176 8 Design of Ligand‐Controlled Genetic Switches Based on RNA Interference
RNP motif
Tr igger protein
Top view
RNA motif
(a)
(b)
Switch X with
trigger protein
Accessible: not functional Inaccessible: functional
Knockdown
Dicer Dicer
Knockdown
target gene target gene
Switch Y with
trigger protein
Switch X with
trigger protein
of of
Switch Y with
trigger protein
~2.6
Å/bp
30°/bp
dsRNA
+
Figure 8.3 3D design scheme of the protein‐responsive shRNA switch. (a) Protein‐responsive
shRNA switches are three‐dimensionally designed by connecting an RNP motif to the
corresponding dsRNA in silico. After specifying the position of the devices with reference to
the Dicer cleavage sites and comparing the locations of the bound proteins of the X and Y
switches, the bound trigger protein on switch X rotates ~30° in a counterclockwise direction
around the axis of the dsRNA and is located ~2.6 Å more distant from the Dicer cleavage sites
than switch Y. (b) Dicer can access and process switch Y via trigger protein binding; the
switch then induces the knockdown of its target gene via RNAi (left). Dicer is inaccessible to
switch X in the presence of the trigger protein because the RNP interaction faces Dicer and
inhibits its access (right). The prevention of Dicer function causes the derepression of gene
knockdown.