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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, nwater(RLocal), and (B) number of EG molecules, nEG(RLocal), 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).
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Figure 8: (A) Number of water molecules, nwater(RLocal), and (B) number of EG molecules, nEG(RLocal), 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).

Mentions: Figure 8 shows the numbers of water molecules, nwater(RLocal), and EG molecules, nEG(RLocal), in the local regions. Upon addition of EG, the number of waters in contact with the backbone atoms in HP, nwater(HP-backbone), decreased and nEG(HP-backbone) increased most significantly, and nEG(TBA-base) changed the least. Changes in nwater were consistent with changes in ρwater shown in Figure 7A. Our data indicate that EG more readily replaces water near Watson–Crick base pairs than around G-quartets.


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, nwater(RLocal), and (B) number of EG molecules, nEG(RLocal), 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).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 8: (A) Number of water molecules, nwater(RLocal), and (B) number of EG molecules, nEG(RLocal), 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).
Mentions: Figure 8 shows the numbers of water molecules, nwater(RLocal), and EG molecules, nEG(RLocal), in the local regions. Upon addition of EG, the number of waters in contact with the backbone atoms in HP, nwater(HP-backbone), decreased and nEG(HP-backbone) increased most significantly, and nEG(TBA-base) changed the least. Changes in nwater were consistent with changes in ρwater shown in Figure 7A. Our data indicate that EG more readily replaces water near Watson–Crick base pairs than around G-quartets.

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