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Brovarets O.O.,NASU Institute of Molecular Biology and Genetics | Brovarets O.O.,Research and Educational Center State Key Laboratory of Molecular and Cell Biology | Brovarets O.O.,Taras Shevchenko National University
Ukrain'skyi Biokhimichnyi Zhurnal | Year: 2013

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. Source


Brovarets O.O.,NASU Institute of Molecular Biology and Genetics | Brovarets O.O.,Research and Educational Center State Key Laboratory of Molecular and Cell Biology | Brovarets O.O.,Taras Shevchenko National University
Ukrain'skyi Biokhimichnyi Zhurnal | Year: 2013

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. Source


Brovarets O.O.,NASU Institute of Molecular Biology and Genetics | Brovarets O.O.,Research and Educational Center State Key Laboratory of Molecular and Cell Biology | Brovarets O.O.,Taras Shevchenko National University | Zhurakivsky R.O.,NASU Institute of Molecular Biology and Genetics | And 4 more authors.
Physical Chemistry Chemical Physics | Year: 2014

We have scrupulously explored the tautomerisation mechanism via the double proton transfer of the A*·Asyn Topal-Fresco base mispair (Cs symmetry), formed by the imino and amino tautomers of the adenine DNA base in the anti- and syn-conformations, respectively, bridging quantum-mechanical calculations with Bader's quantum theory of atoms in molecules. It was found that the A*·Asyn ↔ A·A*syn tautomerisation is the asynchronous concerted process. It was established that the A*·Asyn DNA mismatch is stabilized by the N6H⋯N6 (6.35) and N1H⋯N7 (6.17) hydrogen (H) bonds, whereas the A·A*syn base mispair (Cs) by the N6H⋯N6 (8.82) and N7H⋯N1 (9.78) H-bonds and the C8H⋯HC2 HH-bond (0.30 kcal mol-1). Using the sweeps of the energies of the intermolecular H-bonds, it was observed that the N6H⋯N6 and N1H⋯N7/N7H⋯N1 H-bonds are anti-cooperative and mutually weaken each other in the A*·Asyn and A·A*syn mispairs. It was revealed that the A·A*syn DNA mismatch is a dynamically unstable structure with a short lifetime of 1.12 × 10-13 s and any of its 6 low-frequency intermolecular vibrations can develop during this period of time. This observation makes it impossible to change the tautomeric status of the A bases upon the dissociation of the A*·Asyn base mispair into the monomers during DNA replication. © 2014 the Owner Societies. Source


Brovarets O.O.,NASU Institute of Molecular Biology and Genetics | Brovarets O.O.,Research and Educational Center State Key Laboratory of Molecular and Cell Biology | Brovarets O.O.,Taras Shevchenko National University | Zhurakivsky R.O.,NASU Institute of Molecular Biology and Genetics | And 4 more authors.
Journal of Molecular Modeling | Year: 2013

The biologically important tautomerization of the Hyp·Cyt, Hyp·Thy and Hyp·Hyp base pairs to the Hyp*·Cyt* , Hyp·Thy*and Hyp*·Hyp*base pairs, respectively, by the double proton transfer (DPT) was comprehensively studied in vacuo and in the continuum with a low dielectric constant (ε = 4) corresponding to hydrophobic interfaces of protein-nucleic acid interactions by combining theoretical investigations at the B3LYP/6-311++G(d,p) level of QM theory with QTAIM topological analysis. Based on the sweeps of the energetic, electron-topological, geometric and polar parameters, which describe the course of the tautomerization along the intrinsic reaction coordinate (IRC), it was proved that the tautomerization through the DPT is concerted and asynchronous process for the Hyp·Cyt and Hyp*·Thy base pairs, while concerted and synchronous for the Hyp·Hyp homodimer. The continuum with ε = 4 does not affect qualitatively the course of the tautomerization reaction for all studied complexes. The nine key points along the IRC of the Hyp·Cyt↔Hyp*·Cyt*and Hyp*·Thy↔ Hyp·Thy*tautomerizations and the six key points of the Hyp·Hyp↔Hyp*·Hyp*tautomerization have been identified and fully characterized. These key points could be considered as electron-topological "fingerprints" of concerted asynchronous (for Hyp·Cyt and Hyp*·Thy) or synchronous (for Hyp·Hyp) tautomerization process via the DPT. It was found, that in the Hyp*·Cyt*, Hyp·Thy*, Hyp·Hyp and Hyp*·Hyp*base pairs all H-bonds are significantly cooperative and mutually reinforce each other, while the C2H.O2 H-bond in the Hyp·Cyt base pair and the O6H.O4 H-bond in the Hyp*·Thy base pair behave anti-cooperatively, i.e., they become weakened, while two others become strengthened. © 2012 Springer-Verlag Berlin Heidelberg. Source


Brovarets O.O.,NASU Institute of Molecular Biology and Genetics | Brovarets O.O.,Research and Educational Center State Key Laboratory of Molecular and Cell Biology | Brovarets O.O.,Taras Shevchenko National University | Zhurakivsky R.O.,NASU Institute of Molecular Biology and Genetics | And 4 more authors.
Molecular Physics | Year: 2014

We provide a pathway for the tautomerisation of the biologically important hypoxanthine·adenine (Hyp·Ade) nucleobase pair (Cs) formed by the keto tautomer of the Hyp and the amino tautomer of the Ade into the Hyp*·Ade* base pair (Cs) formed by the enol tautomer of the Hyp and the imino tautomer of the Ade by applying quantum-mechanical calculations and Bader's Quantum Theory of Atoms in Molecules analysis. It was found out that the dipole active Hyp·Ade↔Hyp*·Ade* tautomerisation occurs via the asynchronous concerted double proton transfer (DPT) through the TSHyp·Ade↔Hyp*·Ade* (Cs). Based on the sweeps of the energies of the intermolecular H-bonds along the intrinsic reaction coordinate, it was established that the N6H···O6 H-bond (5.40) is cooperative with the N1H···N1 H-bond (6.99) in the Hyp·Ade base pair, as well as the O6H···N6 H-bond (11.50) is cooperative with the N1H···N1 H-bond (7.28 kcal·mol-1) in the Hyp*·Ade* base pair, mutually strengthening each other. The Hyp*·Ade* base pair possesses an extremely short lifetime 2.68·10-14 s, which is predetermined by the negative value of the Gibbs free energy of the reverse barrier of its tautomerisation, and all of the six low-frequency intermolecular vibrations cannot develop during this period of time. Consequently, the Hyp·Ade→Hyp*·Ade* DPT tautomerisation cannot serve as a source of the rare tautomers of the bases. © 2014 Taylor & Francis. Source

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