In the first few strategy guides I looked at, I haven’t seen anything about how to distribute G-U pairs when we’re required to include a minimum.
If you’re working on a large molecule, is it better to scatter single G-U’s all over, or to group them?
Is it better to put them in short stacks or long stacks?
Here is a little advice for the GU-placement. Know we don’t have a 100 % perfect method to place them yet. This is just general advice.
It is generally safer placing GU’pairs in longer strings and to spread them out. If you do put them next to each other, make sure they line up and are not crossed opposite to each other. And do only do this in designs with real long strings, like 7 basepairs or longer. And I’m still not advising it, just saying that you might get away with it.
There is a short section on GU-placement in section 8 in here.
I have written a couple of strategies on GU-placement according to what I see as good and bad.
Also go watch “Past labs”, under “RNA lab” in the menu. Here you can check for yourself how GU-pairs are placed in a legal way. Wacth the winners and shift to shape data view. If the stem is blue where the GU-pair is placed, and for the neighbour basepair/s, then it is placed in a stable way. Here is a post on how to read the shape data
Good luck with the lab designing!
It’s definitely better to put them on the long stacks. Usually, you should scatter them all over, but on the long stacks, you can group them all the way across sometimes, if you put the U’s and A’s all in rows.