation.
Article in Journal of the American Chemical Society, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
25 citing papers in PubMed, 54 citations in OpenAlex.
- Effects of Loop Nucleobase Substitution on G-Quadruplex Thermal Stability in Aqueous Glycine Betaine, Proline, TMAO, and Urea Solutions.Biomolecules · 2026Article
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- Crowding beyond excluded volume: A tale of two dimers.Protein science : a publication of the Protein Society · 2025Article
- Quantifying Amide-Aromatic Interactions at Molecular and Atomic Levels: Experimentally-determined Enthalpic and Entropic Contributions to Interactions of Amide spbioRxiv : the preprint server for biology · 2023Article
- Progress in application of terahertz time-domain spectroscopy for pharmaceutical analyses.Frontiers in bioengineering and biotechnology · 2023Review
- Combined Effects of Methylated Cytosine and Molecular Crowding on the Thermodynamic Stability of DNA Duplexes.International journal of molecular sciences · 2021Article
- Experimentally determined strengths of favorable and unfavorable interactions of amide atoms involved in protein self-assembly in water.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Urea-aromatic interactions in biology.Biophysical reviews · 2020Review
- Energetic, Structural and Dynamic Properties of Nucleobase-Urea Interactions that Aid in Urea Assisted RNA Unfolding.Scientific reports · 2019Article
- Structure of human telomere G-quadruplex in the presence of a model drug along the thermal unfolding pathway.Nucleic acids research · 2018Article
- Quantifying Interactions of Nucleobase Atoms with Model Compounds for the Peptide Backbone and Glutamine and Asparagine Side Chains in Water.Biochemistry · 2018Article
- Preferential Binding of Urea to Single-Stranded DNA Structures: A Molecular Dynamics Study.Biophysical journal · 2018Article
- The mechanism and high-free-energy transition state of lac repressor-lac operator interaction.Nucleic acids research · 2017Article
- Experimental Atom-by-Atom Dissection of Amide-Amide and Amide-Hydrocarbon Interactions in HJournal of the American Chemical Society · 2017Article
- Aspects of Weak Interactions between Folate and Glycine Betaine.Biochemistry · 2016Article
- Basis of Protein Stabilization by K Glutamate: Unfavorable Interactions with Carbon, Oxygen Groups.Biophysical journal · 2016Article
- Separating chemical and excluded volume interactions of polyethylene glycols with native proteins: Comparison with PEG effects on DNA helix formation.Biopolymers · 2015Article
- Chemical Interactions of Polyethylene Glycols (PEGs) and Glycerol with Protein Functional Groups: Applications to Effects of PEG and Glycerol on Protein Processes.Biochemistry · 2015Article
- Dispersion interactions between urea and nucleobases contribute to the destabilization of RNA by urea in aqueous solution.The journal of physical chemistry. B · 2015Article
- Quantitative assessments of the distinct contributions of polypeptide backbone amides versus side chain groups to chain expansion via chemical denaturation.Journal of the American Chemical Society · 2015Article
Corrections and comments
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Authors and funding
12 authors at 2 institutions in 1 country.
Funding
Abstract
Urea destabilizes helical and folded conformations of nucleic acids and proteins, as well as protein-nucleic acid complexes. To understand these effects, extend previous characterizations of interactions of urea with protein functional groups, and thereby develop urea as a probe of conformational changes in protein and nucleic acid processes, we obtain chemical potential derivatives (μ23 = dμ2/dm3) quantifying interactions of urea (component 3) with nucleic acid bases, base analogues, nucleosides, and nucleotide monophosphates (component 2) using osmometry and hexanol-water distribution assays. Dissection of these μ23 values yields interaction potentials quantifying interactions of urea with unit surface areas of nucleic acid functional groups (heterocyclic aromatic ring, ring methyl, carbonyl and phosphate O, amino N, sugar (C and O); urea interacts favorably with all these groups, relative to interactions with water. Interactions of urea with heterocyclic aromatic rings and attached methyl groups (as on thymine) are particularly favorable, as previously observed for urea-homocyclic aromatic ring interactions. Urea m-values determined for double helix formation by DNA dodecamers near 25 °C are in the range of 0.72-0.85 kcal mol(-1)m(-1) and exhibit little systematic dependence on nucleobase composition (17-42% GC). Interpretation of these results using the urea interaction potentials indicates that extensive (60-90%) stacking of nucleobases in the separated strands in the transition region is required to explain the m-value. Results for RNA and DNA dodecamers obtained at higher temperatures, and literature data, are consistent with this conclusion. This demonstrates the utility of urea as a quantitative probe of changes in surface area (ΔASA) in nucleic acid processes.
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