Quromen

I am talking about the one near to the dna bands, sky blue colored

I ran dna in a 1% agaraose gel and in 1x TAE, i saw a strange blue region somewhere in the middle of the gel. I used ethidium bromide to visualize DNA. what could that blue region be? I tried to move gel around thinking that it may be the UV light that i am using, but that did not change. I even used another UV machine and had same result.

i would tell there was contamination with nuclease that caused the smearing

Contamination

Makes me laugh brother, go read and understand the complexity of the cellular physiology. Putting pile of parts does not make a working machine. Cell is even more complex than that, mentioned earlier cells needs specialized cues to function properly.

Lets say there is a bacteria X with 10 different types of plasmid in it. And i want to isolate each of the plasmid and identify them. How can i isolate each of these 10 plasmid without contamination? Can it be done based on size, Centrifugation based on the kb of the plasmid? I need to know the way to isolate each plasmid separately.