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hello all,

I am doing GST pull down experiment, where my protein tagged with N-terminal GST. and its purified and desalted.

when i am doing interaction using Cell lysate (Hela or 293T) containing my pray protein, and after interaction,while doing immunoprobing (Mab) for pray protein i am getting non-specific bands for GST fused protein also, very prominent,

i am preclearing cell lysate before interaction. i used differnt salt and buffer compositions, but still the problem persist.

i even precleared my antibody also, but then also it didnt work.......

plz gimme some suggestions.

thank you

pankaj

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1 Answer

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If I understand you correctly, your monoclonal Ab for your prey protein is also recognizing your GST-fused bait protein, right? If so, then you have some troubleshooting ahead of you.

First of all, just to make sure, are your bait and prey proteins different?

Then, have you run all the necessary negative controls? What do you see in each condition? -- GST bait protein incubated with buffer but no lysate -- lysate incubated with beads (if you're using them) but no GST-fused bait protein -- lysate incubated with GST alone (not fused to your bait protein) -- simple WB with your mAb using whole lysate -- do you get just the one specific band? -- simple WB with your mAb using buffer in the lane but no lysate -- do you get any signal?

Next, how big are your prey and GST-fused bait proteins? What species are your antibodies? Could it be that the nonspecific band your mAb sees is not actually your GST fusion protein but something else, like heavy chain or light chain?

When you say that you preclear your cell lysate, what conditions do you use, for how long, and what are you using for the preclearing (e.g., unconjugated beads)? How did you preclear your antibody?

After you answer these questions, then hopefully we will be able to figure out what is the problem and how to resolve it.

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