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?
RNA is unstable at basic pH. I have never heard of it being unstable at high salt.
You can simply try it by yourself. Keep aliquot of RNA as you have it and mix other aliquot with high salt. After some time check on agarose gel.
But as you're going to use sodium chloride, I wouldn't expect any problem.
Hi there,
Apart from the impact of the increase of ionic strength on RNA structure stability, there is no problem as the RNA-protein complexes are covalent.
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