Optimization of Y3H readout by selection. (A) An RNA insert (red) selected in isolation for proper folding to interact with target (gray polygon)/activation domain (white triangle) fusion protein. (B) Selection for flanking RNA sequences (black) that enhance proper local tertiary structure context (gray) for the RNA insert. (C) Selection for flanking RNA sequences that enhance proper global folding of display RNA. (D) Selection for flanking RNA sequences that promote accessibility of the RNA insert to target the protein-binding domain. (E) Selection for flanking RNA sequences that enhance access of bound target protein to transcriptional cofactors. (F) Selection for flanking RNA sequences that destabilize a competing complex with yeast protein “X” (black rectangle), enhancing accessibility of RNA insert.
