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Sequences
You can download all Scaffold and staples sequences here.
Figure 1: The sequencing data of the scaffold.
Figure 2: The expected secondary structure of the RNA scaffold predicted with CLC Main Worckbench. The colors indicate base pair probabilities of the different parts of the structure going from 100% to 0% in the order purple, blue, cyan, green, yellow and red.
Figure 3: 2D blueprint of the structures used for the FRET experiments. The edges are consecutively numbered from 5’ to 3’ of the scaffold. Z and V staples are colored blue and green, respectively. The T-linkers are not shown. The purple sequences are the modified staples with Cy3 (green) and Cy5 (orange). The staples forming the lock are colored grey, but the lock and toehold are not shown.
Figure 4: Dicer substrate octahedron design blue print. Four staple strands have a 2 nt 3' overhang (yellow), the rest of the staple strands (blue) have no overhangs. The scaffold (red) runs through the structure in the same way as in the RNA/DNA hybrid structure. The black frames indicate which sides are intended to be cut by Dicer. 5' and 3' indicate the ends of the scaffold strand.
