We perform Co-Immunoprecipitation with HA-tag and anti-HA magentic beads (Pierce).We have a mild washing protocol (4 washing steps , 5min) and usally we detected many proteins binding unspecific by mass spectrometry (untagged control). Now we added a 30 min incubation step at 4°C with benzonase to our protocol and the backround is almoust "empty". Only a little number of proteins with a very low intensity still bind unspecific to beads. I allready performed a GO-Enrichment of all proteins I´ve lost by benzonase treatment, and they are not specific DNA/RNA - binding.
Would DNA or RNA bind to the surface of magentic beads at all?
Does somebody have an idea what could have happend?
I really dont have a explaination for that....
thanks for all ideas
My guess is that the nucleic acids in your extract are mediating a non-specific interaction between proteins in the extract and the beads. This could involve electrostatic interactions with the anionic backbone of the nucleic acids, hydrogen bonding with the bases, and/or hydrophobic interactions with the bases.
My guess is that your magnetic beads suck, they are not properly prepared to make them hydrophilic enough to reduce nonspecific interactions.
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