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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

Ratio of solvent accessible surface areas, RSASA, of DNAs measured as a function of probe radius (rp) 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).
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Figure 11: Ratio of solvent accessible surface areas, RSASA, of DNAs measured as a function of probe radius (rp) 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).

Mentions: Another new finding in this study is the preferential binding of EG to HP. Fewer EG molecules were held around TBA than around HP (Figure 3B), and EG formed very few hydrogen bonds with G-quartet bases (Figure 9B). In addition, the number of hydrogen bonds between EG and the atoms in G-quartet did not increase with increasing EG concentration. To investigate why EG molecules more easily access the surface of HP than that of TBA, we calculated the relative solvent accessible surface areas (RSASA) of DNAs as a function of a spherical probe of radius, rp:(12)\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy}\usepackage{upgreek}\usepackage{mathrsfs}\setlength{\oddsidemargin}{-69pt}\begin{document}}{}\begin{equation*} R_{SASA} = \frac{{SASA(r_p )}}{{SASA(r_0 )}}. \end{equation*}\end{document}In Equation (12), SASA(rp) and SASA(r0) are the solvent accessible surface areas measured with probe radius rp and r0. r0 is the referenced probe radius, set to be 1.4 Å for this calculation; this value is often used as the probe radius of a water molecule for the calculation of solvent accessible surface area (69,70). As shown in Figure 11, RSASA for TBA decreased more significantly with increasing rp than those for other structures. The gyration radius of EG was about 2.4 times that of water, which were calculated by cpptraj module in Amber14 (64). These results indicated that the pocket sizes on the surface of TBA were relatively small for large cosolute, such as EG, but large enough for small molecule, such as water, to bind. As a result, EG could easily access the surface of HP compared to the surface of 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)

Ratio of solvent accessible surface areas, RSASA, of DNAs measured as a function of probe radius (rp) 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).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 11: Ratio of solvent accessible surface areas, RSASA, of DNAs measured as a function of probe radius (rp) 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).
Mentions: Another new finding in this study is the preferential binding of EG to HP. Fewer EG molecules were held around TBA than around HP (Figure 3B), and EG formed very few hydrogen bonds with G-quartet bases (Figure 9B). In addition, the number of hydrogen bonds between EG and the atoms in G-quartet did not increase with increasing EG concentration. To investigate why EG molecules more easily access the surface of HP than that of TBA, we calculated the relative solvent accessible surface areas (RSASA) of DNAs as a function of a spherical probe of radius, rp:(12)\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy}\usepackage{upgreek}\usepackage{mathrsfs}\setlength{\oddsidemargin}{-69pt}\begin{document}}{}\begin{equation*} R_{SASA} = \frac{{SASA(r_p )}}{{SASA(r_0 )}}. \end{equation*}\end{document}In Equation (12), SASA(rp) and SASA(r0) are the solvent accessible surface areas measured with probe radius rp and r0. r0 is the referenced probe radius, set to be 1.4 Å for this calculation; this value is often used as the probe radius of a water molecule for the calculation of solvent accessible surface area (69,70). As shown in Figure 11, RSASA for TBA decreased more significantly with increasing rp than those for other structures. The gyration radius of EG was about 2.4 times that of water, which were calculated by cpptraj module in Amber14 (64). These results indicated that the pocket sizes on the surface of TBA were relatively small for large cosolute, such as EG, but large enough for small molecule, such as water, to bind. As a result, EG could easily access the surface of HP compared to the surface of 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