T-hairpin structure found in the RNA element involved in piRNA biogenesis

Solution structures of tj-17–32, T-hairpin. (A) Superposition of ten lowest energy structures. The stem region, U17–G20, and C28–A31 are superposed. Each molecule was colored gradually from 5′ in blue to 3′ in red, except for U21, U26, and U27 in magenta, purple, and light-sea green, respectively. (B) The minimized average structure. (C) The secondary structure of tj-17–32, T-hairpin. Each residue was colored as in A and B. (D) Structural fluctuations during the MD simulations. The lowest energy structure (1–65 nsec, blue), the second lowest energy structure (1–100 nsec, orange) and the third lowest energy structure of tj-17–32 (1–100 nsec, gray) are shown.