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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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Averaged electrostatic potential (in arbitrary units) around DNA as a function of minimum distance from DNA, rmin, 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 10: Averaged electrostatic potential (in arbitrary units) around DNA as a function of minimum distance from DNA, rmin, 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: As shown in Figure 10, folded DNA structures created more negative electrostatic potentials, V(rmin), around them than those around unfolded structures (V(rmin = 2 Å) of −21.7 for HP, −22.4 for TBA, −20.2 for unHP and −19.4 for unTBA). V(rmin) around unHP was more negative than that around unTBA regardless of rmin, reflecting the difference in net charges of the molecules (−15 for unHP and −14 for unTBA). On the other hand, near the folded TBA (rmin < 4 Å), V(rmin) values were more negative than those around folded HP, although the net charge of HP was also more negative than that of TBA (−15 for HP and −14 for TBA). V(rmin) values around HP and TBA were reversed at rmin > 4 Å, and these values approached the values around their unfolded DNA structures at 20 Å from DNA. To confirm that the strong electrostatic potential around TBA was due to its structural geometry, we calculated the average distance distribution of the number of DNA atoms from the shell surface. The lengths from the shell surface in which all DNA atoms were included were 30 Å for TBA, 40 Å for HP, 50 Å for both unTBA and unHP (Supplementary Figure S3). As expected, the length for TBA was shortest among other structures.


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)

Averaged electrostatic potential (in arbitrary units) around DNA as a function of minimum distance from DNA, rmin, 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

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

Figure 10: Averaged electrostatic potential (in arbitrary units) around DNA as a function of minimum distance from DNA, rmin, 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: As shown in Figure 10, folded DNA structures created more negative electrostatic potentials, V(rmin), around them than those around unfolded structures (V(rmin = 2 Å) of −21.7 for HP, −22.4 for TBA, −20.2 for unHP and −19.4 for unTBA). V(rmin) around unHP was more negative than that around unTBA regardless of rmin, reflecting the difference in net charges of the molecules (−15 for unHP and −14 for unTBA). On the other hand, near the folded TBA (rmin < 4 Å), V(rmin) values were more negative than those around folded HP, although the net charge of HP was also more negative than that of TBA (−15 for HP and −14 for TBA). V(rmin) values around HP and TBA were reversed at rmin > 4 Å, and these values approached the values around their unfolded DNA structures at 20 Å from DNA. To confirm that the strong electrostatic potential around TBA was due to its structural geometry, we calculated the average distance distribution of the number of DNA atoms from the shell surface. The lengths from the shell surface in which all DNA atoms were included were 30 Å for TBA, 40 Å for HP, 50 Å for both unTBA and unHP (Supplementary Figure S3). As expected, the length for TBA was shortest among other structures.

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