Electronic and molecular structure of M-DNA fragments

Yury V Rubin, Leonid F Belous, Capital A Cyrillicnatolij Capital A Cyrillic Yakuba
Journal of Molecular Modeling 2011, 17 (5): 997-1006
To study M-DNA molecular structure (such DNA with transition metal ions placed between the nucleic bases is able to conduct the electric current) and its conductivity mechanisms, we carried out ab initio quantum-mechanical calculations of electronic and spatial structures, thermodynamic characteristics of adenine-thymine (АТ) and guanine-cytosine (GC) base pair complexes with Zn(2+) and Ni(2+). To take into account the influence of the alkaline environment, calculations for these complexes were also carried out with hydroxyl and two water molecules. Computations were performed at MP2 level of theory using 6-31+G* basis set. Analogous calculations were carried out for (AC)(TG) stacking dimer of nucleic acid base pairs with two Zn(2+). The calculation of the interaction energy in complexes has shown the preference of locating the metal ion (instead of the imino proton) between bases in M-DNA. The electronic transition energy calculation has revealed the reduction of the first singlet transition energy in АТ and GC complexes with Ni(2+) from 4.5 eV to 0.4 - 0.6 eV. Ni(2+) orbitals take part in the formation of HOMO and LUMO on the complexes investigated. It was shown that charges of metal ions incorporated into complexes with nucleic bases and in dimer decrease significantly.

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