Immunoaffinity purification of FLAG epitope-tagged bacterial alkaline phosphatase using a novel monoclonal antibody and peptide elution.

The FLAG epitope is an eight amino acid peptide (AspTyrLysAspAspAspAspLys) that is useful for immunoaffinity purification of fusion proteins. A monoclonal antibody (anti-FLAG M1) that binds the FLAG epitope in a calcium-dependent manner and requires an N-terminal FLAG sequence has been described previously. We describe the use of a second anti-FLAG monoclonal antibody (anti-FLAG M2) in immunoaffinity purification of N-terminal Met-FLAG and C-terminal FLAG fusion to bacterial alkaline phosphatase. Although binding of an anti-FLAG M2 monoclonal antibody to the FLAG epitope is not calcium-dependent, bound fusion proteins can be eluted by competition with FLAG peptide.