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The physico-chemical “anatomy” of the tautomerization through the DPT of the biologically important pairs of hypoxanthine with DNA bases: QM and QTAIM perspectives

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Abstract

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.

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Acknowledgments

This work was partly supported by the State Fund for Fundamental Research of Ukraine within the Ukrainian-Russian (project № F40.4/039) and Ukrainian-Slovenian research bilateral projects for 2011-2012 years. O.O.B. was supported by the Grant of the President of Ukraine to support scientific research of young scientists for 2012 year from the State Fund for Fundamental Research of Ukraine (project № GP/F44/086) and by the Grant of the President of Ukraine for talented youth for 2012 year from the Ministry of Education and Science, Youth and Sports of Ukraine. Authors thank Bogolyubov Institute for Theoretical Physics of the National Academy of Sciences of Ukraine for providing calculation resources and software. This work was performed using computational facilities of joint computer cluster of SSI “Institute for Single Crystals” and Institute for Scintillation Materials of National Academy of Sciences of Ukraine incorporated into Ukrainian National Grid.

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  1. Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotnoho Str, 03680, Kyiv, Ukraine

    Ol’ha O. Brovarets’, Roman O. Zhurakivsky & Dmytro M. Hovorun

  2. Research and Educational Center “State Key Laboratory of Molecular and Cell Biology”, 150 Zabolotnoho Str, 03680, Kyiv, Ukraine

    Ol’ha O. Brovarets’, Roman O. Zhurakivsky & Dmytro M. Hovorun

  3. Department of Molecular Biology, Biotechnology and Biophysics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, 2 Hlushkova Ave, 03127, Kyiv, Ukraine

    Ol’ha O. Brovarets’ & Dmytro M. Hovorun

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Brovarets’, O.O., Zhurakivsky, R.O. & Hovorun, D.M. The physico-chemical “anatomy” of the tautomerization through the DPT of the biologically important pairs of hypoxanthine with DNA bases: QM and QTAIM perspectives. J Mol Model 19, 4119–4137 (2013). https://doi.org/10.1007/s00894-012-1720-9

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