Effects of Stem Length and Core Placement on shRNA Activity
Author Information
Author(s): Mcintyre Glen J, Yu Yi-Hsin, Lomas Mehnaaz, Fanning Gregory C
Primary Institution: Johnson and Johnson Research Pty Ltd
Hypothesis
How is the suppressive activity of expressed shRNA altered when changing the length of the stem, and how does suppressive activity relate to the placement of a predetermined siRNA core within the shRNA stem?
Conclusion
There is no fixed correlation between stem length and suppressive activity, and core placement at the base terminus is critical for activity.
Supporting Evidence
- Stem lengths ranged from 19 to 29 base-pairs, with 19 bp being the most common.
- Short and long shRNAs were both found to be potent suppressors.
- Core placement at the base terminus was critical for shRNA activity.
Takeaway
This study found that making the stem of a special RNA shorter or longer doesn't always make it work better; where you put the important part of the RNA matters more.
Methodology
The study tested more than 91 hairpins targeting HIV-1, varying in both stem length and sequence composition, measuring suppressive activities as a reduction in GFP fluorescence.
Potential Biases
Potential bias in the selection of hairpins and targets could affect the generalizability of the findings.
Limitations
The study primarily focused on specific targets (HIV-1 Tat and Vpu) and may not generalize to all shRNA designs.
Statistical Information
P-Value
p<0.001
Confidence Interval
95%
Statistical Significance
p<0.001
Digital Object Identifier (DOI)
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