A UV Resonance Raman Study of Hairpin Dimer Helices of d(A-G)10 at Neutral pH Containing Intercalated dA Residues and Alternating dG Tetrads

摘要

The structure of the oligonucleotide d(A-G)₁₀ in 0.6 M Na+, pH 7.0 has been investigated with UV resonance Raman (UVRR) spectroscopy. Variable wavelength excitation was used to distinguish the spectral contributions of dG and dA residues. Both classes of residues show UVRR hyperchromism with increasing temperature, reflecting unstacking of the bases. The dG residues melt relatively cooperatively with a T_m of ～42°C. Unstacking is non-cooperative for the dA residues, increasing linearly between 4 and 80°C. G-tetrads at low temperature are indicated by UVRR frequency shifts of modes associated with C₆=O and C₂-NH₂ of the dG residues, and of vibrations involving N₇, all sites of H-bonding. However, there are no indications of interbase H-bonds for the dA residues, showing they do not form H-bonded tetrads. Most of the bases are oriented anti about the glycosyl bond, but at 4°C a fraction of the residues are syn. These results, together with the findings by Shiber et al. [Shiber,M.C., Braswell,E.H., Klump,H. and Fresco,J.R. (1996) Nucleic Acids Res. 24, 5004–5012] that d(A-G)₁₀ under comparable conditions has the molecular weight of a dimer, support a model in which two hairpins interact to form a helical structure with G-tetrads and intercalated dA residues.