Investigations of Zn(II) complexes with DNA/RNA bases by means of quantum chemical calculations

Abstract

The interaction of Zn 2+ ions with the five purine and pyrimidine bases of DNA and RNA, i.e., adenine (Ade), cytosine (Cyt), guanine (Gua), thymine (Thy) and uracil (Ura) has been studied using ab initio SCFHF computations with minimal basis set. Energy optimized structures of the possible complexes of the metal ion with the bases and the corresponding interaction energies have been determined. Zn 2+ coordinating simultaneously to the carbonyl oxygen and to one nitrogen in guanine or cytosine gives rise to the highest values of binding energy, followed by the nitrogen sites of adenine and guanine. The least favoured complexes are those involving binding of Zn 2+ to oxygen sites of thymine and uracil. One exception in this series of relative interaction energies is the position O4 in thymine. Most of the resulting geometrical features are similar to those found in previous studies on complexes of the bases with alkali and alkaline earth metal ions. The electronic structure of the coordinated ligands was analysed to obtain a picture of the H-bonding ability between the molecules in the Watson-Crick base pairs AT and GC in the presence of zinc ions. The results show that for Zn 2+ bound to guanine via N3 and N7, the H-bonds in GC are stabilized and also when Zn 2+ is coordinated to O2 of thymine (uracil) the H-bonds in AT(U) are stabilized, whereas for N3 coordination in adenine the AT(U) base pair is destabilized. For N7 coordination in adenine, it has been assumed that the coordination does not significantly change the interaction between Ade and Thy (Ura).