**1. Introduction**

High-fidelity DNA replication is a central issue in molecular biology [1]. During DNA replication, spontaneous point mutations [2–4] arise with frequencies 10−9 ÷ 10−11 [5–8] in functioning of living cells.

Thus, without clear understanding of basic mechanisms of the origin of spontaneous point mutations [32–34], it is difficult to develop a management strategy of genome instability and produce physico-chemical explanations of evolution [35, 36]; to design highly efficient mutagens—analogs of the nucleotide bases with targeted action for different purposes, in particular, for antiviral and anticancer therapy [37, 38]; to essentially increase precision of DNA-based nanodevices of biomolecular electronics as information carriers [39, 40]; to create synthetic macromolecular structures able to replicate with predetermined accuracy [41] and so on.

Renaissance of the Tautomeric Hypothesis of the Spontaneous Point Mutations in DNA: New Ideas…

http://dx.doi.org/10.5772/intechopen.77366

33

Here, we aim to reveal at the microstructural level the molecular grounds of intrinsic DNA

All geometric, energetic and vibrational calculations of the considered base mispairs and transition states (TSs) of their conversion have been performed by Gaussian'09 package [42] using B3LYP [43, 44] and MP2 [45] levels of quantum-mechanical (QM) theory combined with a wide variety of basis sets followed by the intrinsic reaction coordinate (IRC) calculations in the forward and reverse directions from each ТS using Hessian-based predictor-corrector integration algorithm [46] in vacuum and in the continuum with ε = 4, which is characteristic for the active center of the DNA polymerase [47, 48]. Bader's quantum theory of Atoms in Molecules (QTAIM) was applied to analyze the electron density distribution [49]. Physico-chemical parameters have been estimated by the known formulas of physico-chemical kinetics [50].

**3.1. Classical mechanisms of DNA base tautomerization** *via* **DPT along two** 

C·CH3

participation of DNA bases and side chains of the amino acids (m-methyl group) [55].

We established from the physico-chemical point of view that the generally accepted mechanism of the DPT along intermolecular H-bonds [22–29] cannot be the source of formation of mutagenic tautomers of DNA bases in the А·T(WC) and G·C(WC) Watson-Crick (socalled Löwdin's mechanism) [51–53] and G·T(w) wobble [54] base pairs, and also in the

At this point, the А\*·T\* Löwdin's base pair is dynamically unstable and has a lifetime that is 6 orders of magnitude less than the characteristic time spent by DNA polymerase on the forced dissociation of the DNA base pairs into the bases (~10−9 s [32, 51, 52]). The short-lived G\*·C\* Löwdin's base pair escapes the DNA polymerase. The other final tautomerized complexes containing mutagenic tautomers of DNA bases are dynamically unstable: the value of the zero-point energy of the corresponding vibrational mode, in which frequency becomes imaginary at the transition state, is higher than the value of the reverse barrier (**Table 1**).

COOH and m<sup>9</sup>

G·CH3

COOH complexes by the

mutability without involvement of external agents.

**2. Computational methods**

**3. Results and discussion**

COOH, m<sup>9</sup>

m1 T·CH3

**intermolecular H-bonds in H-bonded complexes**

A·CH3

COOH, m1

Nowadays, it is reliably known that the root cause of the origin of the spontaneous point mutations is the formation in the very tight, slightly deformable base pair recognition pocket of the high-fidelity DNA polymerase in its close state of the "wrong" DNA base pairs (i.e., mismatches) able to acquire in the process of thermal fluctuations the conformation of the correct Watson-Crick DNA base pair (i.e., enzymatically competent conformation), which guarantees their incorporation into the chemical structure of the synthesized DNA double helix [4].

In the literature, two approaches are currently presented, according to physico-chemical principles of the occurrence of the mispairs leading to spontaneous point mutations in DNA. One of them is the "tautomeric hypothesis" suggested by J. Watson and F. Crick [9], which consists in the spontaneous tautomeric transition of the DNA bases from canonical to mutagenic tautomeric forms leading to the formation of the adenine·cytosine (A·C\*)/A\*·C and guanine·thymine (G\*·T)/G·T\* (here and below, mutagenic tautomers are marked with asterisk) Watson-Cricklike mispairs with correct enzymatically competent conformation [10] containing mutagenic tautomers [11–13]. Despite great advances in experimental, in particular X-ray analysis [14, 15], NMR, in particular relaxation dispersion measurements [11–13, 16–18], and theoretical [19–21] investigations, there is no unique approach to the physico-chemical mechanisms enabling DNA bases in the canonical tautomeric form to acquire rare or mutagenic tautomeric form before the dissociation of the Watson-Crick nucleobase pairs into the monomers by the replication machinery in order to produce mispairs resulting in further misincorporations and as a result the spontaneous point mutations at the DNA replication. It is generally accepted in the literature that mutagenic tautomers of the DNA bases can arise *via* the double proton transfer (DPT) along intermolecular H-bonds in the Watson-Crick [22–25] and wobble [26] base pairs, and also in the protein-DNA complexes [27]. However, some authors also consider as the source of the origin of the spontaneous transitions the formation of the ionized DNA base pairs [28].

On contrary, according to second approach, other researchers believe that spontaneous point mutations arise due to the formation of the incorrect base pairs involving only DNA bases in the main, canonical tautomeric form—so-called wobble or shifted A·C and G·T base pairs [29, 30]. However, the mechanisms of their adaptation to the enzymatically competent sizes in the very tight, slightly deformable base pair recognition pocket of the high-fidelity DNA polymerase remain unclear [30, 31].

The common feature of these approaches is the absence of the general physico-chemical theory according the nature of these mispairs causing spontaneous point mutations, and the emergence of each of them is considered as a unique phenomenon. In the literature, there are no attempts or ideas aimed at combining these approaches into a unique, internally noncontradictory conception. Nevertheless, creation of such a microstructural theory is an interdisciplinary challenge with fundamental and applied consequences.

Thus, without clear understanding of basic mechanisms of the origin of spontaneous point mutations [32–34], it is difficult to develop a management strategy of genome instability and produce physico-chemical explanations of evolution [35, 36]; to design highly efficient mutagens—analogs of the nucleotide bases with targeted action for different purposes, in particular, for antiviral and anticancer therapy [37, 38]; to essentially increase precision of DNA-based nanodevices of biomolecular electronics as information carriers [39, 40]; to create synthetic macromolecular structures able to replicate with predetermined accuracy [41] and so on.

Here, we aim to reveal at the microstructural level the molecular grounds of intrinsic DNA mutability without involvement of external agents.
