Biopolym. Cell. 2002; 18(3):258-261 .
Short Communications
Stabilization of Watson-Crick base pairs of DNA by protonation: quantum-chemical study
1Potyahaylo A. L., 1Hovorun D. M.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680


By means of semi-empirical quantum-chemical method AMI the protonation of Watson-Crick, base pairs at the positions that don't participate in H-binding has been found to stabilize these pairs. The greatest effect has been observed upon the protonation of Thy O2 and O4 atoms of the pair Ade:Thy with the proton transfer from Thy N3 to Ade N1 and significant changes in the pair geometrical structure. The maximal geometrical changes occur in the pair Gua:Cyt (O2) which opens, being stabilized by only one H-bond N4H...O6 (two other H-bonds are broken). The protonation of DNA bases and their Watson-Crick pairs is assumed to be a multifunctional physico-chemical mechanism, which is possibly used for both preservation of genetic information (DNA base pairs' stabilization to prevent their modification) and DNA replication (DNA-polymerase provides base pairs with canonical status that improves at the same time their ability for complementary pairing). Besides, the protonation of Cyt O2 atom in the pair Gua:Cyt is likely to be a common mechanism of action of proteins responsible for DNA untwisting.


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