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.

Formation of a Thymine‐HgII‐Thymine Metal‐Mediated DNA Base Pair: Proposal and Theoretical Calculation of the Reaction Pathway

“…[36,16] As already mentioned, the base pair in IS4 was protonated, whereas the experimentally observed base pair was neutral. The extraordinary stability of IS4 was puzzling because the occurrence of the N3-Hg II -O4 linkage would be in conflict with the experiment.…”

“…[15][16][17][18] These experimental data enabled us to propose and calculate the mechanistic pathway for the formation of the T-Hg II -T DNA base pair in this study. Thus, the character of a metal linkage remains usually unclear.…”

“…[3] Understanding the bonding of metals to NAs is clearly essential for the targeted, rational design of novel materials based on M-NAs. 2010, 16,[13218][13219][13220][13221][13222][13223][13224][13225]. Promising proposals and functional materials include, for example, electric sensors, charge-transport Abstract: A reaction mechanism that describes the substitution of two imino protons in a thymine:thymine (T:T) mismatched DNA base pair with a Hg II ion, which results in the formation of a (T)N3-Hg II -N3(T) metal-mediated base pair was proposed and calculated.…”

“…However, other pseudo-base pairs linked with different metals have also been prepared by employing suitable organic compounds that substitute the role of natural bases. [16,17] The B-form of Hg II -DNA containing consecutive T-Hg II -T base pairs was determined recently by means of NMR spectroscopic analysis. [11,12] The imidazole ring in the imidazole-Ag I -imidazole pseudo-base pair appeared to be a functional alternative to normal cytosine.…”

Hg²⁺-Trapping Beads: Hg²⁺-Specific Recognition through Thymine–Hg(II)–Thymine Base Pairing

“…[22][23][24][25] New insights were recently reported by Ono and colleagues. 20,26,27) Although extensive structural and theoretical studies on the structure of this base pair in a DNA oligomer have been performed, [28][29][30][31][32][33][34][35][36][37][38][39][40][41] the experimental structure of the T-Hg(II)-T base pair from NMR and Raman spectroscopy was recently reported 27,42) (see the chemical structure of the T-Hg(II)-T base pair for that shown within Fig. 1b).…”