**3.1. Classical mechanisms of DNA base tautomerization** *via* **DPT along two intermolecular H-bonds in H-bonded complexes**

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 m1 T·CH3 COOH, m<sup>9</sup> A·CH3 COOH, m1 C·CH3 COOH and m<sup>9</sup> G·CH3 COOH complexes by the participation of DNA bases and side chains of the amino acids (m-methyl group) [55].

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**).


It was established that the A·G↔A\*·G\* [56], A·C\*↔A\*·C [57], G\*·T↔G·T\* [58], C·T↔C\*·T\* [59], G·G\*syn↔G\*·G\*syn [60], A\*·Asyn↔A·A\*syn [61] and A\*·G\*syn↔A·G\*syn [62] tautomerization processes occur without changing the tautomeric status of the initial DNA base pairs, since the terminal, tautomerized base pairs are dynamically unstable: low-frequency intermolecular vibrations cannot develop during their lifetime (**Figure 1**, **Table 1**). Hence, these transforma-

**Figure 1.** Geometrical structures of the three stationary structures (reagent, transition state and product) describing the progression of the tautomerization *via* DPT along intermolecular H-bonds in some mispairs (B3LYP/6–311++G(d,p) level

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

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

35

During the tautomerization of the dynamically stable short Т·Т\* [63] and С·С\* [64] mispairs, as well as long А·А\* [65] and G·G\* [66] mispairs, mutagenic tautomers are distributed among the monomers with equal probability. This is important for understanding the consolidation of point mutations in subsequent rounds of DNA replication (**Figure 1**, **Table 1**). Short-lived, low-populated А\*·С and G·T\* mispairs are "providers" of the long-lived enzymatically competent А·С\* [57] and G\*·T base pairs [58], respectively, at the origin of the replication errors in DNA. Moreover, comparisons between calculated distances of intermolecular H-bonds with data from X-ray experiments [14, 15] show that incorrect А·С and G·T base pairs with Watson-Crick geometry occur in the А·С\* and G\*·T tautomeric forms in the active center of

Transition from vacuum to continuum with ε = 4, characteristics for the hydrophobic interfaces of the protein-DNA complexes, does not significantly influence the course of these tautomerization reactions and does not change the character of the obtained conclusions and generalizations.

Obtained data evidence that tautomeric hypothesis faces significant obstacles that could not be overcome without going beyond the classical framework that mutagenic tautomers of nucleotide bases are generated in the complexes by DPT protons along neighboring intermolecular H-bonds.

tions do not generate mutagenic tautomers.

of theory, ε = 1).

the high-fidelity DNA polymerase in its closed state.

a The Gibbs free energy of the product relatively the reactant of the tautomerization reaction (T = 298.15 K).

b The electronic energy of the product relatively the reactant of the tautomerization reaction.

c The Gibbs free energy barrier for the forward reaction of tautomerization.

<sup>d</sup>The electronic energy barrier for the forward reaction of tautomerization.

e The Gibbs free energy barrier for the reverse reaction of tautomerization.

f The electronic energy barrier for the reverse reaction of tautomerization.

g The lifetime of the product of the tautomerization reaction.

**Table 1.** Energetic (kcal·mol−1) and kinetic (in s) characteristics of the tautomeric transformations of the canonical Watson-Crick, wobble, model protein-DNA complexes, incorrect long, short and Watson-Crick-like mispairs of nucleotide bases *via* the DPT along the neighboring intermolecular H-bonds in vacuum.

#### **3.2. Can mutagenic tautomers of the DNA bases be formed** *via* **the DPT in Watson-Crick-like mispairs?**

Further, we investigated the physico-chemical mechanisms of the DNA bases tautomerization through the DPT along intermolecular H-bonds of incorrect DNA base pairs.

Renaissance of the Tautomeric Hypothesis of the Spontaneous Point Mutations in DNA: New Ideas… http://dx.doi.org/10.5772/intechopen.77366 35

**Figure 1.** Geometrical structures of the three stationary structures (reagent, transition state and product) describing the progression of the tautomerization *via* DPT along intermolecular H-bonds in some mispairs (B3LYP/6–311++G(d,p) level of theory, ε = 1).

It was established that the A·G↔A\*·G\* [56], A·C\*↔A\*·C [57], G\*·T↔G·T\* [58], C·T↔C\*·T\* [59], G·G\*syn↔G\*·G\*syn [60], A\*·Asyn↔A·A\*syn [61] and A\*·G\*syn↔A·G\*syn [62] tautomerization processes occur without changing the tautomeric status of the initial DNA base pairs, since the terminal, tautomerized base pairs are dynamically unstable: low-frequency intermolecular vibrations cannot develop during their lifetime (**Figure 1**, **Table 1**). Hence, these transformations do not generate mutagenic tautomers.

