The kDNA preparations we get from TopoGEN sometimes have what looks like a small bit of decatenated kDNA. Why is this?
Kinetoplast DNA (KDNA) is mitochondrial DNA from an insect tyrpanosome and is a conglomerate of mostly 2.5 kilobase minicircles interlocked as a collection of catenanes. Since the KDNA is isolated from the whole cell, there can be a carry over of host (genomic) DNA. The amount of host DNA will vary somewhat from lot to lot but should not exceed 20% of the total. A small amount of this high molecular weight cell DNA will not interfere with topo II assays because the decatenation products do not comigrate with the contaminating host DNA. In some cases, if the gels are run for very short times, under conditions where the resolution is poor, there may be complications; however, this can be corrected by running the dye front further down the gel. It is also important to include a KDNA marker (negative control) in each and every gel to be sure that you do not count stray bands as topo II activity.
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