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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) 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).
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Figure 4: (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).

Mentions: To investigate the solvent properties near DNAs, we focused on the water molecules in the first hydration shell around DNA. From the results of water and EG density profiles as shown in Figure 3, we defined the region within 2.0 Å < rmin < 4.0 Å as the first hydration shell around DNA, region RDNA, and calculated thermodynamic parameters for a water molecule in this region. No significant differences in water densities outside this area were observed. Figure 4A shows the number of water molecules, nwater(RDNA), and Figure 4B shows the averaged relative number density of water molecules, ρwater(RDNA) / ρ0, in the region RDNA. For both HP and TBA, nwater(RDNA) values around the folded structures were smaller than those around the unfolded structures. These results show that dehydration occurred upon formation of base pairs and base quartets from the unfolded structures. The difference in nwater(RDNA) for TBA and unTBA was larger than that for HP and unHP for all EG concentrations, whereas ρwater(RDNA) around the DNA in the absence of EG were almost the same (within 3%) for all DNA structures. The decreases in nwater(RDNA) and ρwater(RDNA) / ρ0 for HP upon addition of EG were larger than those for TBA, unHP and unTBA. These results were consistent with the result shown in Figure 3B: EG replaced water molecules around HP more readily than it did water molecules around TBA.


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) 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).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Figure 4: (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).
Mentions: To investigate the solvent properties near DNAs, we focused on the water molecules in the first hydration shell around DNA. From the results of water and EG density profiles as shown in Figure 3, we defined the region within 2.0 Å < rmin < 4.0 Å as the first hydration shell around DNA, region RDNA, and calculated thermodynamic parameters for a water molecule in this region. No significant differences in water densities outside this area were observed. Figure 4A shows the number of water molecules, nwater(RDNA), and Figure 4B shows the averaged relative number density of water molecules, ρwater(RDNA) / ρ0, in the region RDNA. For both HP and TBA, nwater(RDNA) values around the folded structures were smaller than those around the unfolded structures. These results show that dehydration occurred upon formation of base pairs and base quartets from the unfolded structures. The difference in nwater(RDNA) for TBA and unTBA was larger than that for HP and unHP for all EG concentrations, whereas ρwater(RDNA) around the DNA in the absence of EG were almost the same (within 3%) for all DNA structures. The decreases in nwater(RDNA) and ρwater(RDNA) / ρ0 for HP upon addition of EG were larger than those for TBA, unHP and unTBA. These results were consistent with the result shown in Figure 3B: EG replaced water molecules around HP more readily than it did water molecules around TBA.

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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Related in: MedlinePlus