I am performing agarose gel electrophoresis of plasmid which is 2.5-3 kb in size. I am getting more than 3 bands, after restriction I got single band at 3.5kb in size. Electrophoresis conditions- 0.5X TBE, constant voltage 150V. why am I getting more than 3 bands after agarose gel electrophoresis of plasmid?
The closed plasmid comes in three different forms: nicked-relaxed, supercoiled and circular single-stranded. All three forms have a different tertiary structure and thus they run differently on the gel. This should look like this (image from here, there you also find a more detailed explanation):
When you digest the vector you linearize all the forms and they all have the same tertiary form.