Figure 5

Hairpins with mismatched or bulged bases in the sense stem are less potent gene suppressors. (a) Introduced mutations were either changes of a C residue to a U residue (from 1 to 5) or an A residue to a G residue (from 1 to 5) and were compared against the normal (perfectly matched) shRNA with no mutations ("Normal"). All alterations were in the sense strand only (designed to give rise to the non-active siRNA 'passenger' strand), whilst the anti-sense strand of the shRNA stem (designed to give rise to the active siRNA 'guide' strand) remained the same, and perfectly complementary to the target in all variations. (b) Reduction in suppressive activity (relative to the perfectly matched shRNA) was minimal for 1 to 2 mismatched bases but more notable for the constructs with the recommended 3 to 4 mismatched bases, and most obvious where the mutation is increased to 5 bases.