Determining the main mechanisms of transformation of biologically important base
pairs is a globally important task for establishing the mechanism and nature of point
mutations. The primary cause of spontaneous point mutations is the formation of irregular
pairs of DNA bases in the recognition pocket of DNA polymerase. For a long time it
was thought that mutations in the human body occur only due to external factors such as
UV-radiation, ionization, radioactive influences and so on. But a study of the structure
of DNA nature has shown that self-transformations occur inside the molecule due to the
transfer of a proton through hydrogen bonds. One of the theories of mutations is the
tautomeric theory proposed in 1963 by Lowdin. His assumption stemmed from the
ability of nucleotide bases to tautomerize, namely the transition of base pairs to the
protonated state G*·C* (an asterisk indicates a protonated base. A pair of protonated
bases is called Lowdin base pairs). According to his theory, the protonated base leads to
the formation of a minor pair of bases during replication. This hypothesis gave impact to
the study of the existence of minor tautomeric forms of base pairs. To date, a large number
of non-Watson-Crick bases pairing mechanisms by empirical methods have been shown.
It is currently believed that the mutagenic effect is characteristic only of those base
pairs whose lifetime corresponds to the time interval between replications, which is about
10-10s. It is determined that the A*·T* base pairs dissociate before the next replication
process begins , and the G·C base pairs are able to transform into Lowdin conformation
and lead to minor base pairs during the next replication cycle. It is very difficult to establish the fact of proton transfer in one base pair, which is
a part of nucleic acid, by empirical methods. Therefore, non-empirical (ab initio)
quantum-chemical calculation methods are widely used to model the deep mechanisms
of tautomeric transitions. This dissertation aims to investigate the mechanisms of tautomeric and
conformational variability of canonical G·C base pairs using quantum chemical
calculations and to establish new tautomeric structures of G·C base pair.
More than 50 mechanisms of tautomeric and conformational transitions of base
pairs were modeled with the quantum-chemical approaches, transient states of their
mutual transformation were revealed, and more than 80 new tautomeric and8
conformational variations of the G·C base pair were established. All the considered
mechanisms should be considered as processes occurring in the hydrophobic pocket of
the polymerase. Geometries of all investigated DNA base pairs and transition states were optimized
using the Gaussian’09. With the help of quantum chemical calculations, various forms of G·C base pairs
and ways of their transformation were investigated. The objects of the study were
optimized using the density functional theory under normal conditions (ε=1,
T=298.15 K), at the level of the theory B3LYP/6-311++G (d,p). Correlation effects were
taken into account by calculating energies at one point, at the level of the theory MP2/6-
311++G(2df,pd). The free Gibbs energy of the reaction G was calculated at the level of the theory at
which the optimization took place. For all studied structures, at the level of B3LYP
theory, a correction factor of 0.9668 was applied, and at the level of MP2 - 0.9531.
Transition states of tautomeric transformations of G·C base pairs were identified
by the method of synchronous quasi-Newtonian directional transfer STQN. The correspondence of stationary points to the
transition state on the potential energy hypersurface (PES) was established in the
presence of imaginary frequencies (νi) in their vibrational spectra.
The path of the tautomerization reaction was determined by calculating the system
changes from the transition state in the forward and reverse directions along the internal
reaction coordinate (IRC) according to the HPC integration algorithm (Hessian-based
predictor-corrector integration algorithm). The interaction energy (Eint) in base pairs was
defined as the difference between the base dimer energy and the energies calculated
separately for each base. The quantum theory of Bader's "Atoms in Molecules"
(QTAIM) was used to analyze the electron density distribution, using the AIMAll
package taking into account the wave functions obtained at the level of theory
MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p). The standard theory of transition
states was used to estimate the activation barriers and reverse barriers of tautomerization
reactions. All new tautomeric transformations
(approaching or shifting bases in pairs) are due to the intrinsic properties of G·C
nucleotide base pairs, all conformational rearrangements involve the rotation of base pairs
relative to each other without proton transfer.
