FIGURE 2.

Secondary structure predictions and in-gel FRET analysis of selected RNA aptamers. (A,B) Secondary structure prediction for RNA aptamers of (A) SI and (B) SIM series. Two types of structure are shown for each RNA, with a canonical aminoacceptor (AA) stem and with an alternative F-stem. (Red) Nucleotides corresponding to the tRK1 AA-stem; (blue) to the D-arm; (purple) to the TΨC stem–loop; (black) stably selected substitutions and variable regions; fluorophore positions are shown by splashes; (Fl) fluorescein. (C) In gel FRET analysis of two selected RNA aptamers, (left panel) SI 56 and (right panel) SIM 92. Radioactive signals, p32, and fluorescence (ex. 488 nm, em. 520 nm), Fl, of increasing amounts of RNAs labeled by donor fluorophore only (Fl-RNA) or by both donor and acceptor fluorophores (FlDy-RNA), in a native 12% PAGE.