A UV resonance Raman study of d(A(+)-G)10, a single-stranded helix without stacked or paired bases

UV resonance Raman spectroscopy has been utilized to directly observe structural features of the recently described nucleic acid single-stranded helix d(A(+)-G)10. An absence of base stacking is confirmed by invariant hypochromic ratios of dominant vibrational modes for the oligomer relative to its constituent monomers as the structure is thermally denatured. The N1 of dA residues is protonated, as determined by similarity to the ring-stretching vibrations for protonated adenine and its derivatives. Selective resonance enhancement of Raman vibrational modes from dA and dG residues shows frequency shifts upon thermal denaturation that confirm the participation of the exocyclic amino of dA but not dG residues in H-bonding. Conformationally sensitive glycosyl bond modes suggest anti residue conformations.