[Strategy market] Brourd's 2-2 loop strategy

Here is the natural continuation of Brourd’s 1-1 loop strategy. I think Brourd’s idea explains why the GU/UG puzzle trick for the 2-2 loop, don’t work in lab.

G and U are attracted, if opposite to each other. Even if in a 2-2 loop. Which means attraction between structures, we want to stay apart.

This is Wisdaves design WisTest from Shape test lab:

On the shapedata you can see, that the 2-2 loop joins basepairs, as there is no yellow nucleotides in the loop ring.

So far none of the GU/UG 2-2 loops have worked.

The Eterna energy model don’t allow for GC-pairs to be opposite each other in the 2-2 loop, so those we don’t have to worry about. The same appear to be the case with AU-pairs across each other.

I would like a strategy that says:

Give -1 pr. each GU pair opposite each other in a 2-2 multiloop.

So for the first picture shown, give all in all -2.

Dear Eli,

Your strategy has been added to our implementation queue with task id 77. You can check the schedule of the implementation here.

Thanks for sharing your idea!

EteRNA team