Blocking is a puzzle-solving strategy that involves identifying unwanted base pairs and making changes that prevent them from forming. Typically, the unwanted pairs involve bases that should be unpaired in the target structure.
How to Block
- Identify the unwanted base pairs. Press spacebar to view your RNA in natural mode. Use CTRL+click to highlight new base pairs that form. Press spacebar again to view your RNA in "target mode". Look for highlighted bases in loop regions.
- Change bases to prevent unwanted base pairs from forming. If A's in a loop are pairing with U's somewhere else in the molecule. Try changing the A's to U or C. This is particularly useful in bulges.
In the picture on the right, nucleotide 169 is a blocking point, with an A instead of a U at that spot, the puzzle would be unstable.
Note that base 172 is also a blocking point, with this A properly mismatching the A at 332.
"The C Trick"residue is used to "block" a bulge. This prevents the formation of the unwanted structure shown in the top panel.