I carried out digestion of vector pLentiv2 (14kb) with restriction enzyme BsmBI at 37C for 3 hours, and performed a gel extraction to purify the cut DNA fragment for cloning. I ran both the uncut vector in lane 2 and the cut vector in lane 3 on a 0.8% agarose gel. They travelled the same distance on the gel and I'm confused as to whether this is supposed to happen or if the digestion was unsuccessful. Could i proceed with cloning with the cut vector ?
I presume the enzyme only cleaves it one time, in which case I would not worry much that they are running with similar size. Nicked circle and linear DNA do run at about the same size. However it would appear that your restriction digestion has resulted in a significant degree of degradation of the plasmid as evidenced by the smear running below the band. This is something that you should be highly concerned about. It may be that you have a poor DNA prep or it may be that you have introduced a contaminating nuclease somewhere.
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