gen synthesizer 6 /14
in this proble, we need to make only two pairs
and i plug in U(upper part) and A( lower part) in first pair.
It seems OK
BUT when i changed order like A(upper), U(lower), screen show me that it can not be folded into target structure.
AU pair and UA pair is same, right?
then Why this change cause this problem?
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The orientation of the RNA matters. You can see that the free energy number between the AU pair and the GC pair change when you orientate the AU pair (If you can’t see those numbers, press G to activate them).
Another reason for what you saw, is that the U in your AU pair might have binded to another A base in the natural mode when you used an AU pair, but couldn’t bind to it when you used a UA pair.
If I didn’t explain this properly please tell me and I will elaborate, but you will learn more about this later in the progression.
And when you ask your next question, please write the question in the title (in this case something like “Is AU different than UA?”), just so it would be easier to understand from the main page.
ok thank you for your reply.