[Strategy Market] AU pairs are indifferent
Note : This is a submission in the EteRNA Strategy Market
The alignment (parallel or criss-cross or random) of AU pairs does not have a big stability impact for a design when
- within stacks that are not in junctions or next-to-junctions - of stacks and loops
- the “string” (or its two halves) is not symmetrical in the sense of aldo’s mismatches ( http://getsatisfaction.com/eternagame… ).
While this is the case the AU pairs can be substituted with the same amount (or that n-1*) of GU pairs, or an appropriate amount of GC pairs. While being plainly useful for the design’s energy, these “indifferent” pairs, or their substitutes, are the most mobile options for tweaking towards better folding-likelihood in my experience.
*to allow for parallel structure.