plasmid prep with protein? contamination - (Aug/10/2007 )

I am trying to isolate fosmid DNA using an alkaline plasmid prep (from Sambrook's Molecluar Cloning book). The preps from some of the clones have a lot of white debris. I am not sure if this is protein, it almost looks like soap, it floats to the top of the tube once dislodged for the side. I would like to get rid of it or avoid the problem. Repeated phenol-chloroforms help remove this stuff, but it there any adjustments I can make to the buffer that will help precipitate more of this protein? out earilier. This same clone preps have also clogged Qiagen maxi-prep filters, after 3 spins to remove the cell debris.

well there is spining harder...and longer. (after solution 3 in alkaline lysis)
also be gentle when moving the solution, to avoid break these white lumps
for maxiprep, my lab also employ gause filters to removed the larger lumps.

i would suggest you to buy sterile compresses. They act as very good filter

centrifuge at higher xg and for longer. Manytimes we fish out the white stuff with a pipette tip so that it doesnot clog the maxiprep filters.