(A) Representative model of the internal loop, 5′AAGC/3′AGGA, from the B. mori R2 retrotransposon 5′ RNA. Loop residues are shown in color, and closing pairs are shown in gray. The AA, AG, GG, and CA pairs can be described in the Leontis-Westhof notation as S/H, H/S, H/S, and W/W, respectively. (B) The structures of the four pairs of the B. mori R2 internal loop in the NMR model. The pairs are shown down the axis of the helix without rotation of the duplex about the long axis. Short dashed lines connect potential hydrogen-bond donors and acceptors that are within 2.2 Å in the modeled structures. Long dashed lines connect potential hydrogen-bond donors and acceptors that are >2.5 Å apart. The dotted line from G16H1 goes to a nonbridging oxygen between A4 and A5. As discussed in the text, the G6 and G16 base pair may exchange with similar conformations.
