| | Re: How can we justify the appearance of supercoiled plasmid
It sounds like a lot of you are saying HOW to deal with supercoiled DNA in gel electrophoresis, but not WHY it is there. That is what I assume the question "how can we justify the appearance of super coiled plasmid DNA on a gel?" is asking.
I can think of three reasons, but I don't know how accurate they are.
1. Salt concentration of your reagents used in the miniprep could have an impact. For example, if your reagents were mixed wrong and the salt concentration is too high, your plasmid will supercoil. I don't feel comfortable just making up some kind of explanation for what kind of biochemistry is going on there.
2. Vector problem? I can't describe what, though.
3. Something in the bacterial growth medium?