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Binding of metal ions and water molecules to nucleic acid bases: The influence of water molecule coordination to a metal ion on water–nucleic acid base hydrogen bonds

Authorized Users Only
2019
Authors
Andrić, Jelena M.
Stanković, Ivana
Zarić, Snežana D.
Article (Published version)
Metadata
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Abstract
The interactions of nucleic acid bases with non-coordinated and coordinated water molecules were studied by analyzing data in the Protein Data Bank (PDB) and by quantum chemical calculations. The analysis of the data in the crystal structures from the PDB indicates that hydrogen bonds involving oxygen or nitrogen atoms of nucleic acid bases and water molecules are shorter when water is bonded to a metal ion. These results are in agreement with the quantum chemical calculations on geometries and interaction energies of hydrogen bonds; the calculations on model systems show that hydrogen bonds of nucleic acid bases with water bonded to a metal ion are stronger than hydrogen bonds with non-coordinated water. These calculated values are similar to the strength of hydrogen bonds between nucleic acid bases. The results presented in this paper may be relevant to understand the role of water molecules and metal ions in the process of replication and stabilization of nucleic acids and also to u...nderstand the possible toxicity of metal ion interactions with nucleic acids.

Keywords:
Coordinated water / Crystal structures / Hydrogen bonds / Metal ion / Nucleic acid bases
Source:
Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials, 2019, 75, 301-309
Publisher:
  • International Union of Crystallography
Funding / projects:
  • Noncovalent interactions of pi-systems and their role in molecular recognition (RS-172065)
Note:
  • Supplementary information: https://cer.ihtm.bg.ac.rs/handle/123456789/4863
Related info:
  • Referenced by
    https://cer.ihtm.bg.ac.rs/handle/123456789/4863

DOI: 10.1107/S2052520619001999

ISSN: 2052-5206

WoS: 000470735800003

Scopus: 2-s2.0-85066938589
[ Google Scholar ]
2
URI
http://cherry.chem.bg.ac.rs/handle/123456789/3675
https://cer.ihtm.bg.ac.rs/handle/123456789/3521
Collections
  • Radovi istraživača / Researchers' publications
Institution/Community
IHTM
TY  - JOUR
AU  - Andrić, Jelena M.
AU  - Stanković, Ivana
AU  - Zarić, Snežana D.
PY  - 2019
UR  - http://cherry.chem.bg.ac.rs/handle/123456789/3675
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/3521
AB  - The interactions of nucleic acid bases with non-coordinated and coordinated water molecules were studied by analyzing data in the Protein Data Bank (PDB) and by quantum chemical calculations. The analysis of the data in the crystal structures from the PDB indicates that hydrogen bonds involving oxygen or nitrogen atoms of nucleic acid bases and water molecules are shorter when water is bonded to a metal ion. These results are in agreement with the quantum chemical calculations on geometries and interaction energies of hydrogen bonds; the calculations on model systems show that hydrogen bonds of nucleic acid bases with water bonded to a metal ion are stronger than hydrogen bonds with non-coordinated water. These calculated values are similar to the strength of hydrogen bonds between nucleic acid bases. The results presented in this paper may be relevant to understand the role of water molecules and metal ions in the process of replication and stabilization of nucleic acids and also to understand the possible toxicity of metal ion interactions with nucleic acids.
PB  - International Union of Crystallography
T2  - Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials
T1  - Binding of metal ions and water molecules to nucleic acid bases: The influence of water molecule coordination to a metal ion on water–nucleic acid base hydrogen bonds
VL  - 75
SP  - 301
EP  - 309
DO  - 10.1107/S2052520619001999
ER  - 
@article{
author = "Andrić, Jelena M. and Stanković, Ivana and Zarić, Snežana D.",
year = "2019",
abstract = "The interactions of nucleic acid bases with non-coordinated and coordinated water molecules were studied by analyzing data in the Protein Data Bank (PDB) and by quantum chemical calculations. The analysis of the data in the crystal structures from the PDB indicates that hydrogen bonds involving oxygen or nitrogen atoms of nucleic acid bases and water molecules are shorter when water is bonded to a metal ion. These results are in agreement with the quantum chemical calculations on geometries and interaction energies of hydrogen bonds; the calculations on model systems show that hydrogen bonds of nucleic acid bases with water bonded to a metal ion are stronger than hydrogen bonds with non-coordinated water. These calculated values are similar to the strength of hydrogen bonds between nucleic acid bases. The results presented in this paper may be relevant to understand the role of water molecules and metal ions in the process of replication and stabilization of nucleic acids and also to understand the possible toxicity of metal ion interactions with nucleic acids.",
publisher = "International Union of Crystallography",
journal = "Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials",
title = "Binding of metal ions and water molecules to nucleic acid bases: The influence of water molecule coordination to a metal ion on water–nucleic acid base hydrogen bonds",
volume = "75",
pages = "301-309",
doi = "10.1107/S2052520619001999"
}
Andrić, J. M., Stanković, I.,& Zarić, S. D.. (2019). Binding of metal ions and water molecules to nucleic acid bases: The influence of water molecule coordination to a metal ion on water–nucleic acid base hydrogen bonds. in Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials
International Union of Crystallography., 75, 301-309.
https://doi.org/10.1107/S2052520619001999
Andrić JM, Stanković I, Zarić SD. Binding of metal ions and water molecules to nucleic acid bases: The influence of water molecule coordination to a metal ion on water–nucleic acid base hydrogen bonds. in Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials. 2019;75:301-309.
doi:10.1107/S2052520619001999 .
Andrić, Jelena M., Stanković, Ivana, Zarić, Snežana D., "Binding of metal ions and water molecules to nucleic acid bases: The influence of water molecule coordination to a metal ion on water–nucleic acid base hydrogen bonds" in Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials, 75 (2019):301-309,
https://doi.org/10.1107/S2052520619001999 . .

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