PUF-11 binds high-affinity sites of each RNA class with comparable affinities in vitro. (A) RNAs from each class that bound PUF-11 with high affinity in the three-hybrid assay. The sequences of the synthetic RNA oligonucleotides used for EMSAs are shown. The core binding element of each RNA is highlighted. Numbering begins with +1 at the first U of the core UGU trinucleotide. (B) EMSAs with purified recombinant GST–PUF-11. Protein concentrations are indicated above the gel. Two complexes of different electrophoretic mobilities were observed: The complex migrates slower than free RNA. The fraction of RNA bound was plotted against protein concentration to obtain apparent Kd values for each RNA.
