see designations in Table 5

80 Quantum Chemistry – Molecules for Innovations

those of the Watson–Crick base pairs. These values for the irregular base pair as distinguished from the Watson–Crick base pairs reflect the distortion of double helix conformation and can be factor taking into account the recognition of the structural

Detailed study of the geometric characteristics for the optimized mutagenic and Watson– Crick base pairs leads to the following results. The distance between the bonds joining the bases to the deoxyribose groups in the Gua\*·Thy and Gua·Thy\* mutagenic base pairs is close to the corresponding canonical distance in the Gua·Cyt base pair, and the corresponding distance in the Ade\*·Cyt and Ade·Cyt\* base pairs is close to that in the Ade·Thy base pair. Moreover, in each pair of stereoisomers (Gua\*·Thy, Gua·Thy\* and Ade\*·Cyt, Ade·Cyt\*), the N9–C1-C1 and N1–C1–C1 glycosidic angles are close to the corresponding value in one of the Watson–Crick canonical base pairs. Analogous conclusions were made earlier by Topal and Fresco (Topal & Fresco, 1976) and Danilov et al. (Danilov et al., 2005), who studied each of the above-mentioned mutagenic base pairs by model building and by ab initio methods, respectively, and showed that these pairs are sterically compatible with the Watson–Crick

Finally, according to the molecular mechanism of recognition of the complementary base pairs of nucleic acids by DNA polymerase (Li & Waksman, 2001), the key role in the selection of the correct substrate is the interactions of the certain amino acid residues in the recognition site of DNA polymerase with the invariant arrangement of the N3 purine and O2 pyrimidine atoms (Beard & Wilson, 1998, 2003; Poltev et al., 1998). These hydrogenbonding interactions may provide a means of detecting misincorporation at this position. Our data show that the structural invariants of the mutagenic nucleotide pairs are very close to those of the correct nucleotide pairs. In other words, the mutual position of the atoms and atomic groups is practically the same both for the correct and the irregular pairs, so that the DNA polymerase (more exactly its recognizing site) can play the role of additional matrix under the inclusion of the nucleotides. Therefore, we conclude that the formation of the DNA mutagenic base pairs satisfies the geometric constraints of the standard double helical DNA. If these mutagenic base pairs would be incorporated into a standard Watson–Crick double helix, the helix would not likely experience significant distortion and its stability

The comparison of the formation energies of the canonical and mutagenic base pairs (Table 6) shows that the Löwdin's Ade\*·Thy\* base pair, which electronic formation energy is -33.80 kcal/mol, is the most stable among all the studied base pairs. At the same time, the formation of the Gua\*Thy and Ade\*·Cyt mispairs is more favorable than that of the AdeThy canonical base pair, GuaThy\* and Ade·Cyt\* mispairs which have -14.92; -33.39 and -23.50 kcal/mol formation energy, respectively (Table 6). From the other point of view, it may evidence that dissociation of the Gua\*Thy and Ade\*·Cyt mispairs will be complicated during the strand separation. These data therefore confirm that Ade·Cyt\* and Gua\*·Thy mispairs are suitable candidates for the spontaneous point mutations arising in DNA (Fig. 6). The Ade\*·Cyt and Gua·Thy\* lifetimes (3.4910-11 s and 3.5910-13 s, accordingly) are too short comparably with the time of one base pair dissociation during the enzymatic DNA replication (10-9 s). This means that these mispairs will "slip away" from replication machinery: they transfer to Ade·Cyt\* and Gua\*·Thy accordingly (Fig. 6). In this way

Ade\*·Cyt and Gua·Thy\* mispairs act as intermediates in this reaction.

invariants of the sugar-phosphate backbone by the polymerase.

base pairs.

would not be greatly deteriorated.

