scholarly journals Urea Destabilizes RNA by Forming Stacking Interactions and Multiple Hydrogen Bonds with Nucleic Acid Bases

2009 ◽  
Vol 131 (49) ◽  
pp. 17759-17761 ◽  
Author(s):  
U. Deva Priyakumar ◽  
Changbong Hyeon ◽  
D. Thirumalai ◽  
Alexander D. MacKerell
Keyword(s):  
Nucleic Acid ◽  
Hydrogen Bonds ◽  
Stacking Interactions ◽  
Nucleic Acid Bases ◽  
Multiple Hydrogen Bonds

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

2019 ◽  
Vol 75 (3) ◽  
pp. 301-309
Author(s):  
Jelena M. Andrić ◽  
Ivana M. Stanković ◽  
Snežana D. Zarić
Keyword(s):  
Nucleic Acid ◽  
Hydrogen Bonds ◽  
Nucleic Acids ◽  
Metal Ions ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Metal Ion ◽  
Water Molecules ◽  
Nucleic Acid Bases ◽  
Coordinated Water

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.

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