Many games have the ability to support user-developed add-ons. In the case of this game, an API that permits one to write algorithmic solvers would be very cool. I can see automating some algorithms to get a puzzle at least part of the way to solved and then letting the brain take over for the final tweaking. It would not be too hard to write a simulated annealing approach that uses the energy levels and the solution criteria as “goodness” measures if one could access the puzzles this way.
It would need functions to iterate over the list of nucleotides, identify if a nucleotide is supposed to be in a stack or a loop, query the size of the loop, switch iteration to the nucleotide it is supposed to be paired with, query the energy levels and solution criteria status, set nucleotides and flip nucleotide pairs. Maybe some others I have not yet thought of. Ideally this would be a little window one could pull up and write the code in Python, Ruby or Javascript (or something similar) and have it saved to the users account as a macro they could apply to a puzzle.
A macro need not satisfy the puzzle to be useful. For instance, the simplest macro could be used to just set up all the initial A<>U pairs that seems to be a typical starting move for many and let the brain take over from there.
edit: thought of some additional functions.