DFT Studies of the Zinc Complexes of DNA Bases

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The metal cation interactions with DNA nucleobases have been studied by a variety of experimental and theoretical method. It is known that the coordinated metal ions play a significant role in the biological action of nucleic acids. Especially, metal cations interact with the DNA bases, destroying the hydrogen bonding between the base pairs. Therefore, the structure of DNA is changed. So, the metal cations affect syntheses, replication and cleavage of DNA. Cerda and Wesdemiotis have reported the alkali metal ions (Li, Na and K) affinities of the DNA bases, but they do not show the information on the binding site of the metal. Burda et al. have studied on the interaction of guanine and adenine with Zn at the Hartree-Fock (HF) and MollerPlesset second-order perturbation theory (MP2). However the results are not sufficient to predict the preferred location of the binding sites. They also do not present investigation on the interaction of the zinc cation with thymine and cytosine. Actually, we can locate the structures for various zinc cation complexes including the some bridged formations. In the present study, as a continuation of our study on the binding of metal cations with DNA bases we report a DFT investigation on the interaction of Zn with DNA bases. We focus in this study our attention on the geometrical structures, association sites and association energies for the Zn complexes of DNA bases to describe the structural and energetic features of these complexes. DFT calculations in this study are carried out at B3LYP level of theory using the Gaussian03 series of program. The geometry optimizations are performed with the 6-31G(d,p) basis set using energy gradient method and all structures are fully optimized without any constraint. Vibration frequencies are also calculated to confirm that all the stationary points correspond to true minima on the potential energy surface. The stationary conformers are obtained by verifying that all the harmonic frequencies are real. All energies are calculated with single point at the B3LYP level of theory with the 631++G(d,p) basis set using the optimized geometry calculated with 6-31G(d,p) to obtain reasonable energies. In order to obtain accurate association energies, basis set superposition errors (BSSE) are also subtracted from the calculated association energies in the full counterpoise (CP) approximation. The zinc cation association energies (ΔE) are obtained by subtracting the sum of the energies of the base [E(B)] and zinc cation monomer [E(Zn)] from the energy of the full optimized base-Zn complex [E(B-Zn)].