I have just learned to do co-ip and I have encountered some problems. I transfected HEK 293T cells with FLAG-protein and HA-protein and performed an anti-FLAG IP and my negative control (HA-protein only) keeps getting pulled down in the IP, I believe this is due to non-specific binding to the beads. As a result I cannot get a conclusive answer as to whether my proteins interact
I am considering washing the lysates with increasing concentration of salt in the wash buffer.
Any other suggestions as to how I can fix this problem?