We tried to run uncut and cutted plasmid DNA using the High sensitivity DNA chip using Bioanalyzer 2100. The uncut plasmids showed peaks as expected, BUT we were not able to see anything on the uncut plasmid, like it was empty. We run agarose gels from the same samples, so the uncut plasmid was there, for sure. We repeated the bioanalyzer runs and the results were exactly the same. My question is, can we actually succesfully run uncut plasmid DNA using any of the Bioanalyzer chips? Or there is a special sample preparation that has to be done for this particular purpose? If we can't, What is the issue? It has anything to do with the supercoil formation?
We are looking forward for your input, since we were considering the use of the bioanalyzer for plasmid quality control. Please, advice! Thanks!