I would like to know if the biotin labels affect the binding of the antigen to the antibody. For example, if all the asp and glu carboxyl groups are changed on a protein, then will the antibody still recognize it and be able to bind?

Biotinylation probably won’t affect binding to an antibody although there are certainly risks. If you are using a monoclonal antibody they might be more site specific, especially with the N terminus (which will likely be modified by our biotinylation reagent). Additionally, the larger your antigen, the less likely biotinylation will inhibit binding. Really the only way to know is to try it, we have a lot of experience labeling proteins and antibodies and this really is the best way to modify without changing the biomolecule too much. Other reagents will not be as controllable and use more harmful chemistries that could harm your protein. I would recommend using lower biotinylation levels (depending on the size of your antigen, I would recommend not adding more than 10 molar equivalents) and it should work out fine. This reagent specifically labels amine groups on Lysine residues. The beauty of our linking reagent is that there is no reduction or oxidation step that would alter the hydroxyl groups on Asp or Glu residues. The kit has been developed so that only 3–8 biotins are labeled onto the antibody. There are about 50 Lys residues on any given antibody, so if you are only modifying three of them, the probability that you are hitting the antigen binding site is low. While we cannot guarantee that the antigen binding site is not being labeled, rendering it inactive, we rarely see a case where labeling causes the antibody to become inactive.