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. 2014 Sep;20(9):1410–1418. doi: 10.1261/rna.043950.113

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© 2014 Herrera-Carrillo et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society

This article, published in RNA, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.

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FIGURE 2. — Design of shRT5 mutants with a terminal G-C or G-U base pair and varying stem length. The shRT5 with a 19-bp stem and 5-nt loop (19/5) was used as template. The shRNA stem length was reduced/increased at the bottom of the hairpin, resulting in shRT5 variants 15/5–23/5 that do not affect the complementarity with the probe used in Northern blotting. In this shRNA length series, the terminal top base pair G-C was modified to G-U. The predicted Dicer and Ago2 cleavage sites are marked with black and gray arrows, respectively. Predicted RNA fragment lengths upon Ago2 and Dicer processing are shown below the structures.