# [Market strategy] Direction of GC-pairs in asymmetric multiloops

Asymmetic multiloop = multiloop with different numbers of nucleotides between the multiloop arms.

I would like a strategy for designs with asymmetric multiloop.

Hypothesis: the shorter between GC-pairs in multiloops, the more opposite turning GC-pairs are allowed. Or the bigger the multiloops become, the more important the direction of GC-pairs become. In asymmetric designs the rule seem to be, that the fewer numbers of nucleotides between the arms the more opposite GC-pairs are allowed.

In a multiloop like in the asymmetri lab, there are 2, 3 and 4 nucleotides between the arms. The tendency is for greater allowance of opposite turning pairs in where there are fewest nucleotides between the multiloop arms.

So I would like a stragety for designs with multiloop with uneven numbers of nucleotides between multiloop arms.

Penalize highest if a gc pair in the multiloop, other than in the neck, turns opposite, the more nucleotides there is between multiloop arms.

Eg. The asymmetri lab. Here the nucleotide distance between multiloop arm is 2,3 and 4.

Here is Penguinâ€™s Taipan (100%) from the asymmetry lab with explanation:

Penalise with

-4 if opposite turning GC-pair is found to the left of multiloop ring where there is 4 nucleotides between multiloop arms

-3 if opposite turning GC-pairs is found to the left of multiloop ring where there is 3 nucleotides between multiloop arms

-1 if opposite turning GC-pairs is found to the left of multiloop ring where there there is two nucleotides between multiloop arms

For theory see Multiloop size and asymmetric multiloops

This is the missing strategy for market stategy nr. 23.

Dear Eli,

Your strategy has been added to our implementation queue with task id 55. You can check the schedule of the implementation here.

ETA of the implementation is 9/5/2011

EteRNA team

I now suspect that it is the two and bases between the stems, that causes this multiloop to behave more relaxed when it comes to orientation of GC-pairs in this multiloop. There seems to be less of a penalty for opposite turning GC-pairs in bigger multiloops. For more about this read here.