I would like to ad a strategy so specific spots in a RNA designs are energeticly alligned with the energy in the neck.
This strategy will only work for designs with a neck a length of 7 nucleotides and in medium sized multiloops, (not in the star lab, the cross lab and the bulged cross lab) Also it will work best in designs with center multiloops connected to at least 3 strings (neck included), which excludes the finger lab.
I have formulate a general strategy. Also I’m aware that energy still pose a problem in programming, so I prepared for that this hypothesis will wait some time before testing.
If collective neck energy is high, don’t allow lowering of energy in multiloop – all GC-pairs should turn in the right direction. Penalize if this is not the case. In other words if energy is at it’s max in the multiloop and hookarea, then the neck should preferably be of collective energy of middle or high. Penalize if that is not the case.
If collective neck energy is low, energy should either be a bit lowered from the max posible in the multiloop – in other words, allow opposite turning GC-pair in multiloop, at neck end, and/or the energy in the hook end of the neck should be a bit lowered. Penalize if energy is not lowered at multiloop end of the neck, and/or lowered at the hook end of the neck.
Other patterns I see:
High energy hook, high energy design
Low energy hook, low energy design
Low energy multiloop, low energy design
I might need a bit of help making a strategy for these tendencies.
Here is the reason why I would like a strategy for the neckarea, that takes into acount what the energy is on overall, in the multiloop connected to the neck, in the hookarea. Here is the theory and data behind: