plasmid profile - difficulties with marker and size of plasmids.. (Jul/10/2007 )

Have any of you worked with the marker 39R?
I have a problem with the lowest band of my gel because it does not fit with the size of my plasmids.. Can it be excessive DNA?
Thanks!

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what do you mean by the lower band ? you mena the 7kpb band ??...

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Thanks for your reply!
My plasmids should be minimum 6 kb.. so are the lower bands something else than plasmids or could there something wrong with my annotation of the marker..?

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Dont compare the linear DNA in the ladder with the circular DNA of plasmid. There is no way the sizes going to match. The lower band in your sample preps could be supercoiled DNA which runs faster than the nicked plasmid. Digest your plasmid with any enzyme and see the size of the linear plasmid and then compare with the ladder.

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Thanks a lot! I know that I can't compare, thats why I have used the 39R plasmid marker. If it possible to have supercoiled DNA in my miniprep plasmid sample, then my problem is solved..! (?)

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