plasmid digestion - problem with enzymes? - (May/27/2013 )
I have digested pUC19 plasmid with BamHI and HindIII enzymes (3h, 37 degrees) and then run the electrophoresis. The circular (uncut) plasmid was about the right size, but the digested samples resulted in a bands of higher molecular weight. BamHI and HindIII are the unique sites so I expected to see linearized plasmid.
The enzymes I used are really old and I want to know if they are still working.
I've attached the photo of my gel - can anyone explain it?
An uncut plasmid preparation contains three forms, cut, nicked and uncut (this occurs spontaneously in a preparation) that all travel through the gel at different speed. Maybe your enzymes are too old and thats why only a fraction or none of have been cut and you see all three forms in your gel. Maybe you should try with new enzymes.
-sorry ignore comment it this was the case all three forms would appear in the same lane.
I will definitely order new enzymes.
Now I want to understand what has happend with the plasmid. Could it be the result of heating: the plasmid was not digested but it has changed it's conformation from circular to nicked.
How old is really old? I've used enzymes that are 5 years old (but stored properly and treated with care) and it's been fine. You could try a sequential digestion (digest with BamHI first, then with HindIII).
I'm new in this lab and I'm not sure about storage conditions. But the other old enzymes from the same freezer work fine. So I am curious about what could've happened with these two.