[Strategy market] [Switch] Zero GU’s as end bases - Switch strategy

Strategy Market Strategy Market - Switches
1

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.

2

Dear Eli,

Your strategy has been added to our implementation queue with task id 146. You can check the schedule of the implementation here.

Thanks for sharing your idea!

EteRNA team

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Just wanted to add, that this strategy might be a little premature. I based it on what data I had, which was too little. I later learned about Rfam - a database over natural RNA, switches included.

Here is what I can say based on what I see in Rfam on Riboswitches. Gu content is relatively low. GU mainly occurs at closing basepair and in short strings too. The GU-pairs in stem are spread out. Not beside each other. And mainly in longer strings. I did find one double same turning GU at a string end, and a triple one inside a string. Ok. I also found one with twisted GU’pairs. So no clear pattern here.