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 Penguin’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.