What are the probable reasons by which there are chances of introducing endotoxin during plasmid isolation? How much chances are there to introduce endotoxin through air?
My understanding is that endotoxin is a general term for bacterial membrane components that can cause an immune response. When you purify plasmid from E. coli, the endotoxin should be removed, but, there is always a potential for a tiny bit to be retained. Whether this matters really depends on what you will do with the plasmid. Qiagen makes a maxiprep kit that has an extra step to eliminate endotoxin which you might want to use. Also, autoclaving everything and using sterile technique is advisable to minimize bacterial contamination from other sources.
Most endotoxins in plasmid preps are not introduced (though they can certainly be introduced by using non-endotoxin-free buffers and plasticware and not keeping sterile technique), but come from the cells themselves from which you purify the DNA. The most important thing then is to use a purification process that eliminates them. The Qiagen kit mentioned above is pretty decent for most purposes.
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