Raman spectroscopic detection of the T-HgII-T base pair and the ionic characteristics of mercury

Developing applications for metal-mediated base pairs (metallo-base-pair) has recently become a high-priority area in nucleic acid research, and physicochemical analyses are important for designing and fine-tuning molecular devices using metallo-base-pairs. In this study, we characterized the Hg-II-mediated T-T (T-Hg-II-T) base pair by Raman spectroscopy, which revealed the unique physical and chemical properties of Hg-II. A characteristic Raman marker band at 1586 cm(-1) was observed and assigned to the C4=O4 stretching mode. We confirmed the assignment by the isotopic shift (O-18-labeling at O4) and density functional theory (DFT) calculations. The unusually low wavenumber of the C4=O4 stretching suggested that the bond order of the C4=O4 bond reduced from its canonical value. This reduction of the bond order can be explained if the enolate-like structure (N3=C4-O4(-)) is involved as a resonance contributor in the thymine ring of the T-Hg-II-T pair. This resonance includes the N-Hg-II-bonded state (Hg-II-N3-C4=O4) and the N-Hg-II-dissociated state (HgII+ N3=C4-O4(-)), and the latter contributor reduced the bond order of N-Hg-II. Consequently, the Hg-II nucleus in the T-Hg-II-T pair exhibited a cationic character. Natural bond orbital (NBO) analysis supports the interpretations of the Raman experiments.