Table 6. Electronic and Gibbs free energies (in kcal/mol) (T=298.15 K) of base pairs obtained at the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of theory in vacuum#

Fig. 6. Interconversion of Ade·Cyt\*↔Ade\*·Cyt and Gua\*·Thy↔Gua·Thy\* mispairs involving mutagenic tautomers of DNA bases. Relative Gibbs free energies (T=298.15 K, in vacuum) are obtained at the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of theory and reported near each structure in kcal/mol. The dotted lines indicate H-bonds AH…B (their lengths H…B are presented in angstroms), while continuous lines show covalent bonds

The obtained Gibbs free energies of interaction indicate that Gua\*·Thy and Ade·Cyt\* are more favorable than Gua·Thy\* and Ade\*·Cyt. It was established that the Ade\* Cyt and Gua\*·Cyt\* base pairs are metastable and easily (i.e., without facing significant barrier) "slip" into the energetically more favorable Ade Cyt\* and Gua·Cyt base pairs, respectively. The comparison of reverse electronic barriers of interconversion with the zero-point energies of competent vibrational modes (Table 7) of the tautomerized complexes allows concluding that Ade\*Thy\* and GuaThy\* complexes are dynamically unstabletheir electronic barriers of the reverse transition are noticeably lower than zero-point energy of corresponding vibrational modes.

Elementary Molecular Mechanisms of the Spontaneous Point

and GuaThy\* as stable structures.

concrete physico-chemical content.

thermodynamic and kinetic criteria:

(several ms);

Mutations in DNA: A Novel Quantum-Chemical Insight into the Classical Understanding 83

In this context, a topic of current importance is the search of novel physico-chemical mechanisms of tautomerisation of DNA bases in Watson-Crick base pairs: the pioneering, but encouraging steps have been already made in this direction (Brovarets', 2010; Cerón-Carrasco

It was found that a specific interaction of a single water molecule with the site of mutagenic tautomerisation in each of four canonical DNA bases could transform to into mutagenic tautomeric form in a definite time notably less than ~4·10-4 s. The most vulnerable point of this model of origin of replication error in DNA is a complete lack of experimental and especially theoretical support for a probability of the penetration of water molecules at a replication fork per one Watson-Crick base pair. Most likely such a probability is very low, since a compact, essentially hydrophobic organization of replisome (Marians, 2008;

In this work it was found that among all purine-pyrimidine base pairs with Watson-Crick geometry involving one base in mutagenic tautomeric form - AdeCyt\*, Gua\*Thy, Ade\*Cyt and GuaThy\*, GuaThy\* mispair is dynamically unstable and Ade\*Cyt mispair has very small lifetime (<<10-9 s) and therefore plays an intermediate role in DNA replication cycle, "sliding down" to the AdeCyt\* mispair. This fact substantially alters the Löwdin's scheme (Löwdin, 1963, 1965, 1966) of replication point errors fixation arising due to the prototropic tautomerism of DNA bases, which treats all four base pairs AdeCyt\*, Ade\*Cyt, Gua\*Thy

In our opinion, the results reported here not only provide more evidence in support of Watson and Crick classical tautomeric hypothesis of point mutations, but also fill it with

By combining the data from the literature with our findings, we concluded that the tautomeric mechanism of the origin of mutations in DNA should satisfy the following





Finishing our conclusions, we hope that this theoretical study gives valuable and thorough information on the chemically intriguing and biologically relevant questions of the DNA bases tautomerism. Our results presented here are believed to provide a new insight into the molecular nature of spontaneous point mutations in DNA and also be a promising and

within the range of 10-8-10-11, that agrees fully with biological experimental data.

forcibly dissociate a Watson-Crick base pair into monomers (several ns);

perspective tool for experimentalists working in the field of DNA mutagenesis.

energy of the complex with canonical tautomer participation;

et al., 2009a, 2009b, 2011; Cerón-Carrasco & Jacquemin, 2011; Kryachko & Sabin, 2003).

Pomerantz & O'Donnell, 2007) is supposed to minimize this probability.

