Using gel electrophoresis how do you determine if you have a pure plasmid preparation?

Answer 1

dkstringer's right; the smear he mentions is the genomic DNA which will be all sorts of different sizes. A clean gel with only the appropriate band(s) tells you it's a good prep. It's often useful to do a linearizing cut, too, to get an accurate size reading. That should also take care of the potentially confusing supercoiled band.

Answer 2

Actually....when you run plasmid DNA that has not been cut by a restriction endonuclease through an agarose gel you're likely to see two bands...one representing the supercoiled DNA which runs a little faster then the band that isn't supercoiled.

If you see a smear or several bands(more then 2) then the prep isn't very pure.

Answer 3

load different amounts in different lanes. On staining, you should see only a single band in the gel. Additionally, cut the plasmid with a restriction endonuclease that you know cuts the plasmid in a single site. On electrophoresis, you should still see only a single band.

Answer 4

There will be only one spot on the paper showing only one substance is present