I routinely purify FLAG-tagged protein-RNA complexes that have been crosslinked with formaldehyde using FLAG peptide. Alternatively, it is possible to elute proteins from FLAG resins using high salt (3M NaCl) buffers.
My question is: is RNA integrity preserved at such high salt concentrations? I believe protein-RNA interactions should remain stable due to formaldehyde crosslinking but I am afraid high salts could trigger RNA fragmentation. Does anyone have any experience on eluting protein-RNA complexes with this method?