title: The physicochemical essence of the purine·pyrimidine transition mismatches with Watson-Crick geometry in DNA: A·C* versa A*·C. A QM and QTAIM atomistic understanding.
abstract: It was established for the first time by DFT and MP2 quantum-mechanical (QM) methods either in vacuum, so in the continuum with a low dielectric constant (ε = 4), typical for hydrophobic interfaces of specific protein-nucleic acid interactions, that the repertoire for the tautomerisation of the biologically important adenine · cytosine* (A · C*) mismatched DNA base pair, formed by the amino tautomer of the A and the imino mutagenic tautomer of the C, into the A*·C base mispair (∆G = 2.72 kcal mol(-1) obtained at the MP2 level of QM theory in the continuum with ε = 4), formed by the imino mutagenic tautomer of the A and the amino tautomer of the C, proceeds via the asynchronous concerted double proton transfer along two antiparallel H-bonds through the transition state (TSA · C* ↔ A* · C). The limiting stage of the A · C* → A* · C tautomerisation is the final proton transfer along the intermolecular N6H · · · N4 H-bond. It was found that the A · C*/A* · C DNA base mispairs with Watson-Crick geometry are associated by the N6H · · · N4/N4H · · · N6, N3H · · · N1/N1H · · · N3 and C2H · · · O2 H-bonds, respectively, while the TSA · C*↔ A* · C is joined by the N6-H-N4 covalent bridge and the N1H · · · N3 and C2H · · · O2 H-bonds. It was revealed that the A · C* ↔ A* · C tautomerisation is assisted by the true C2H · · · O2 H-bond, that in contrast to the two others conventional H-bonds exists along the entire intrinsic reaction coordinate (IRC) range herewith becoming stronger at the transition from vacuum to the continuum with ε = 4. To better understand the behavior of the intermolecular H-bonds and base mispairs along the IRC of the A · C* ↔ A* · C tautomerisation, the profiles of their electron-topological, energetical, geometrical, polar and charge characteristics are reported in this study. It was established based on the profiles of the H-bond energies that all three H-bonds are cooperative, mutually strengthening each other. The nine key points, providing a detailed physicochemical picture of the A · C* ↔ A* · C tautomerisation, were revealed and thoroughly examined along the IRC. It was shown that the A* · C base mispair with the population ~1 % obtained at the MP2 level of QM theory in the continuum with ε = 4 is thermodynamically and dynamically stable structure. Its lifetime was calculated to be 5.76 · 10(-10) s at the MP2 level of QM theory in the continuum with ε = 4. This lifetime, from the one side, enables all six low-frequency intermolecular vibrations to develop, but, from the other side, it is by order less than the time (several ns) required for the replication machinery to forcibly dissociate a base pair into the monomers during DNA replication. This means that the A* · C base mispair "slips away from the hands" of the replication machinery into the A · C* mismatched base pair. Consequently, the authors came to the conclusion that exactly the A · C* base mispair is an active player of the point mutational events and is effectively dissociated by the replication machinery into the A and C* monomers in contrast to the A* · C base mispair, playing the mediated role of a provider of the A · C* base mispair in DNA that is synthesised.
authors.affiliation: a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Akademika Zabolotnoho Street, 03680 Kyiv , Ukraine.
authors.forename: Ol'ha O
authors.initials: OO
authors.lastname: Brovarets'
authors.forename: Dmytro M
authors.initials: DM
authors.lastname: Hovorun
mesh_terms: D000465:Algorithms; D020137:Base Pair Mismatch; D020029:Base Pairing / Q000235:genetics; D055598:Chemical Phenomena; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D007536:Isomerism; D008956:Models, Chemical; D015394:Molecular Structure; D011687:Purines / Q000737:chemistry*; D011743:Pyrimidines / Q000737:chemistry*; D011789:Quantum Theory; D013816:Thermodynamics
chemical_list: D011687:Purines; D011743:Pyrimidines; D004247:DNA; C030986:pyrimidine; C030985:purine
keywords: DFT and MP2 levels of QM theory; QTAIM analysis; cooperativity of the H-bonds; mutagenic tautomers; purine·pyrimidine transition mismatches; spontaneous point mutations in DNA; tautomerisation via the DPT