Tag Archives: intermolecular hydrogen bonds
Structural and energetic properties of the four configurations of the А•Т and G•C DNA base pairs
O. O. Brovarets’
Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv;
Research and Educational Center “State Key Laboratory of Molecular and Cell Biology”, Kyiv, Ukraine;
Institute of High Technologies, Taras Shevchenko National University of Kyiv, Ukraine;
e-mail: brovarets@list.ru
Using the methods of non-empirical quantum chemistry at the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of theory it was established for the first time, that Hoogsteen, reverse Hoogsteen, Watson-Crick and reverse Watson-Crick configurations of the A·T and G·C DNA base pairs are isoelectronic and isomorphic structures with similar dynamic properties. Based on these results, non-ionisation mechanism of the Hoogsteen “breathing” of the G·C DNA base pair, namely transformation of the tautomerised (Löwdin’s) G*·C* base pair with Watson-Crick geometry into the Hoogsteen electroneutral G*·C* H base pair stabilized by the three O6H…N4, N3H…N7 and C8H…O2 H-bonds, was postulated. It is suggested that such scenario activates only in those cases, when DNA is not located in aqueous solution, but works together with proteins and cytosine protonation at the N3 atom is precluded.
Under what conditions does G•C watson-crick DNA base pair acquire all four configurations characteristic for A•T watson-crick DNA base pair?
O. O. Brovarets’
Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv;
Research and Educational Center “State Key Laboratory of Molecular and Cell Biology”, Kyiv, Ukraine;
Institute of High Technologies, Taras Shevchenko National University of Kyiv, Ukraine;
e-mail: brovarets@list.ru
At the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of theory it was established for the first time, that the Löwdin’s G*·C* DNA base pair formed by the mutagenic tautomers can acquire, as the A·T Watson-Crick DNA base pair, four biologically important configurations, namely: Watson-Crick, reverse Watson-Crick, Hoogsteen and reverse Hoogsteen. This fact demonstrates rather unexpected role of the tautomerisation of the one of the Watson-Crick DNA base pairs, in particular, via double proton transfer: exactly the G·C→G*·C* tautomerisation allows to overcome steric hindrances for the implementation of the above mentioned configurations. Geometric, electron-topological and energetic properties of the H-bonds that stabilise the studied pairs, as well as the energetic characteristics of the latters are presented.