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. 2006 Jul;12(7):1254–1261. doi: 10.1261/rna.29906

FIGURE 2.

FIGURE 2.

Specifier Loop region of the glyQS 5′-UTR. (A) Native sequences for the 5′- and 3′-sides of the bottom portion of Stem I. Nucleosides with asterisks (*) are conserved among T box RNAs. Native sequence A•U pairs in red were substituted with G•C base pairs. (B) The biomolecular model RNAs. The Specifier half molecule contains the Specifier Loop with the glycine codon GGC. The sequences were altered to increase the stability of the complex between the Common and Specifier half molecules, including the addition of a predicted base pair between C35 and G94 denoted with open circles (○). The Specifier half molecule was synthesized with 2-aminopurine (2AP) substituting for A either 5′ or 3′ to the codon, at position 98 or position 102 (green circled “A”). The 2AP (inset) fluorescence was used to monitor interactions. The 17-nt ASLGlyGCC is shown in the secondary structure determined from NMR analyses (F. Vendeix and P.F. Agris, unpubl.).