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Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory.

Nakano M, Tateishi-Karimata H, Tanaka S, Tama F, Miyashita O, Nakano S, Sugimoto N - Nucleic Acids Res. (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan Advanced Institute for Computational Sciences, RIKEN, 7-1-26, Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.

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(A) Normalized average free energy of a water molecule relative to bulk water in the first hydration shell around DNA, ΔGw(RDNA), as a function of EG concentration for HP (filled red circles with solid line), TBA (filled black triangles with solid line), unHP (open red circles with dashed line) and unTBA (open black triangles with dashed line). (B) Difference in ΔGw(RDNA) between folded and unfolded structures, ΔΔGw(RDNA), for HP versus unHP (red squares) and TBA versus unTBA (black diamonds). All energies are shown in kcal/mol/water at 298 K.
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Figure 5: (A) Normalized average free energy of a water molecule relative to bulk water in the first hydration shell around DNA, ΔGw(RDNA), as a function of EG concentration for HP (filled red circles with solid line), TBA (filled black triangles with solid line), unHP (open red circles with dashed line) and unTBA (open black triangles with dashed line). (B) Difference in ΔGw(RDNA) between folded and unfolded structures, ΔΔGw(RDNA), for HP versus unHP (red squares) and TBA versus unTBA (black diamonds). All energies are shown in kcal/mol/water at 298 K.

Mentions: (A) Number of water molecules in the region RDNA, nwater(RDNA), and (B) relative number density of water molecules in the region RDNA to the density of bulk water, ρwater(RDNA) / ρ0, at different EG concentrations for HP (filled red circles with solid lines), TBA (filled black triangles with solid lines), unHP (open red circles with dashed lines) and unTBA (open black triangles with dashed lines). Standard errors of the mean (SEM), which were calculated with the average values for every 10 ns data from 50 ns to 100 ns MD simulations, are enough small within the sizes of symbols (also in Figures 5–9).


Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory.

Nakano M, Tateishi-Karimata H, Tanaka S, Tama F, Miyashita O, Nakano S, Sugimoto N - Nucleic Acids Res. (2015)

(A) Normalized average free energy of a water molecule relative to bulk water in the first hydration shell around DNA, ΔGw(RDNA), as a function of EG concentration for HP (filled red circles with solid line), TBA (filled black triangles with solid line), unHP (open red circles with dashed line) and unTBA (open black triangles with dashed line). (B) Difference in ΔGw(RDNA) between folded and unfolded structures, ΔΔGw(RDNA), for HP versus unHP (red squares) and TBA versus unTBA (black diamonds). All energies are shown in kcal/mol/water at 298 K.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4666364&req=5

Figure 5: (A) Normalized average free energy of a water molecule relative to bulk water in the first hydration shell around DNA, ΔGw(RDNA), as a function of EG concentration for HP (filled red circles with solid line), TBA (filled black triangles with solid line), unHP (open red circles with dashed line) and unTBA (open black triangles with dashed line). (B) Difference in ΔGw(RDNA) between folded and unfolded structures, ΔΔGw(RDNA), for HP versus unHP (red squares) and TBA versus unTBA (black diamonds). All energies are shown in kcal/mol/water at 298 K.
Mentions: (A) Number of water molecules in the region RDNA, nwater(RDNA), and (B) relative number density of water molecules in the region RDNA to the density of bulk water, ρwater(RDNA) / ρ0, at different EG concentrations for HP (filled red circles with solid lines), TBA (filled black triangles with solid lines), unHP (open red circles with dashed lines) and unTBA (open black triangles with dashed lines). Standard errors of the mean (SEM), which were calculated with the average values for every 10 ns data from 50 ns to 100 ns MD simulations, are enough small within the sizes of symbols (also in Figures 5–9).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan Advanced Institute for Computational Sciences, RIKEN, 7-1-26, Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.

Show MeSH
Related in: MedlinePlus