Figure 6

TGE deletions, dual hexamer spacing requirements and upstream partial consensus elements define GLD-1 dimer binding. A. The two TGE region of the tra-2 mRNA 3' UTR is shown with the 28-nt TGE boundaries delineated and the three canonical 5'-UACUCA-3' hexamers underlined. Bars beneath the sequence correspond to the regions tested and are colored according to the calculated inhibition constant. RNAs with a K_i^app ≤ 15 nM are represented by black bars and RNAs that compete with the native TGE RNA less effectively are represented by grey bars. Each RNA is listed by the position in the sequence with the corresponding K_i^app value. B. The spacing requirements for canonical hexamer placement in a 28-nt poly-uridine background. Consensus 5'-UACUCA-3' hexamers are displayed as red boxes. The relative position of each hexamer is shown with the numbers indicating nucleotide spacing between hexamers and hexamer distance from either the 5' or 3' end. C. High-affinity GLD-1 binding and the effects of various dinucleotide insertions upstream of a canonical hexamer in a poly-uridine background. Each RNA contains a single 5'-UACUCA-3' hexamer (red boxes) positioned 6 nucleotides from the upstream partial motif, with the numbering referring to the hexamer boundary distances from the 5' and 3' ends. The partial motif sequences are given and are shown schematically within the white boxes. Uridine residues are indicated by dots. The effect of added A or C residues was evaluated in comparison to 5'-UUUUUU-3'.