In reply to Dave Garnett:
> (In reply to Jimbo W)
>
> Are you using monoclonals or polyclonal sera? (I'm sure you know this, but although polyclonals are messier they tend to be better for IP) If monoclonals you must know what epitopes they see, don't you? Where did you get the antibodies from?
>
> If you can't find out, I guess it might save you a lot of time to try IPing some native GFP and RFP to check how much cross-reactivity there is, but I can't believe this information isn't already available.
>
> BTW, you don't really mean Protein A do you? That could complicate things!
Thanks Dave. Yes I should have said protein x and y! We make our own sheep Gfp polyclonal which is great in western blot and had been for ip as well. However for the reasons you suggest, I've been looking for alternatives. I also have rabbit and chicken polyclonals from abcam, which I use for ChIP and IF respectively, but I don't have a GFP monoclonal. However, the RFP ab I'm using is from chromatek, and it is a rat monoclonal:
http://chromotek.com/en/reagents/conventional-antibodies/rfp-antibody-5f8/
Which I don't know the epitope, but which they are explicit about being specific for RFP and not GFP.
We have some of this companies GFP trap beads in the unit, that people use for mass spec, but they're expensive, though for IP they claim they should be very specific. I also wonder whether I could pre incubate my Gfp polyclonal coupled to beads in a lysate from cells expressing RFP alone.
I'm setting up an expt. today to test this out. However, I've discovered another potential issue, which is that we use the eGFP, and this does not have the non dimerising mutations. While the mCherry should be monomeric, I'm now worried about the potential that these might dimerise together, Gfp and RFP. I can't find anything specific on the literature about this, but I think it is unlikely. However for my understanding, I wonder if you can tell me whether something that dimerises inefficiently like Gfp, uM kd I think, could this be rendered problematic by locally high concentration such as when using multiple Gfp derivatives on proteins known to complex, or worse could Gfp dimerisation enhance an interaction of Gfp on a proteon known to interact with itself. Does that make sense? If there is a potential for Gfp and mCherry to dimerise, can I get round this in Ips by using a large volume for my dynabead pull downs?
Sorry for the length! Need to make sure I get this right! Thanks for your help.. ..I've presumed before that you have worked in biotech, so appreciate the advice very much.