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Figure 4 | BMC Molecular Biology

Figure 4

From: The effects of stem length and core placement on shRNA activity

Figure 4

Target-matched sequence at the base terminus is critical for activity. All hairpins were designed around position 56 of Tat (or 59 as indicated in the final set). (A) The same Tat56-19, 21, 23, 25, 27 and 29 bp hairpins as tested before, representing the span of commonly employed stem lengths, were reused here for comparison (shown with open bars). (B - C) For a constant stem length of 29 bp, inverted sequence was introduced at either the loop terminus or base terminus in 2 bp increments. (D) A 21 bp siRNA core was progressively re-positioned at each of 9 possible positions in the stem of a 29 bp hairpin. All values are averages from at least 3 independently repeated experiments with 95% Confidence Intervals (CI) shown. (E) The Tat56-29 shRNA was transiently expressed in 293a cells from which small RNA species were extracted and cloned. One hundred and thirty four individual ssRNA species were cloned and six were found that originated from the Tat56-29 hairpin. The remaining sequences were bacterial in origin or unidentified.

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