Fig. 5.

PUF-8 binds to pal-1 3′ UTR in vitro. (A) Schematic illustration of pal-1 3′ UTR showing the two regions used in gel mobility shift assays. The dotted bar represents the full-length 3′ UTR; Red line on the left part corresponds to Region 1 and the green line on the right is Region 2. See Fig. S1 for the complete sequence of pal-1 3′ UTR. (B) Electrophoretic mobility patterns of radiolabeled Region 1 and Region 2 of pal-1 3′ UTR RNA in the presence of MBP:PUF-8. L pal-1 – radiolabeled pal-1 3′ UTR; UL pal-1 – unlabeled pal-1 3′ UTR; NS RNA – unlabeled non-specific RNA; and 100x – number of times molar excess over L pal-1. (C) Electrophoretic mobility shift of the radiolabeled Region 1 and Region 2 of pal-1 3′ UTR RNA incubated with increasing concentrations of MBP::PUF-8. In both cases, the protein concentrations were: 1ane 1 – no protein; lane 2 – 0.02 nM, lane 3 – 0.04 nM, lane 4 – 0.06 nM and lane 5 – 0.08 nM. In both (B) and (C), the shifted band is indicated by the arrow. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)