Secondary structure of the Class I GTP aptamer. Lines connect base-pairing partners in the P1 and P2 stems. Positions in the recognition bulge (L1, residues 8–16; L3, residues 29–34) are colored according to whether they are invariant (red), two-base varying (green), or unconserved (black) (Carothers et al. 2004). The terminal base pair of the outer stem P1 (A7:A35) and inner stem P2 (G17:U28) are noncanonical pairs and are colored in the same way. For sites that are two-base varying, the tolerated substitution is shown below the position. The lines connecting aptamer residues to the GTP ligand indicate positions for which we detected intermolecular aptamer-GTP NOEs.
