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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) Relative number density of water molecules, ρ(RLocal)/ρ0, (B) normalized free energy of a water molecule, ΔGw(RLocal), (C) normalized interaction energy between water and DNA, ΔEsww(RLocal), (D) normalized interaction energy between water molecules, ΔEwww(RLocal), (E) normalized translational entropy term, TΔStrw(RLocal) and (F) normalized orientational entropy term, TΔSorw(RLocal), in RLocal as a function of EG concentration for HP-backbone (filled red circles with solid lines), TBA-backbone (filled black triangles with solid lines), HP-base (open red circles with dashed lines) and TBA-base (open black triangles with dashed lines). Energies plotted in panels C, D, E and F are shown in kcal/mol/water at 298 K.
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Figure 7: (A) Relative number density of water molecules, ρ(RLocal)/ρ0, (B) normalized free energy of a water molecule, ΔGw(RLocal), (C) normalized interaction energy between water and DNA, ΔEsww(RLocal), (D) normalized interaction energy between water molecules, ΔEwww(RLocal), (E) normalized translational entropy term, TΔStrw(RLocal) and (F) normalized orientational entropy term, TΔSorw(RLocal), in RLocal as a function of EG concentration for HP-backbone (filled red circles with solid lines), TBA-backbone (filled black triangles with solid lines), HP-base (open red circles with dashed lines) and TBA-base (open black triangles with dashed lines). Energies plotted in panels C, D, E and F are shown in kcal/mol/water at 298 K.

Mentions: To evaluate local hydration properties in more detail, we focused on two Watson–Crick base pairs within HP (C4-G13 and T5-A12) and one G-quartet within TBA (involving G2, G5, G11 and G14) as shown in Figure 1A and B, respectively; these are internal pairs in order to eliminate contributions from loop and terminal regions. We will refer to the voxels around the base atoms in these nucleotides as HP-base and TBA-base and to the voxels around the phosphate groups as HP-backbone and TBA-backbone. The distances from the center of voxel to the designated atom of DNA were 2 Å < rmin < 4 Å. We defined these regions as the local regions, RLocal. Figure 7 shows the thermodynamic parameters of a water in the region RLocal obtained by GIST analysis. The density of waters around base atoms was highest for TBA (ρwater(TBA-base)) as shown in Figure 7A, even though guanine bases are tightly packed in the quadruplex. In our definitions of RLocal and RDNA, the inner area of TBA was excluded, because the region was too small to hold water molecules.


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) Relative number density of water molecules, ρ(RLocal)/ρ0, (B) normalized free energy of a water molecule, ΔGw(RLocal), (C) normalized interaction energy between water and DNA, ΔEsww(RLocal), (D) normalized interaction energy between water molecules, ΔEwww(RLocal), (E) normalized translational entropy term, TΔStrw(RLocal) and (F) normalized orientational entropy term, TΔSorw(RLocal), in RLocal as a function of EG concentration for HP-backbone (filled red circles with solid lines), TBA-backbone (filled black triangles with solid lines), HP-base (open red circles with dashed lines) and TBA-base (open black triangles with dashed lines). Energies plotted in panels C, D, E and F are shown in kcal/mol/water at 298 K.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 7: (A) Relative number density of water molecules, ρ(RLocal)/ρ0, (B) normalized free energy of a water molecule, ΔGw(RLocal), (C) normalized interaction energy between water and DNA, ΔEsww(RLocal), (D) normalized interaction energy between water molecules, ΔEwww(RLocal), (E) normalized translational entropy term, TΔStrw(RLocal) and (F) normalized orientational entropy term, TΔSorw(RLocal), in RLocal as a function of EG concentration for HP-backbone (filled red circles with solid lines), TBA-backbone (filled black triangles with solid lines), HP-base (open red circles with dashed lines) and TBA-base (open black triangles with dashed lines). Energies plotted in panels C, D, E and F are shown in kcal/mol/water at 298 K.
Mentions: To evaluate local hydration properties in more detail, we focused on two Watson–Crick base pairs within HP (C4-G13 and T5-A12) and one G-quartet within TBA (involving G2, G5, G11 and G14) as shown in Figure 1A and B, respectively; these are internal pairs in order to eliminate contributions from loop and terminal regions. We will refer to the voxels around the base atoms in these nucleotides as HP-base and TBA-base and to the voxels around the phosphate groups as HP-backbone and TBA-backbone. The distances from the center of voxel to the designated atom of DNA were 2 Å < rmin < 4 Å. We defined these regions as the local regions, RLocal. Figure 7 shows the thermodynamic parameters of a water in the region RLocal obtained by GIST analysis. The density of waters around base atoms was highest for TBA (ρwater(TBA-base)) as shown in Figure 7A, even though guanine bases are tightly packed in the quadruplex. In our definitions of RLocal and RDNA, the inner area of TBA was excluded, because the region was too small to hold water molecules.

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