The solution structure of the hairpin formed by d(TCTCTC-TTT-GAGAGA)

The 15-residue oligonucleotide d(TCTCTC-TTT-GAGAGA) forms a hairpin structure with a loop of three thymidine residues at neutral pH or above. The three-dimensional solution structure of this oligonucleotide has been determined by means of two-dimensional nuclear magnetic resonance methods. Interproton distance constraints derived from NOEs, in combination with torsion angle constraints obtained from J-coupling constants were used in the variable target function program DIANA to derive the hairpin structure. It was found that hairpins with two different loop conformations fit the NMR data, i.e. an equilibrium between these two conformational states can only fully explain the NOE data available. In one state, loop residue T7 is turned into the minor groove, while in the second state residue T8 is in the minor groove. In both conformations the phosphate backbone changes its direction by 180 degrees between residues T9 and G10. Concomitantly, torsion angles zeta of T9 and alpha of G10 both adopt a gauche(+) conformation and gamma of residue G10 adopts a trans conformation to induce this complete change in the direction of the backbone.