Biopolymers and cell. 2002; 18 (3): 258 - 261

Stabilization of Watson-Crick base pairs of DNA by protonation: quantum-chemical study

A. L. Potyahaylo, D. M. Hovorun

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 Me Nl 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 mul¬tifunctional 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 GuaCyt is likely to be a common mechanism of action of proteins responsible for DNA untwisting.