Getting rid of RNA & RNAse contamination in DNA sample for PCR - (May/16/2007 )
The bacterial DNA I extracted for use in PCR has RNA in it- I've added RNAse to get rid of it, but now I'm stuck with RNAse in my PCR template that'll chew up my Taq polymerase. How can I purify my DNA to use in PCR??
I don't really know...but I thought I would answer just to sympathise!
Hopefully someone with an idea will come along soon...
i extract my bact DNA using standard genomic extraction protocol... add RNase too andthey are OK. RNA is more unstable compare to DNA and tend to degrade faster. when you do PCR, the high temperature and the up and down temperature of PCR cycles... should degrade most of the RNA. That is why doing RNA work needs extra care to prevent RNA from degradation.
By the way, is it really your RNase cause Taq not working? or something else? shouldn't you wash your DNA pellete with 70% ethanol and 100% ethanol while you precipitate you DNA after extraction? if the washing is OK, you shouldn't hv any remaining RNase in your pure DNA?
If you want to get rid of your RNase you can phenol:chloroform extract your DNA after the RNase digestion.
There is no way a RNase can chew up your Taq polymerase. Taq polymerase is a protein enzyme, not a ribozyme.
The only way your RNase can cause problems in PCR is if it,s not clean and have traces of DNase in it.
agree with u
agreed with auldmok.
Just use the phenol chloroform method.
thanks for the replies everyone,
i'm going to keep the RNAse in the PCR reaction and see what happens...
normally the RNAse should not affect your PCR. Except you need to take in count the glycerol that came with your RNAse.
if you're so afraid, do the pH chlo method. Otherwise, look for bead-coupled RNases. I know ambion sell someone, but it may exist cheaper