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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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Related in: MedlinePlus

Whole MD systems and grid inhomogeneous solvation theory (GIST) analysis regions for (A) HP, (B) TBA, (C) unHP and (D) unTBA, and (E) the definition of GIST analysis RDNA used in this study. DNA strands are shown in black stick models, and oxygen atoms of water molecules are shown as gray dots. Rectangular boxes in panels A, B, C and D represent the GIST analysis regions for each system. In panel 2E, rmin is the minimum distance between DNA atom and the center of voxel, and RDNA (colored in gray around DNA) is the GIST analysis region in this study.
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Figure 2: Whole MD systems and grid inhomogeneous solvation theory (GIST) analysis regions for (A) HP, (B) TBA, (C) unHP and (D) unTBA, and (E) the definition of GIST analysis RDNA used in this study. DNA strands are shown in black stick models, and oxygen atoms of water molecules are shown as gray dots. Rectangular boxes in panels A, B, C and D represent the GIST analysis regions for each system. In panel 2E, rmin is the minimum distance between DNA atom and the center of voxel, and RDNA (colored in gray around DNA) is the GIST analysis region in this study.

Mentions: To investigate the thermodynamic parameters of the water molecules around DNA, we used the GIST program included in cpptraj module in AMBER 14 (64). We set the GIST grid size to 0.5 Å3, and set the GIST analysis region to cover the whole DNA structure with a margin of at least 7 Å. The box sizes were 36 × 34 × 49 Å3 for HP, 39 × 32 × 41 Å3 for TBA, 35 × 35 × 58 Å3 for unHP and 35 × 35 × 56 Å3 for unTBA, respectively. Locations of GIST analysis regions relative to the MD systems are shown in Figure 2A–D. In this study, as the first step to investigate the effects of environment on the thermal stabilities of DNA structures, we focused on the thermodynamic properties of water molecules around DNA, although it is expected that the interaction between cosolutes and DNA is also important. We removed all potassium ions and EG molecules from the simulation boxes before applying GIST analysis because GIST assumes that the solute of interest comprises all molecules in the simulation box except for 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)

Whole MD systems and grid inhomogeneous solvation theory (GIST) analysis regions for (A) HP, (B) TBA, (C) unHP and (D) unTBA, and (E) the definition of GIST analysis RDNA used in this study. DNA strands are shown in black stick models, and oxygen atoms of water molecules are shown as gray dots. Rectangular boxes in panels A, B, C and D represent the GIST analysis regions for each system. In panel 2E, rmin is the minimum distance between DNA atom and the center of voxel, and RDNA (colored in gray around DNA) is the GIST analysis region in this study.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 2: Whole MD systems and grid inhomogeneous solvation theory (GIST) analysis regions for (A) HP, (B) TBA, (C) unHP and (D) unTBA, and (E) the definition of GIST analysis RDNA used in this study. DNA strands are shown in black stick models, and oxygen atoms of water molecules are shown as gray dots. Rectangular boxes in panels A, B, C and D represent the GIST analysis regions for each system. In panel 2E, rmin is the minimum distance between DNA atom and the center of voxel, and RDNA (colored in gray around DNA) is the GIST analysis region in this study.
Mentions: To investigate the thermodynamic parameters of the water molecules around DNA, we used the GIST program included in cpptraj module in AMBER 14 (64). We set the GIST grid size to 0.5 Å3, and set the GIST analysis region to cover the whole DNA structure with a margin of at least 7 Å. The box sizes were 36 × 34 × 49 Å3 for HP, 39 × 32 × 41 Å3 for TBA, 35 × 35 × 58 Å3 for unHP and 35 × 35 × 56 Å3 for unTBA, respectively. Locations of GIST analysis regions relative to the MD systems are shown in Figure 2A–D. In this study, as the first step to investigate the effects of environment on the thermal stabilities of DNA structures, we focused on the thermodynamic properties of water molecules around DNA, although it is expected that the interaction between cosolutes and DNA is also important. We removed all potassium ions and EG molecules from the simulation boxes before applying GIST analysis because GIST assumes that the solute of interest comprises all molecules in the simulation box except for 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.

Show MeSH
Related in: MedlinePlus