ArticleNucleic acids research2015
Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Protein crowders remodel RNA electrostatics, hydration, and dynamics: a challenge to steric crowding models.Nucleic acids research · 2026Article
- Exploring Nucleic Acid Structure and Function with Molecular Dynamics and Fragment Molecular Orbital Methods.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Enzyme Reactions Are Accelerated or Decelerated When the Enzymes Are Located Near the DNA Nanostructure.ACS applied materials & interfaces · 2025Article
- 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
- Nearest-neighbor parameters for the prediction of RNA duplex stability in diverse in vitro and cellular-like crowding conditions.Nucleic acids research · 2023Article
- Detection of Trace Amounts of Water in Organic Solvents by DNA-Based Nanomechanical Sensors.Biosensors · 2022Article
- Article
- 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
- Duplex DNA Is Weakened in Nanoconfinement.Journal of the American Chemical Society · 2020Article
- Article
- Effects of Environmental Factors and Metallic Electrodes on AC Electrical Conduction Through DNA Molecule.Nanoscale research letters · 2017Article
- Ectoine protects DNA from damage by ionizing radiation.Scientific reports · 2017Article
- Topological impact of noncanonical DNA structures on Klenow fragment of DNA polymerase.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Ectoine can enhance structural changes in DNA in vitro.Scientific reports · 2017Article
- Newly characterized interaction stabilizes DNA structure: oligoethylene glycols stabilize G-quadruplexes CH-π interactions.Nucleic acids research · 2017Article
- In What Ways Do Synthetic Nucleotides and Natural Base Lesions Alter the Structural Stability of G-Quadruplex Nucleic Acids?Journal of nucleic acids · 2017Review
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7 authors.
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Abstract
In conditions that mimic those of the living cell, where various biomolecules and other components are present, DNA strands can adopt many structures in addition to the canonical B-form duplex. Previous studies in the presence of cosolutes that induce molecular crowding showed that thermal stabilities of DNA structures are associated with the properties of the water molecules around the DNAs. To understand how cosolutes, such as ethylene glycol, affect the thermal stability of DNA structures, we investigated the thermodynamic properties of water molecules around a hairpin duplex and a G-quadruplex using grid inhomogeneous solvation theory (GIST) with or without cosolutes. Our analysis indicated that (i) cosolutes increased the free energy of water molecules around DNA by disrupting water-water interactions, (ii) ethylene glycol more effectively disrupted water-water interactions around Watson-Crick base pairs than those around G-quartets or non-paired bases, (iii) due to the negative electrostatic potential there was a thicker hydration shell around G-quartets than around Watson-Crick-paired bases. Our findings suggest that the thermal stability of the hydration shell around DNAs is one factor that affects the thermal stabilities of DNA structures under the crowding conditions.
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