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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

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 stabiliti...

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Autores principales: Nakano, Miki, Tateishi-Karimata, Hisae, Tanaka, Shigenori, Tama, Florence, Miyashita, Osamu, Nakano, Shu-ichi, Sugimoto, Naoki
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4666364/
https://www.ncbi.nlm.nih.gov/pubmed/26538600
http://dx.doi.org/10.1093/nar/gkv1133
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author Nakano, Miki
Tateishi-Karimata, Hisae
Tanaka, Shigenori
Tama, Florence
Miyashita, Osamu
Nakano, Shu-ichi
Sugimoto, Naoki
author_facet Nakano, Miki
Tateishi-Karimata, Hisae
Tanaka, Shigenori
Tama, Florence
Miyashita, Osamu
Nakano, Shu-ichi
Sugimoto, Naoki
author_sort Nakano, Miki
collection PubMed
description 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. To understand how cosolutes, such as ethylene glycol, affect the thermal stability of DNA structures, we investigated the thermodynamic properties of water molecules around a hairpin duplex and a G-quadruplex using grid inhomogeneous solvation theory (GIST) with or without cosolutes. 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. Our findings suggest that the thermal stability of the hydration shell around DNAs is one factor that affects the thermal stabilities of DNA structures under the crowding conditions.
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spelling pubmed-46663642015-12-02 Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory Nakano, Miki Tateishi-Karimata, Hisae Tanaka, Shigenori Tama, Florence Miyashita, Osamu Nakano, Shu-ichi Sugimoto, Naoki Nucleic Acids Res Chemical Biology and Nucleic Acid Chemistry 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. To understand how cosolutes, such as ethylene glycol, affect the thermal stability of DNA structures, we investigated the thermodynamic properties of water molecules around a hairpin duplex and a G-quadruplex using grid inhomogeneous solvation theory (GIST) with or without cosolutes. 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. Our findings suggest that the thermal stability of the hydration shell around DNAs is one factor that affects the thermal stabilities of DNA structures under the crowding conditions. Oxford University Press 2015-12-02 2015-11-03 /pmc/articles/PMC4666364/ /pubmed/26538600 http://dx.doi.org/10.1093/nar/gkv1133 Text en © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Chemical Biology and Nucleic Acid Chemistry
Nakano, Miki
Tateishi-Karimata, Hisae
Tanaka, Shigenori
Tama, Florence
Miyashita, Osamu
Nakano, Shu-ichi
Sugimoto, Naoki
Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory
title Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory
title_full Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory
title_fullStr Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory
title_full_unstemmed Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory
title_short Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory
title_sort thermodynamic properties of water molecules in the presence of cosolute depend on dna structure: a study using grid inhomogeneous solvation theory
topic Chemical Biology and Nucleic Acid Chemistry
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4666364/
https://www.ncbi.nlm.nih.gov/pubmed/26538600
http://dx.doi.org/10.1093/nar/gkv1133
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