During the tautomerization of the dynamically stable short Т·Т\* [63] and С·С\* [64] mispairs, as well as long А·А\* [65] and G·G\* [66] mispairs, mutagenic tautomers are distributed among the monomers with equal probability. This is important for understanding the consolidation of point mutations in subsequent rounds of DNA replication (**Figure 1**, **Table 1**). Short-lived, low-populated А\*·С and G·T\* mispairs are "providers" of the long-lived enzymatically competent А·С\* [57] and G\*·T base pairs [58], respectively, at the origin of the replication errors in DNA. Moreover, comparisons between calculated distances of intermolecular H-bonds with data from X-ray experiments [14, 15] show that incorrect А·С and G·T base pairs with Watson-Crick geometry occur in the А·С\* and G\*·T tautomeric forms in the active center of the high-fidelity DNA polymerase in its closed state.

Transition from vacuum to continuum with ε = 4, characteristics for the hydrophobic interfaces of the protein-DNA complexes, does not significantly influence the course of these tautomerization reactions and does not change the character of the obtained conclusions and generalizations.

**3.2. Can mutagenic tautomers of the DNA bases be formed** *via* **the DPT in** 

The Gibbs free energy of the product relatively the reactant of the tautomerization reaction (T = 298.15 K).

The electronic energy of the product relatively the reactant of the tautomerization reaction.

The Gibbs free energy barrier for the forward reaction of tautomerization. <sup>d</sup>The electronic energy barrier for the forward reaction of tautomerization.

The Gibbs free energy barrier for the reverse reaction of tautomerization.

The electronic energy barrier for the reverse reaction of tautomerization.

*via* the DPT along the neighboring intermolecular H-bonds in vacuum.

The lifetime of the product of the tautomerization reaction.

**Tautomeric transition ∆G<sup>a</sup> ∆E<sup>b</sup> ∆∆GTSy**

A·T↔A\*·T\* [51–53] 11.95 12.26 10.29 12.40 −1.66 0.14 6.5 × 10−15 G·С↔G\*·С\* [52] 9.22 8.22 9.69 13.28 0.47 5.06 1.6 × 10−13

G·T↔G\*·T\* [54] 11.78 12.12 9.47 12.58 −2.31 0.46 2.1 × 10−15

A·A\*↔A\*·A [65] 0.00 0.00 7.01 10.33 7.01 10.33 1.8 × 10−8 A·G↔A\*·G\* [56] 10.07 9.58 9.63 11.46 −0.44 1.88 4.8 × 10−14 G·G\*↔G\*·G [66] 0.00 0.00 5.51 8.33 5.51 8.33 8.2 × 10−10 A·C\*↔A\*·C [57] 3.99 3.64 8.17 10.53 4.18 6.89 1.1 × 10−10 G\*·T↔G·T\* [58] 1.22 1.19 2.63 5.61 2.63 5.61 8.1 × 10−13 C·C\*↔C\*·C [64] 0.00 0.00 8.28 10.83 8.28 10.83 1.5 × 10−7 C·T↔C\*·T\* [59] 9.15 8.99 9.55 11.38 0.40 2.39 2.1 × 10−13 T·T\*↔T\*·T [63] 0.00 0.00 4.64 8.18 4.64 8.18 1.6 × 10−10 G·G\*syn↔G\*·G\*syn [60] 11.02 11.15 9.07 12.17 −1.96 1.02 4.1 × 10−15 A\*·Asyn↔A·A\*syn [61] 13.98 14.71 14.15 16.43 0.16 1.72 1.1 × 10−13 A\*·G\*syn↔A·G\*syn [62] 1.89 2.20 2.42 4.60 0.52 2.40 2.2 × 10−13

COOH [55] 5.63 6.48 7.24 10.45 1.60 3.97 1.9 × 10−12

COOH [55] 8.21 7.23 6.68 8.52 −1.53 1.29 6.1 × 10−15

COOH [55] 3.35 2.91 6.12 7.43 2.77 4.52 1.6 × 10−11

COOH [55] 1.93 2.75 2.08 5.96 0.15 3.21 1.0 × 10−13

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

34 Mitochondrial DNA - New Insights

**MP2/cc-pVQZ//MP2/6–311++G(d,p)**

COOH↔m1

COOH↔m<sup>9</sup>

COOH↔m1

COOH↔m<sup>9</sup>

**MP2/cc-pVQZ//B3LYP/6–311++G(d,p)**

m1 T·CH3

m<sup>9</sup> A·CH3

m1 C·CH3

m<sup>9</sup> G·CH3

a

b

c

e

f

g

**MP2/6–311++G(3df,2pd)//M05/6–311++G(2df,pd)**

T\*·CH3

A\*·CH3

C\*·CH3

G\*·CH3

**<sup>c</sup> ∆∆ETS**

**<sup>d</sup> ∆∆G<sup>e</sup> ∆∆E<sup>f</sup> τ<sup>g</sup>**

tion through the DPT along intermolecular H-bonds of incorrect DNA base pairs.

Further, we investigated the physico-chemical mechanisms of the DNA bases tautomeriza-

**Table 1.** Energetic (kcal·mol−1) and kinetic (in s) characteristics of the tautomeric transformations of the canonical Watson-Crick, wobble, model protein-DNA complexes, incorrect long, short and Watson-Crick-like mispairs of nucleotide bases

**Watson-Crick-like mispairs?**

Obtained data evidence that tautomeric hypothesis faces significant obstacles that could not be overcome without going beyond the classical framework that mutagenic tautomers of nucleotide bases are generated in the complexes by DPT protons along neighboring intermolecular H-bonds.
