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CoIP using Ni NTA, my non-his-tagged protein bind to beads! - (Jan/13/2011 )

Hi all,

I am frustrated by the CoIP recently. I am doing mammalian CoIP which I transfect protein A (with cmyc tag) and protein B (His tag)to 293 cells. I am using qiagen Ni-NTA agarose column.
Before I have done the Y-2-H screening, confirmed in the same system and then in vitro coimmunoprecipitation using TNT recticulocyte. Now come to the mammalian CoIP.
Please remember I have no problem in doing same CoIP several months ago. Beofore, the protocol is more or less the same as the Qiagen provided except that I have incubated the beads with 1% BSA for 1 hr before I added to lysate. However, since I have seen in the forum that the BSA in fact has no use in blocking the non-specific binding in the Ni-NTA agarose beads, so I stop using it.
I don't know if it is the reason behind but recently, I found that my protein A (has cmyc tag at N-term also His-tag at C-term BUT I have already added the stop codon in front of it and sequence has been checked) can bind to beads and being eluted out!!!! More weird thing is that I set up the transfection for the CoIP is like (1). Protein A plasmid + Protein B plasmid (2). Protein A + empty vector for roundup the plasmid amount. What I find out is the protein A band appear in the setup (2) is obviously stronger than (1). Moreover, the non-specific bands appeared were more than before. Theoretically, only protein B can be pulldown by Ni-NTA but not the protein A.
Anyone has any suggestions to me? I am really discouraged and don't want to do anymore, you know each time the experiment takes such a long time........ :(


Does anyone think that blocking with 1% BSA can help?