For RNA isolation, I use the phenol-chloroform extraction method. To avoid DNA contamination I've used the DNaseI enzyme. But I'm not sure how long after I can do the DNase treatment. Should I do the treatment right after the isolation procedure or after isolation, can I keep my samples at -80 and then apply DNAse treatment?
Short answer: Yes
A bit longer answer:
Typically, you perform DNase treatment after the RNA purification is finished to remove DNA that has remained in the sample. Whether you perform the DNase treatment right away after the RNA purification or after freezing (and then thawing) the samples should not make a difference. Just do not forget to inactivate the DNase afterwards :-)
you could treat them at either time, immediately or after storage at -80. just keep in mind for the DNase I that you have if you need to add EDTA when heat-inactivating. i like invitrogen's enzyme better than ambion's with the deactivation beads, always gave terrible organic carryover.
I agree with the previous answers. I typically use turbo DNase to remove any remaining DNA after isolation (either same day or after they have been frozen).
I typically clean-up the RNA by doing acid phenol extraction to remove DNase and any remaining DNA or an RNA clean-up kit. I try to avoid heat inactivation due to RNA hydrolysis via divalent cations. Unless you add enough EDTA to chelate any divalent ions present in the reaction buffer.
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