You could try degrading the RNA with RNase to release the protein.

Thanks Adam! However, I actually need both the dsRNA and the protein. I am trying to confirm a protein-RNA interaction. Any idea?

Elution of the complex depends upon what tag your protein has and what resin it is bound to. However, I suggest sodium chloride or potassium chloride concentration of no greater than 50 mM and 15% (v/v) glycerol. The buffer can be about 50 mM (pH between about 6 to 8) preferably but within the buffering range of the buffers. If your protein is bound to Ni-NTA, the initial buffer pH has to be greater than 7.6 for the protein to even be bound to the resin. It can be eluted with low pH such as sodium acetate (pH 5.5) or it can be eluted with imidazole at about pH 8.

I am not sure how imidazole affects stability of nucleic acid complexes, but I know from experience that high concentrations of salts inhibit binding of the nucleic acid complexes because the salt binds instead.

Adron Ung Thanks! I was actually considering 0.2M Glycine-HCL at pH 2.5. The Na-Ac at pH 5.5 is a great idea. Using 400mM Nacl may help too with the eltuion. FYI, I am using antibody (Agarose GFP-Trap from Chromotek) based pulldown.

The Agarose GFP trap is very high affinity for GFP like picomolar level. So I don't know that pH 5.5 would be good enough to separate your GFP tagged protein from the resin. It depends on how the antibody works.

The gentlest cleavage would be to use a specific protease to cleave a recognition sequence on your GFP tagged protein. If you PCR molecular clone in a plasmid a TEV sequence between the GFP and your protein, you can use the TEV protease to cleave the cleave off GFP. Just use a lot of TEV protease and wait a day or two to allow complete cleavage. Depending upon salt concentration and buffer components, might actually take two days. You could do this at pH 8.

I don't like your idea of using 400 mM NaCl. The salt binds instead electrostatically, your protein binds the negatively charged chloride instead of the negatively charged phosphates of the double helix of RNA.

Adron Ung The reason for using high salt (400-700mM, NaCl) is the same that you explained. Salt binds to protein thereby releasing the RNA from the complex. I will try a few things and will update you about which one works. Hopefully one of the protocols will :)

Anindya Ganguly , Oh I must have not understood. I thought you wanted to pull down the protein-dsRNA complex. Do you just want to know what protein is bound to the RNA so separating the protein from the RNA would make sense?

Adron Ung Yes, You're right. I think there's no easy way of getting both of them from the same elute. More so, when I will be using different gel based methods for protein and RNA identification respectively. Will use the same pulldown but two different elution mechanism for protein and RNA resp.