I can see how this is a problem for ribosomal proteins.  One can't make proteins without ribosomes, so you can't ever get an "untouched" control protein to test the answer to your question experimentally.

I'm afraid the most plausible explanation ("null hypothesis") needs to be that there is still some RNA there.  The absorbance method is necessarily less sensitive than the fluorescence method.  (Absorbance is like trying to see a star against daylight -- fluorescence is like seeing it against the night sky).  So it makes sense that with a good prep containing little RNA, the absorbance can't see it, but the fluorescence can.

There's no such thing as "cleared" :)  The best it's going to get is "good enough for your purpose".  So, you should probably try to set a standard for how good is good enough.  Quantify how much RNA is still there with a standard.  

Hello Emily,

                      I didn't understood your problem. Are you interested in getting a purified RNA or Protein? If you want to get rid of RNA, then i think RNAase treatment will do the job for you. And if you are interested in RNA then you can get rid of protein by phenol chloroform precipitation method.

Thanks both forma your answers. 

Dear Manojkumar i am interested un purify proteín. I already used  RNAse/DNAse treatment after sonication and then I have isolated ny protein by IMAC with nickel, and additionally I washed it with 2M NaCl to eliminate nucleic ácid. According with Nanodrop my protein isla cleaned but with fluorescence (BrEt) I still see conramination bit less. I think Jhon is right...because of my protein is ribosomal( translation activity) its affinity with RNA is too high. I will start my next assay with this resulta. Thanks