FIGURE 2.

In vitro selection of the reporter RNA. (A) The predicted secondary structure of the parental molecule used for the in vitro selection. Part of a streptavidin-binding aptamer (blue) is linked to part of an aptamer selected to be a good editing substrate (underlined). The 21 positions that were randomized for the selection are in lowercase, and the three U's that are guided into the editing site are indicated in red. (B) Progression of the in vitro selection. Radiolabeled pre-edited RNAs from the indicated cycles of selection were treated in a streptavidin-coated microtiter plate with mitochondrial extract in the presence or absence of the indicated nucleotide cofactors. After washing the plate, eluted RNA was analyzed on a denaturing gel. The size corresponding to the three U insertions expected from accurate editing is indicated. (C) The sequence of the RNAs obtained from the selection. The number of identical clones is indicated in parentheses. The maroon bases represent positions that differ from the starting parental sequence, and the nucleotides that had been deleted during the selection are indicated by a maroon dash. Other colors are as described above. Nucleotides are numbered relative to the pre-edited sequence of RNA A.