I want to check if there is RNA that is still bound to proteins in the organic phase, when performing RNA extraction using TRIZOL or Phenol-Chloroform. Is there a way to recover or visualize/quantify that RNA?
Or are all protein-RNA interactions broken?
Definitely in TRIZOL or similar, all interactions are broken since the reagents contain derivatives of the denaturing agent guanidium. Phenol/chloroform is usually applied after Proteinase K digest, so there is no question of bound protein.
If you have an unusual protocol or purpose, please post more details and I'll be happy to have a look.
Best,
A.
Definitely in TRIZOL or similar, all interactions are broken since the reagents contain derivatives of the denaturing agent guanidium. Phenol/chloroform is usually applied after Proteinase K digest, so there is no question of bound protein.
If you have an unusual protocol or purpose, please post more details and I'll be happy to have a look.
Best,
A.
Thank you everyone!
@anna: I work with yeast in which I have a wild type strain and a mutant strain(a gene of interest deleted, the protein is known to affect RNA-Protein interactions). When I use the Trizol method for RNA isolation, I find that the RNA isolated is consistently lower in the mutant strain compared to the wild type strain for the same amount of cells. I am not sure if this is because of difference in transcription/degradation or if its because of RNA sticking more to the proteins in the mutant strain and being lost while extraction.
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