I had a problem when trying to clone a 1.8kb insert into a 8.3kb vector. I first digested both insert and vector and purfied from the GEL. Then I did a rapid ligation and transformation afterwards. But I can not even see a single clone.
One thing to add: I checked the ligation on the GEL. I can see negative control (no ligase) with clear two bands. For others, I can see smear bands with larger size (bigger than the insert + vector). [see attached pics]
I speculate that this ligation might works but not properly, but I do not know the possible reason.
I would like to ask you: if the ligation is successful, what band would you see on the GEL? Is there something wrong if I see smear bands with unexpected larger size?