DFT investigation of the mismatched base pairs (T-Hg-T)3, (U-Hg-U)3, d(T-Hg-T)2, and d(U-Hg-U)2.

Mismatched T:T and U:U base pairs in DNA and RNA duplexes represent the preferred target for mercury(II) cations. In this work, the structural, energetic, and electronic properties of the metallo base pairs T-Hg-T and U-Hg-U were investigated using density functional theory. In order to evaluate the geometric and energetic effects on the stacking interaction, the systems (T-Hg-T)3 and (U-Hg-U)3 systems as well as the dinucleotide systems d(T-Hg-T)2 and d(U-Hg-U)2 were examined. Results show that the exchange-correlation functionals B3LYP-D3 and M06-L yield reasonable information on these systems that is in agreement with the available experimental data.