Biopolym. Cell. 2005; 21(1):70-79.
http://dx.doi.org/10.7124/bc.0006DF
Molecular Biophysics
The molecular mechanism of the spontaneous substitution mutations caused by tautomerism of bases: Post Hartree-Fock study of the DNA rare base pairs
1Danilov V. I., 1Hovorun D. M., 2Kurita N.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680
  2. Toyohashi University of Technology
    1-1 Hibarigaoka Tenpaku-cho, Toyohashi, Aichi 441-8580

Abstract

Gas-phase gradient optimization of the DNA rare base pairs containing lactam-lactim and amino-imino tautomers was carried oat using the Hartree-Fock (HF), Density Functional Theory (DFT) and the second-order Moller-Plesset perturbation (MP2) methods at the 6-31G(d, p) basis set. It is shown that full geometry optimization at the MP2 level leads to an intrinsically nonplanar propeller-twisted and buckled geometry of G*-T and G-T* base pairs. The nonplanarity of the pairs is caused by pyramidalization of the amino nitrogen atoms, which is underestimated by the HF and DFT methods. This justifies the importance of geometry optimization at the MP2 level for obtaining reliable prediction of the charge distribution, molecular dipole moments and geometrical structure of the base pairs. The comparison of the formation energies for the rare base pairs shows the energetical preference of the G*-T and A-C* base pairs as compared with the G-T* and A*-C ones, respectively. It is detected that the stabilization energies of the G-T* and A*-C base pairs describing the interaction between monomers are essentially larger than those of the G*-T and A-C* base pairs, respectively. An analysis of the decomposition members for molecular HF interaction energies by Morokuma-Kitaura (MK) and the Reduced Variational Space (RVS) methods showed that the nature of a larger stability of the G-T* and A*-C base pairs as compared to the G*-T and A-C* ones is due to the electrostatic interactions by 60–65 % and the polarization and charge transfer interactions by 35–40 %.
Keywords: spontaneous mutations, tautomerism, rare base pairs, Hartree-Fock, DFT, Moller-Plesset, geometry optimization, nonplanarity of amino group, propeller-twisted and buckled geometry, Morokuma-Kitaura analysis, interaction energy, stability energy
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