I have biotinylated my antibody and mixed with the magnetic beads. But after mixing I have blocked the conjugated magnetic beads with 1% BSA . I was seeing aggregation of magnetic beads even before and after the blocking .
How exactly did you biotinylate your antibody? I've used Lighting Link kit to biotinylate my antibody and found that the product caused my streptavidin magnetic beads to aggregate.I suspect the kit reactants and side products in the product mixture were to blame; there was no clean up step, as the manufacturer states the product is ready for use without cleanup.
Or...maybe you have too many biotins on your antibody and this is causing it to cross link your particles?