Raman spectroscopic detection of the T-Hg II-T base pair and the ionic characteristics of mercury.

Abstract

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 HgII-mediated T-T (T-HgII-T) base pair by Raman spectroscopy, which revealed the unique physical and chemical properties of HgII. 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 (18O-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-HgII-T pair. This resonance includes the N-HgII-bonded state (HgII-N3-C4=O4) and the N-HgII-dissociated state (HgII+ N3=C4-O4−), and the latter contributor reduced the bond order of N-HgII. Consequently, the HgII nucleus in the T-HgII-T pair exhibited a cationic character. Natural bond orbital (NBO) analysis supports the interpretations of the Raman experiments.