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

The structure of the oligonucleotide d(A-G)(10) in 0.6 M Na+, pH 7.0 h as been investigated with UV resonance Raman (UVRR) spectroscopy, Vari able wavelength excitation was used to distinguish the spectral contri butions of dG and dA residues, Both classes of residues show UVRR hype rchromism with increasing temperature, reflecting unstacking of the ba ses. The dG residues melt relatively cooperatively with a T-m of simil ar to 42 degrees C, Unstacking is non-cooperative for the dA residues, increasing linearly between 4 and 80 degrees C, G-tetrads at low temp erature are indicated by UVRR frequency shifts of modes associated wit h C-6=O and C-2-NH2 of the dG residues, and of vibrations involving N- 7, all sites of H-bonding, However, there are no indications of interb ase H-bonds for the dA residues, showing they do not form H-bonded tet rads, Most of the bases are oriented anti about the glycosyl bond, but at 4 degrees C a fraction of the residues are syn, These results, tog ether with the findings by Shiber ct 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 o f a dimer, support a model in which two hairpins interact to form a he lical structure with G-tetrads and intercalated dA residues.