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However, my PI said something about being concerned that these enzymes didn't cut 100% so she wants to try a different one that will just linearize by cutting inside the promoter? I don't quite understand, but this tool will be useful to me regardless. One of the promoters would be about 400bp in size, while the other would be about 1400. I can cut with enzymes just outside of each of the promoters as we designed them that way. So ideally I'd like a list of enzymes which are unique to one plasmid or the other. The restriction enzyme digest is primarily to confirm the purity of the plasmid isolated from specific colonies. I am dealing with two highly similar plasmids, of similar size (7300 vs 6400) which differ in the promoter used. I am attempting to find a list of enzymes that cut one plasmid, but not another.
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