Plasmid size vs supercoiling

[Johan de Boer]

Hi,
We are trying to isolate a recombinant molecule that consists of about 3.5
kb vector and 2.5 kb insert. When we run the (uncut) plasmid DNA from
minipreps on an ethidiumbromide/agarose gel the major band runs at a
certain position, but one clone runs much slower (at approximately 2.5
and 5 kb linear markers respectively). The faster ones turn out to be
just the vector, when we linearize the DNA with an enzyme that cuts
one of the cloning junctions. The slow running DNA would look promising,
however it looks exactly the same as the others after linearizing it.
Is it possible for a plasmid from two colonies to have such different
supercoiling patterns?
Has anyone seen this before?

Any ideas would really be appreciated

Johan de Boer
jdboer at sol.uvic.ca
Victoria, Canada