The Solution Structure of the Hairpin Formed by d(TCTCTC-TTT-GAGAGA)

Abstract

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.

The Hairpin Structure of a Topoisomerase II Site DNA Strand Analyzed by Combined NMR and Energy Minimization Methods

“…The high P angle values displayed by the T10 and C11 residues are in agreement with earlier observations on the conformation adopted by pyrimidine sugars in DNA loops (Mooren et al, 1994;James & Tinoco, 1993;Boulard et al, 1991). Some RNA hairpin loops exhibit also high P angles, i.e.…”

“…Table 6 gathers the torsion angle values for the so-called turning phosphate, i.e. the position where a change of direction occurs in the phosphate backbone in a variety of reported DNA hairpin loops (Mooren et al, 1994;Boulard et al, 1991;Kuklenyik et al, 1996;Blommers et al, 1991;Hirao et al, 1994). In four of the represented structures (Mooren et al, 1994;Boulard et al, 1991;Kuklenyik et al, 1996;Blommers et al, 1991) the turning phosphate displays a combination z(+)a(+)b(t)g(t) similar to that of T10pC11 in our structure.…”

A single G-to-C change causes human centromere TGGAA repeats to fold back into hairpins.

“…The individual s, C, a, 1, and y values for the 9C-p-1OA backbone conformation in the loop are -170°, 1240, 720, -1080, and -1790, respectively. From crystallographic (25)(26)(27) and NMR (19,(28)(29)(30) studies of various sized loops, it would appear that the last (3') loop phosphodiester that links it to the 5'-end of the stem is generally close to the C(g+) a(g+-t) P3(t-g-) conformation.…”

The Hairpin Elements of Nucleic Acid Structure: DNA and RNA Folding

“…The three-dimensional structure was determined from the distance and torsion angle constraints determined by NMR, using a variable target function approach (DIANA) followed by unconstrained energy minimization (Mooren et al 1993a). Two families of structures are observed.…”