Dear colleagues,

I am trying to figure out the principle of manually designing gRNA in order to clone it into plasmid. I know, that I have to add sticky ends to my oligos to make cloning them into the vector possible. My plasmid after cut would have stick ends like this:

5 'G A A A .................... G T T T T A 3'

3' C T T T G T G G .....................A T 5'

So as I understand my oligo should look like this:

5' C A C C XXXXXXXXXXXXX 3'

..............3' XXXXXXXXXXXXX C A A A 5'

But since now I have been using Benchling to simulate cloning gRNA into the vector, and this tool were adding proper overhangs to my oligos by itself. Now I looked closer at it and I saw, that in some cases it adds additional complementary base pair and I can't figure out why. I attach picture, where you can see two sites of BsmBI cut and how two different gRNA were "cloned" by Benchling. I have marked this base bair which I am talking about by red arrows. So my question is, if there is any pattern that I should follow while designing my oligos manually? In my case part that is cut out by BsmBI doesn't encode anything, its just a space to inserting a filler.