Purified DNA fragments are bigger than unpurified - (Mar/19/2014 )

I'm using the GFX PCR DNA and gel purification kit to purify DNA fragments after enzymatic digestion. When I check the cloning efficiency by PCR the fragments size are ok. After digestion and purification the fragments appear higher in gel. Someone can help me to understand this? 

Double check your cut site to make sure that you are getting the correct dropout size. Salt concentration can have an effect on the migration of DNA in gels, but from your post I would assume that the size difference is significant.

Some restriction enzymes bind to DNA and DNA shows bigger band.

SnapGene software shows you which enzymes bind to DNA.