Here I have a basic question, usually, a linearized plasmid will run slower than CCC plasmid after it was digested by a one-cut R.E.But now my linearized vector runs faster than the integrate one after being digested by one -cut-site R.E. I have change two RE, the same case happened ,these two band runs at the same speed.Who can tell me if it could happen in the normal situation?

Thanks in advance.

Yes, it is quite normal. You should based on the linearized plasmid to judge the size. It is very hard to predict the moving length of the uncut plasmid.

the uncut plasmid also runs as to isoforms, supercoiled and not

I realize this thread is old and kinda dead, but today I noticed something similar though even more strange, so I'll post this anyway. In a 0.7 % gel the linearized vector was slower than the uncut vector (just like I had supposed) but in a 2 % gel it was the other way round!!! If someone has an explanation for this or has made the same experience I'm eager to hear about it...