Phenol-chloroform problem - (Aug/18/2010 )

Hi all! I wanted to purify my sheared genomic DNA from cell lysate, so I conducted a usual phenol-chloroform extraction followed by a chloroform extraction and then ethanol precipitation. The weird thing is during the first phenol-chloroform step, there is no cloudy stuff (proteins) at the phenol interphase, but this cloudy stuff appears during the second chloroform step.

Anyone has an idea what is going on?

I subsequently checked the purified DNA, and it looks fine.

i think that as long as you have checked your DNA and it looked fine, so you don't have to worry ...
maybe you have pipetted those along with the DNA layer in the first step ...
and they were visible to the naked eye, being added to a more organic layer " chloroform " ...
it happened with me too ...
i'll be happy if my thoughts are right .. ??