Why should RNase treatment be followed by phenol chloroform - (Nov/25/2007 )
Following plasmid purification and subsequent agarose gel electrophoresis I determined that my plasmid prep was contaminated with RNA. I have read that I could treat the preparation with RNase which would break down the RNA. Why does this have to be followed by the use of phenol chloroform though - what does the phenol chloroform do to the RNase and how? - many thanks!
To get rid of RNase.
Phenol extraction will get rid of the RNase, although i don't think it is necessary to do so. I always used to make homemade DNA minipreps with a last step of resuspending in TE + RNase. I never cleaned up the preps any further and had no problem with it.
The order of the process really depends on your next application for the material. I'd say having leftover RNase protein contaminating your preps is probably a bad idea and removing the RNA prior to Phenol extraction is best.
UNlike many other enzymes, like DNase for example, RNase is very stable, even taking boiling in its stride (you used to make DNase-free RNase by boiling the RNase prep). The only way to stop it is to physically remove it from the system.