**3.5. Physico-chemical scenarios of the origin of the replication and incorporation point errors in DNA**

each case mostly, one pathway is most probable at the origin of the spontaneous point muta-

**Table 2.** Energetic and kinetic characteristics of the tautomeric transformations of the classical Watson-Crick or wobble DNA base pairs, which are involved into the processes of the spontaneous point mutagenesis, *via* the DPT accompanied

The time necessary to reach 99.9% of the equilibrium concentration between the reactant and the product of the

**Tautomeric conversion ∆G ∆E ∆∆GTS ∆∆ETS ∆∆G ∆∆E τ99.9%**

A·Т(WC)↔A\*·Т↑(w) [68] 9.90 9.59 16.72 16.02 6.82 6.43 1.1 × 10−7 5.4 × 10−8 A·T(WC)↔A·T\*O2↑(w) [68] 10.91 11.25 16.72 16.02 5.81 4.77 2.0 × 10−8 9.9 × 10−9 A·Т(WC)↔A·Т\*↓(w) [68] 13.08 14.84 20.28 20.41 7.20 5.57 2.1 × 10−7 2.5 × 10−10 G·C(WC)↔G·C\*↑(w) [68] 13.35 14.10 30.47 30.74 17.12 16.64 3.95 1.6 × 10−10 G·C(WC)↔G\*·C↓(w) [68] 15.10 16.49 31.08 31.53 15.98 15.04 0.58 1.3 × 10−11 G·C(WC)↔G·C\*↓(w) [68] 15.08 15.96 30.88 31.41 15.80 15.45 0.42 8.8 × 10−12 G·C(WC)↔G\*·C↑(w) [68] 14.85 17.22 24.87 25.64 10.02 8.42 2.5 × 10−5 8.4 × 10−12

A·C(w)↔A·C\*(WC) [69, 70] 4.87 6.77 19.98 18.85 24.84 25.62 4.9 × 10<sup>2</sup> — G·T(w)↔G\*·T(WC) [69, 71] −1.69 −2.46 17.04 16.37 18.73 18.83 8.8 — A·A(w)↔A\*·A(WC) [72] 4.18 1.64 26.89 23.59 22.71 21.94 4.4 × 104 — G·G(w)↔G\*·G(WC) [72] −4.96 −6.75 26.81 26.08 31.77 32.83 5.0 × 107 — A·G(WC)↔A·G\*↓(w) [73] 3.76 6.19 17.01 17.07 13.25 10.88 5.3 × 10−3 — A·G(WC)↔A\*·G↑(w) [73] 14.29 14.09 25.29 24.39 11.00 10.30 1.2 × 10−4 — C·T(WC)↔C\*·T↑(w) [73] 0.56 0.55 17.05 17.36 16.48 16.81 6.8 × 10−7 — C·T(WC)↔C·T\*↓(w) [73] 12.07 14.57 26.64 25.32 14.57 10.75 5.4 × 10−2 — T·T(w)↔T·T\*(WC) [74] 8.98 8.64 31.06 31.90 22.09 23.26 1.6 × 104 — C·C(w)↔C·C\*(WC) [74] −8.90 −10.73 25.38 24.32 34.28 35.05 4.4 × 106 —

**MP2/aug-cc-pVDZ//B3LYP/6–311++G(d,p)**

38 Mitochondrial DNA - New Insights

**MP2/cc-pVQZ//B3LYP/6–311++G(d,p)**

**<sup>a</sup> Nb**

Obtained results are crucial for understanding the microstructural mechanisms of spontaneous transitions and transversions, since they allow us to explain how incorrect purine·pyrimidine, purine·purine and pyrimidine·pyrimidine wobble pairs adapt to the enzymatically competent sizes in the recognition pocket of the high-fidelity DNA polymerase. In particular, established A·C(w) →A·C\*(WC) [70] and G·T(w) → G\*·T(WC) [71] transformations *via* the sequential PT allow us to interpret the X-ray [14, 15] and molecular dynamics simulations data [19] according the acquisition by the wobble A·C(w)/G·T(w) mispairs of the Watson-Crick geometry by their transformation to the A·C\*(WC)/G\*·T(WC) Watson-Crick-like base mispairs by the participation of the C\* and G\* mutagenic tautomers in the recognition pocket of the high-fidelity DNA polymerase. Moreover, we theoretically predicted the G·T(w) → G\*·T(WC) transformation for the wobble G·T(w) base mispair, which was confirmed by an NMR experiment of a DNA duplex [16–18].

tions (**Figures 2** and **3**, **Table 2**).

Populations of the wobble mispairs containing mutagenic tautomers.

by the substantial changes of their geometry in the continuum with ε = 1.

Note: for designations see **Table 1**.

tautomerization reaction, s.

a

b

In the framework of such qualitatively new model conceptions, we were able to shed light on the microstructural mechanisms of the occurrence of point mutations—replication and incorporation point errors.

Thus, the spontaneous mutagenic tautomerization of the Watson-Crick pairs of nucleotide bases into the wobble base mispairs, which includes the A\*, T\*, G\* and C\* mutagenic tautomers, has been established to be the source of the generation of the mutagenic tautomers of the DNA bases arising at the separation of DNA strands. At this juncture, *replication errors* would arise in the following way (as an example, we would consider the case, when A\* belongs to the template strand of DNA): A\* + C → A\*·C → A·C\*, A\* + A → A\*·A → A\*·Asyn, A\* + G → A \*·G → A·G → A\*·G\* → A\*·G\*syn. Similar schemes of structural transformations, which occur directly in the recognition pocket of the high-fidelity DNA polymerase, would take place also for three other cases, when G\*, T\* and C\* belong to the template strand of DNA.

