Effects of mercury(II) on structural properties, electronic structure and UV absorption spectra of a duplex containing thymine-mercury(II)-thymine nucleobase pairs.

Structural properties, electronic structure and UV absorption spectra of mercury(ii) mediated metal-DNA complex, thymine-mercury(ii)-thymine base pair (T-Hg(II)-T), were theoretically and computationally investigated along with experimental data [Ono et al., J. Am. Chem. Soc., 2006, 128(7), 2172-2173]. The results were obtained by density functional theory (DFT) calculations for ground state and time-dependent DFT (TD-DFT) calculations for excited states associated with the polarized continuum model (PCM) in order to account for the bulk solvent effect. The LUMO of T-Hg(II)-T was stabilized due to the presence of Hg(II) since an unoccupied 6p orbital interacted with the 2p orbitals of thymine N3 atoms in the same way as in a pi-conjugated system. Thus, excitations in T-Hg(II)-T involve transitions qualitatively different from those of the thymine-thymine mismatch base pair (T-T). Since conventional DFT functionals lack correct description of dispersion forces, a method previously developed in our research group which combines DFT and a van der Waals correction functional was introduced to study multiple stacking nucleobase pairs. Based on the evaluated distance and the interaction energy between two stacking nucleobase pairs, the selective capturing of Hg(II) ion by T-T compared to other metal ions is explained. The calculated UV absorption spectra of multiple stacking nucleobase pairs reproduced the decrease of absorption around 260 nm and the red-shift of the main peak experimentally observed in the presence of Hg(II) ion. Detailed analysis of the electronic structure revealed that the metal-metal interaction between two Hg(II) in multiple stacking T-Hg(II)-T is the origin of the significant changes in UV absorption spectra.