[Strategy market] Sameturning GC-pairs blocks at multi loops

I have earlier made a strategy about double sameturning GC-pairs. Penalizing if there is too many.

This does not take into account the placements of these double blocks of GC-pairs. It is my experience, that they seem to make trouble if connected to a multiloop, as in this Eterna ensemble Shape test design (97%) design 05, sparse 5.

The GC-pair block makes the otherwise stable and correct turning GC-pair in the multiloop, unstable. GC-pairs in blocks gets higher free negative energy, and higher free negative energy is often stabilizing. But having two GC-pairs turning the same way, makes the string they are on, bond less. A string gets stronger, if basepairs are flipped, compared to each other.

For this strategy, I define multiloops as multiloops having three or more strings. (In multiloops with two strings double GC-pairs is allowed in connection to loop ring.)

Also the multiloop should have at least 1 or more nucleotide between the GC-basepairs in the multiloop ring.

I would like to ban sameturning double GC-pairs, if connected to multiloops.

Give -2 pr each.

Neck area is exception to the rule for banning GC’ blocks at multiloops. Here sameturning double GC-pairs are allowed at multiloop end of the neck.

Dear Eli,

Your strategy has been added to our implementation queue with task id 80. You can check the schedule of the implementation here.

Thanks for sharing your idea!

EteRNA team