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. 2011 May;17(5):957–966. doi: 10.1261/rna.2636911

FIGURE 3.

FIGURE 3.

Effect of bulge size on PKR activation. (A) Global geometry of bent E RNAs containing one [1 × 0], [2 × 0], [4 × 0], and [6 × 0] A-bulge. Approximate bulge angles, based on the studies of Zacharias and Hagerman (1995a) are provided. (B) Native gel mobility analysis of bent E RNAs. Gel was loaded running and RNAs were intentionally loaded from right to left, the direction of increasing mobility. Gel contains 15% acrylamide (29:1), 0.5X TBE, and was run at 300 V, 16°C for 8 h. (C) PKR activation by bent E RNAs with different bulge sizes. Representative data set is provided in gel format, where percent PKR activation is normalized to dsRNA-51, and fold-effects relative to dsRNA-51 are provided. Gel is 10% SDS-PAGE. Experiments were conducted in duplicate. (D) Plot of PKR activation versus A-bulge size for two independent data sets, depicted by filled and open symbols. RNA concentration is at 0.02 μM. The average of these data sets is shown as the trend line.