I have the pairs done but the large and small circles are not coming together and when I try to change the sequences, the blue and red RNA’s don’t join together.
I’m guessing this is the puzzle you are having trouble with:
Generally try place the GC pairs and AU pairs first and then add in the GU’s. If it destabilizes the puzzle, take it out and place it somewhere else.
If that is not enough, try place the GU even if it destabilizes, and flip its surrounding base pairs.
GU’s can line up, but they generally don’t like to cross, unless some rare cases at ends of stems.
Hope this helps.