plasmid prep question - thick white material? (Aug/08/2007 )
i assume that there is RNAse in your resuspension buffer.
But if you are growing a midiprep say 100ml, this is insufficient exposure to RNAse to remove all RNA. Thus it would be better to RNAse treat your DNA as a separate step. (perhaps step 12)
Similarly if you are growing a 100ml prep, the protein contamination in the prep will be more apparent. As you have already suggested, phenol/chloroform extraction should remove this protein. (step 13)
I have experienced the same problems with some of my preps, the amount of the white junk that looks like soap varies depending on the clone I prep. The advice given to me was longer and harder spins ( I always spin at least twice) after lysis and run final supernatant through sterile filters to remove more of this stuff before precipitation. Then I do a couple phenol:chloroform extraction and this remove even more of the white protein(?). The one more ethanol precipitation. Good luck