The strategy should work for FMN, FMN/MS2 switches and microRNA turnoff switches.
Here are a few things that are already made into separate strategies, but are central to this strategy.
- Reward knotting of tails at the ends of the RNA sequence. Preferably minimum 4 base pairs.
This is a variant of my former strategy for tails. Just here I wish that tails should always be made to pair with each other. And penalize if they are not.
- Reward aptamer for being static in one end. Penalize if tails are no tied up with each other.
Similar this is also being a strategy already by jandersonlee. However it is also important here. These two requests above, are often one and the same thing.
Aptamer after static stem of tails
- Is there an aptamer right after the beginning neck which is made of the made of knotted up tails? If so this determines the positioning of the static stem to be after the aptamer gate. Reward - if there is a static stem there.
Example to the right (Blue = static neck followed by aptamer = orange):
No aptamer directly after static stem made of tails
- Reward if there is a static stem after that aptamer gate (grey), which is furthest away from the MS2 sequence.
Example to the right (Static neck = blue placed after the grey aptamer gate, which is the aptamer gate furthest away from the MS2 sequence)
Aptamer gates are typically 3-5 base pairs long. I see the current trend point more towards 4 or 5 than 3 base pairs of length.
Distance from static stem to aptamer gate
The static stem should be next to the aptamer gate - decrease reward the further the static stem is away. (0 base distance is good, 1 base distance is fine and up to 3 regularly fly.)
The static stem should be at least 3 base pair long. 4 or more is better.
The static stem (the one that is not the stem at the non moving end of the aptamer.) shows up before the MS2.
In rare cases there are an equal distance between the MS2 sequence and either of the two FMN sequences, reward placement of static stem near that aptamer gate where neither the aptamer gate nor the FMN sequence pair directly up with the MS2 sequence.