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Immunoprecipitation problem - Protein nonspecific binding to bead (Apr/07/2011 )

Hello~ everybody!
I have a big problem, that is nonspecific binding between my interest protein(desmin) and protein G agarose, protein G sepharose, or protein A agarose when i do the IP assay.
I always blocked 20ul bead each 1.5ml tube with fresh 5%BSA in 500ml PBS overnight before processing IP. Bead is not powder, it's slurry and commercially came from Santa Cruz.
Before Blocking, i washed bead with 1ml PBS for twice from the slurry. Next, taking bead to mix with IGg that can't bind any Ab for at least 1 hour.
When bead is ready, i started the preclering process that puting bead into lysate. The lysate was C2C12 cell and BHK21 line which containing indigenous desmin(intermediate filament),
and centrifugation at 12000rpm for 10 minutes. A lot of desmin exists at pellet, and some of it at supernatant. I took the supernatant for IP assay. Extraction buffer was used for IP buffer, 10mM Tris-HCl PH 8,EDTA 5mM PH 8.08, NaCl 140mM, Triton X-100 1%(or NP-40 1%), protease inhibitor cocktail, phosphatase inhibitor, 2mM PMSF. Sometimes, i added additional 0.1% SDS and 0.5% deoxycholic acid saldium salt as RIPA buffer. Anyway, i always got the same resalt. When 30 minutes preclearing step is done, tube applied to centrifugate at 2500rpm for 3 minutes. I left the supernatnat from pellet, then took it for IP step(Ab 2 hours, bead 2 Hours). The pellet dissolved in sample buffer as the negative control. But negative control always showed that binding between bead and desmin without antibody. I'm trying to Co-IP two proteins, the interacting protein is binding to the agarose G or A beads, so i can't have a negative control.

Any help is appreciated, thanks in advance!

-CCLee49-

You could try increasing the stringence of your IP buffers. Hopefully, the Ab-desmin interaction is stronger than the desmin-bead interaction, so that a higher stringency buffer would eliminate non-specific interactions but still permit the IP. When doing ChIP experiment, we wash with buffers containing up to 500 mM NaCl, and the IP still works.

Hope this helps!

-madrius1-

madrius1 on Fri Apr 8 20:04:56 2011 said:


You could try increasing the stringence of your IP buffers. Hopefully, the Ab-desmin interaction is stronger than the desmin-bead interaction, so that a higher stringency buffer would eliminate non-specific interactions but still permit the IP. When doing ChIP experiment, we wash with buffers containing up to 500 mM NaCl, and the IP still works.

Hope this helps!


I appreciate for your help. Do you suggest me that i can increase the salt stringency? Could you tell me why? I put IgG for completing that bead strongly binding to desmin, but still not working.

-CCLee49-