I would like a strategy that says, give -1 if a GU-basepair as closing basepair for a string (no matter which end), in either of the two shapes of a switch lab puzzle. Give -1 pr extra, if there is more than one.
However, give only half penalty if the GU closing basepair turns up in a string which is longer than 4 nucleotides.
Also give only half penalty for GU’s in connection with a bulge, as I have seen some GU’s do okay in FMN aptamer 2.0, when in connection with a bulge.
A little on the background for this strategy. I have noticed that GU-basepairs at ends of a string often does bad. In Simple RNA Switch, the highest scoring design that has a GU at end position in the string scores 80 %, (Default title by Pmlkjn) and the GU-pair is not stable. Highest scoring one that has a stable GU-pair is at 68%. (First attempt by Flash Dave) and the GU turns up at the end of the 7 nucleotide long string in the unbound shape. I think the longer the string, the more tolerant to GU pairs as closing bases. Highest scoring design with a stable GU end pair is at 68% (My first fold by Bill Zhu). The GU end bases have a habit of showing up in the lower scoring designs and in higher abundance.
A few GU’s at end bases do relatively good, when in connection with a bulge (FMN aptamer 2.0 lab) In our current lab FMN switch 2.0, a GU-end basepair do turn up in high scoring design (Starting point 81%) But the neighbouring basepair is unstable. And though GU’end bases looks as having a certain potential in this lab, I do think that GU’s at endbase position is overall a bad idea, especially in shorter strings.