I think that part of the importance of the identity of the single nucleotide in the bulge in the example boganis was originally using actually has to do with dangling energies in the structure (a 2-2 loop) that would form if one of the pairs to the side of the bulge didn’t form. The need is to make it more energetically favorable to form the single-nucleotide bulge than the 2-2 loop 
Hello, I’m new to this. Why doesn’t this solution or whatever work for http://eterna.cmu.edu/puzzle/Challeng…
Your guide was pointed out to me by somebody – probably Eli – and I found it VERY helpful! Thanks so much for putting it together.
An observation: When there is a loop between two stacks, it seems to like the guanines placed on the 3’ side of the stack – that is, in the direction of increasing nucleotide numbers.
it’s helpful to me , tks u very much
Your sequence isn’t strong enough to hold that shape together. Experiment with the 5 bases you have to work with
This has helped me spend less time on loops.
That looks awesome!
Good strategy i tried it and it works!
The links above didn’t work for me (got a page of comments, but no puzzle) - tweaked the URLs to get them to work:
-
The 1-1 Loop
http://eterna.cmu.edu/game/puzzle/305… -
The Corner Loop
http://eterna.cmu.edu/game/puzzle/306… -
The 2-2 Loop
http://eterna.cmu.edu/game/puzzle/307…
http://eterna.cmu.edu/game/puzzle/305… -
The BIG Loop
http://eterna.cmu.edu/game/puzzle/307…
http://eterna.cmu.edu/game/puzzle/307…