Epitope Masking Prevents Antibody Binding (Immunoprecipitation (CST Guide))

Question

Accepted Answer

No IP signal despite confirmed protein expression in input control. Antibody works in western blot of denatured lysate but fails in native IP conditions. Common causes: 1) Target protein conformation under native conditions obscures antibody epitope binding site 2) Interacting proteins physically block access to antibody recognition region 3) Epitope located in protein-protein interaction interface, masked by binding partners 4) Post-translational modifications alter protein structure hiding the epitope Solutions: 1) Use antibody recognizing different epitope region of target protein (check Source/Purification section on product page) 2) Try N-terminal or C-terminal specific antibodies if current antibody targets internal region 3) Test antibody raised against different immunogen or peptide sequence 4) Consider using tag-based IP system (FLAG, HA, Myc) if epitope masking persists