Hi there,

How do you make plasmid size estimate? Is it on agarose gel? If yes then don't forget plasmid is naturally circular and therefore you have to linearize it (using restriction enzyme cutting only once)  if you want to estimate its size accurately. The circular form of plasmid always tends to run faster on gel than the linear form because the former is more compact.

Hi there,

How do you make plasmid size estimate? Is it on agarose gel? If yes then don't forget plasmid is naturally circular and therefore you have to linearize it (using restriction enzyme cutting only once)  if you want to estimate its size accurately. The circular form of plasmid always tends to run faster on gel than the linear form because the former is more compact.

I agree with liger. You have to cut and make the plasmid linear to estimate actual size. Here you can find some pictures and detailed explanations for migration of linear, circular, open nicked and supercoliled form of plasmids. 

http://users.wmin.ac.uk/~redwayk/lectures/analysis.htm

http://www.vivo.colostate.edu/hbooks/genetics/biotech/gels/agardna.html

Hi.

Otherwise, in case you already used a restriction enzyme, and if the plasmid has 2 restriction sites (e.g. in plasmid + insert) then the plasmid is cut in 2 fragments.

If those 2 fragments have the same size, they can mimic a single smaller fragment on agarose gel. In your case, your observed size is more or less twice as small as the expected size (but not exactly though... are you sure of this 2.7 kbp size ?).