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

• Published in: Nucleic acids research Vol. 40; no. 12; pp. 5766 - 5774
• Main Authors: Uchiyama, Tomomi, Miura, Takashi, Takeuchi, Hideo, Dairaku, Takenori, Komuro, Tomoyuki, Kawamura, Takuya, Kondo, Yoshinori, Benda, Ladislav, Sychrovský, Vladimír, Bouř, Petr, Okamoto, Itaru, Ono, Akira, Tanaka, Yoshiyuki
• Format: Journal Article
• Language: English
• Published: Oxford University Press 01.07.2012
• Subjects: Structural Biology
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gks208

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 ( 18 O-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 (Hg II+ 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.