Are your primers both amplifying the insert?

If so then the unused insert dna may be wetting the growth plates and you are amplifying free template. Primers from the plasmid into the insert are better for proving that insertion has taken place. If this is just a digest problem then take any enzyme that has a cut site in the plasmid but not in the insert and linearise the vector and then cut with the enzyme that appears not to work but first prove that your vector does have the proper insert

Seeing supercoiled plasmid is pretty normal. For the restriction digest, check to see if any of the products are almost exactly the same size (

Thank you for the suggestion, I have used primers in the vector that either side of the insert, and it is showing a perfect band pattern. the problem is digestion and I could see a very thick and single band after digestion.

What does your uncut plasmid look like in relation to the digests? Are you sure it is supercoiled? Supercoiled is generally the good DNA that we want and is easily cut with RE's.

It is possible that the RE does not digest efficiently: Could be due to poor enzyme, poor plasmid preparation. If it is a plasmid problem, prepare a fresh prep and be careful with lysis and agitation of sample.

Try other RE's and use a control for digestion if possible to make sure digests are working. If double digests run single digest controls. Run controls with plasmid/buffer only as the nature of the buffer can effect the way a plasmid separates and can activate nucleases.

XmaI and RsrII digestion. unable to get exact band patterns.

It would be good to know what size the plasmid plus insert is supposed to be and what size of fragments are expected from the single digests

Thank you for the suggestion. I mentioned the expected sizes of bands on gel for individual digestions for the same plasmid. I don't know what is the exact reason behind this kind of unexpected pattern.

I meant what do you expect as opposed to the the observed?