Restriction Analysis - (Mar/27/2006 )
after mini prep i used to perfomr a restriction analysis. The problem is, that restriction is incomplete, even though i use enough amount of restriction enzyme ( 10 U for 2 1/2 hours for 5 µl DNA, which concentration is not even 5 µg DNA!), but as mentioned... incomplete digestion! Could the purity of my plasmid dna be so poor, that the restriction enzyme can't cut competely?
Perhaps your enzyme isn't very good. We had that problem when we changed suppliers of our REs.
You could check the quality of your DNA with a spec or a nanodrop, if you have one.
Or you could, maybe, phenol-chloroform purify, to improve the DNA quality.