Degraded phenol questions - (May/26/2010 )
I've started doing DNA extractions with phenol/chloroform for the first time. I got good DNA concentrations values with A260/A280 values around 2. However, the A230/A260 values are around 0.8-1.
I started looking for a reasons for the low values and came across some information that indicated that phenol turns pinky-brown when it degrades... the same colour ofthe phenol I was using for my extractions.
So my question are these:
1) Is it likely that the degraded phenol caused the high level of protein in the final DNA extract or should I continue to look for other reasons for the low A230/260 value?
2) I am able to get a PCR product out of my DNA extraction with the degraded phenol, should be concerned about quality of the PCR product?
3) Is it worth trying to rescue the DNA extract by trying to remove the protein or will the DNA be too damaged by the phenol to make it worthwhile?
Here is an interest blog about phenol-chloroform extraction (http://bitesizebio.com/2010/05/03/practical-application-of-phenolchloroform-extraction/). It describes briefly what to do with the pink oxidized phenol...
Hope it helps.
Thanks Lsek for this link. It's a great article!