*Incorporation errors* would occur according to the following scenario: in the recognition pocket of the high-fidelity DNA polymerase, it would form the appropriate wobble base mispair

Finally, it becomes clear why spontaneous point errors occur quite rarely. This, in particular, is due to the fact that the mechanisms of their occurrence are kinetically controllable, with the time τ99.9%, which is necessary to reach 99.9% of the equilibrium concentration of the reactant and product, significantly greater than the time that the DNA polymerase spends incorporat-

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

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

41

Based on our own theoretical data, which have been successfully confirmed by experimental data [16–18], one can make an assumption, why the DNA-repair enzymes, "sharpened" precisely for the wobble base mispairs, do not provide 100% accuracy. The reason consists in the ability of this pair to transform into a pair with Watson-Crick geometry, which, figuratively speaking, is a "hiding place" from the enzyme, because it is not recognized by it, thus restrict-

So, obtained data, in principle, enable to understand the mechanism of elimination from the genome of mutagenic tautomers, whose lifetime exceeds by orders of magnitude the time of

Again, established ability of the wobble pair to be formed from the Watson-Crick-like pair involving mutagenic tautomer of the DNA bases enables DNA-repair complex to reveal and

We developed original methodology tracking the evolution of all physico-chemical parameters along the entire reaction pathways: in particular, the electronic energy, the first derivative of the electronic energy by the IRC-dE/dIRC, the dipole moment of the base pair, the distances and the angle of the intermolecular specific contacts (H-bonds or van der Waals contacts), electron density, the Laplacian of the electron density, ellipticity and the energy at the (3,-1) bond critical points of the intrapair specific contacts, the NBO charges of the hydrogen atoms involved in the tautomerization, the glycosidic angles and the distance between the glycosidic hydrogens. This works not only in the stationary structures such as reagent, product and transition state of the tautomerizations *via* the DPT and w↔WC tautomeric reactions *via* the

Additionally, for the first time, we have introduced the conception of the key points (KPs) based on the electron-topological characteristics of the intermolecular bonds, namely the value of the electron density and its Laplacian at the corresponding (3,-1) bond critical points. This approach allows us to comprehensively describe the mechanism of the tautomerization process. Thus, depending on the symmetry and nature of the system, maximum number of KPs could reach 9 and minimal—5, when KPs are degenerated (see **Figures 5** and **6** for illus-

Arrangement of the extrema of the derivative of the energy by IRC—dE/dIRC—coincides with the second and penultimate KPs, where mutual transformations of the H-bond into a covalent bond and *vice versa* occur. These data allow us to separate the pathway of the tautomerization reaction into the zones of reagent, transition state and product of the reaction. In general, these key points could be considered as "fingerprints" of the tautomerization process *via* DPT or PT.

eliminate them from the genome during several cycles of DNA replication.

**3.6. Profiles of the physico-chemical parameters along the IRC of tautomerizations** 

ing one nucleotide into the DNA double helix that is synthesized (~8.3 × 10−4 s [67]).

ing the ultimate accuracy of the repair process.

tration on the example of the 2AP·T(WC)↔2AP·T\*(w)).

cellular DNA replication.

*via* **DPT and PT**

PT [51–74, 78].

**Figure 4.** Structures corresponding to the stationary points on the reaction pathways of the (a) A\*·A(WC)↔A\*·Asyn(TF), (b) G·A(WC)↔G·Asyn, (c) A\*·G\*(WC)↔A\*·G\*syn and (d) G·G\*(WC)↔G·G\*syn *anti*↔*syn* conversions through the large-scale adjustments of the bases relative to each other, obtained at the B3LYP/6–311++G(d,p) level of theory, ε = 1 [77].

tautomerizing into the pair with Watson-Crick architecture of the binding. For the case, when A belongs to the template strand of DNA: A + C → A·C → A·C\*, A +A → A·A → A\*·A → A\*·Asyn, A + G → A·G → A\*·G\* → A\*·G\*syn.

Both processes have two common features—they involve the same pairs, which play the role of intermediates on the path of formation of enzymatically competent conformations of some incorrect pairs, as well as the same set of terminal incorrect pairs, able to acquire the enzymatically competent conformations during the process of thermal fluctuations.

Finally, it becomes clear why spontaneous point errors occur quite rarely. This, in particular, is due to the fact that the mechanisms of their occurrence are kinetically controllable, with the time τ99.9%, which is necessary to reach 99.9% of the equilibrium concentration of the reactant and product, significantly greater than the time that the DNA polymerase spends incorporating one nucleotide into the DNA double helix that is synthesized (~8.3 × 10−4 s [67]).

Based on our own theoretical data, which have been successfully confirmed by experimental data [16–18], one can make an assumption, why the DNA-repair enzymes, "sharpened" precisely for the wobble base mispairs, do not provide 100% accuracy. The reason consists in the ability of this pair to transform into a pair with Watson-Crick geometry, which, figuratively speaking, is a "hiding place" from the enzyme, because it is not recognized by it, thus restricting the ultimate accuracy of the repair process.

So, obtained data, in principle, enable to understand the mechanism of elimination from the genome of mutagenic tautomers, whose lifetime exceeds by orders of magnitude the time of cellular DNA replication.

Again, established ability of the wobble pair to be formed from the Watson-Crick-like pair involving mutagenic tautomer of the DNA bases enables DNA-repair complex to reveal and eliminate them from the genome during several cycles of DNA replication.
