Original Research ARTICLE
Surprising conformers of the biologically important A·T DNA base pairs: QM/QTAIM proofs
- 1Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics (NAN Ukraine), Ukraine
For the first time novel high-energy conformers – А·Т(wWC) (5.36), А·Т(wrWC) (5.97), А·Т(wН) (5.78) and А·Т(wrН) (∆G=5.82 kcal∙mol-1) were revealed for each of the four biologically important А·Т(WC) DNA base pairs – Watson-Crick А·Т(WC), reverse Watson-Crick А·Т(rWC), Hoogsteen А·Т(Н) and reverse Hoogsteen А·Т(rН) at the MP2/aug-cc-pVDZ//B3LYP/6-311++G(d,p) level of quantum-mechanical theory in the continuum with ε=4 under normal conditions. Each of these conformers possesses substantially non-planar wobble (w) structure and is stabilized by the participation of the two anti-parallel N6H/N6H´…O4/O2 and N3H…N6 H-bonds, involving the pyramidalized amino group of the A DNA base as an acceptor and a donor of the H-bonding. The transition states – TSА·Т(WC)↔А·Т(wWC), TSА·Т(rWC)↔А·Т(wrWC), TSА·Т(Н)↔А·Т(wН) and TSА·Т(rН)↔А·Т(wrН), controlling the dipole-active transformations of the conformers from the main plane-symmetric state into the high-energy, significantly non-planar state and vice versa, were localized. They also possess wobble structures similarly to the high-energy conformers and are stabilized by the participation of the N6H/N6H´…O4/O2 and N3H…N6 H-bonds. Discovered conformers of the А·Т DNA base pairs are dynamically stable short-lived structures (lifetime τ = (1.4-3.9) ps). Their possible biological significance and future perspectives have been briefly discussed.
Keywords: А·Т DNA base pair, Watson-Crick, reverse Watson-Crick, Hoogsteen, reverse Hoogsteen, Wobble structure, DNA breathing, DNA pre-melting, Conformational transformation, transition state, quantum-chemical calculations
Received: 25 Nov 2017;
Accepted: 11 Jan 2018.
Edited by:Freddie Salsbury, Wake Forest University, United States
Reviewed by:Sonia Melandri, Università di Bologna, Italy
Mauricio A. Palafox, Complutense University of Madrid, Spain
Copyright: © 2018 Brovarets and Hovorun. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Prof. Dmytro Hovorun, Institute of Molecular Biology and Genetics (NAN Ukraine), Department of Molecular and Quantum Biophysics, Kiev, Ukraine, email@example.com