Using INTRON's DNA-spin Plasmid DNA purification kit to extract plasmids from specific E.Coli strains, my team and I have encountered numerous plasmid dimerizations that lead to over-weighted plasmid DNAs which are hard to identify whether they are the wanted plasmids or other common impurities. We have followed the protocol given by the producer but have not achieved notable success under our lab conditions and we are needing help right now.
What host strain are you using? If you are in a RecA+ host then you are always going to get a mixture of monomer, dimer, trimer etc.
If you are sure the strain is RecA- then you should not be getting dimers if the plasmid is a monomer to begin with. What makes you think you are seeing dimers?
After performing plasmid extraction, we confirm the presence of the product (expected size: 6000-7000 bp) via gel electrophoresis (1% concentration, approximately 30 minutes running time, TAE Buffer, RedSafe applied, 10000bp DNA ladder for indentification) and observe under UV 254nm light, we notice a single DNA product that is over 10000bp, notably larger than our wanted plasmid. This phenomenon has occured for 3 out of 4 times when performing the extraction procedure
I doubt you are getting actual dimers because if recombination was actually occurring you would see a whole panalopy of multimeric forms. I guess it is possible that you are getting some concatemers where plasmids Are intertwined but not dimers.
if it really is a problem then you might try to retransform and/or try a different host like DH5alpha.
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