This strategy is based on the difference in pull each single unpaired nucleotide seems to have on the overall RNA structure.
Sometimes back Brourd were talking about the C-trick that can be used in 1 nt-bulges: ”It can only be used in some puzzles, because unfortunately, the interaction between G and C is very strong, so it can pull puzzles apart with ease.”
I have earlier made strategies that banned nucleotides other than yellow in loop and multiloop ring. Also strategies based on placement of boost. But not a complete strategy weighing the pull on the structure based on the color of the individual nucleotide.
I would like a strategy for all single nucleotides in puzzles (nucleotides not in strings) that says:
Give 0 for single yellow A
Give -1 for single blue U
Give -2 for single red G
Give -3 for single green C
Aptamer ring area excluded and so too the locked part of the hookarea.