1. My overexpression plasmid (empty vector) is 8200 bp. But it is showing 4000-5000 bp always in the agarose gel, which might be for the supercoiled conformation. But this large difference is acceptable?
2. The same plasmid after digestion ( EcoRI & BamHI) becomes 12000+ bp in the agarose gel. Shouldn't it be around 8000-8200 as it becomes linear after digestion? If it becomes 12000+bp which is too big, is this acceptable? and why it becomes bigger.
If the plasmid is really 8kb then the supercoiled version runs much faster, I think around 4-5kb is probably ok. But don't make any serious conclusions from the supercoil size, you need to linearize or digest your plasmid to really know the size.
For your second question, do you see a linear band at 12kb or is the sum of the smaller bands? If you see a single band after digestion at 12kb then that is likely the actual size. If you are just adding up smaller bands and they add to 12kb then maybe you just have some incomplete digestion. Does EcoR1 and BamH1 release the insert?
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