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

Tomomi Uchiyama, Takashi Miura, Hideo Takeuchi, Takenori Dairaku, Tomoyuki Komuro, Takuya Kawamura, Yoshinori Kondo, Ladislav Benda, Vladimír Sychrovský, Petr Bouř, Itaru Okamoto, Akira Ono, Yoshiyuki Tanaka

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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 metallobase- pairs. In this study, we characterized the Hg II-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-Hg II-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.

Original languageEnglish
Pages (from-to)5766-5774
Number of pages9
JournalNucleic acids research
Volume40
Issue number12
DOIs
Publication statusPublished - 2012 Jul

ASJC Scopus subject areas

  • Genetics

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    Uchiyama, T., Miura, T., Takeuchi, H., Dairaku, T., Komuro, T., Kawamura, T., Kondo, Y., Benda, L., Sychrovský, V., Bouř, P., Okamoto, I., Ono, A., & Tanaka, Y. (2012). Raman spectroscopic detection of the T-HgII-T base pair and the ionic characteristics of mercury. Nucleic acids research, 40(12), 5766-5774. https://doi.org/10.1093/nar/gks208