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Immunoprecipitation isolates a single protein from complex mixtures like cell extracts using antibodies specific to the target protein. Antibodies are immobilized on magnetic or agarose beads, then incubated with the protein sample. Low-speed centrifugation precipitates the antibody-protein complex, which is resuspended in mild buffer to release the target protein into solution.

Antibodies are immobilized on magnetic or agarose beads through direct covalent linking or indirectly via antibody-binding recombinant bacterial proteins such as protein A or G. This immobilization allows the antibodies to form complexes with target proteins when the pre-coated beads are incubated with protein samples.

Co-immunoprecipitation uses the same principle as immunoprecipitation to study protein-protein interactions. A member protein from a protein complex serves as bait to separate and identify its other binding partners, revealing the composition and organization of protein complexes in their native state.

Chromatin immunoprecipitation (ChIP) studies protein-DNA or protein-RNA interactions by cross-linking target proteins with DNA using formaldehyde, followed by sonication to obtain smaller chromatin fragments. High-affinity antibodies capture DNA bound to proteins, and cross-linking is reversed using heat, salt, and proteinase K to release DNA for analysis.

Immunoprecipitation has several limitations: antibodies and bacterial proteins may undergo non-specific binding, introducing contaminants; immobilization of antibodies on beads requires optimization and is time-consuming; and bead washing after antigen-antibody complex formation is critical but risks losing the target protein during this step.

After low-speed centrifugation precipitates the antibody-protein complex, the pellet is resuspended in mild buffer with low pH or high salt conditions. These conditions break protein-antibody bonds and release the target protein into solution. A second low-speed centrifugation obtains the purified target protein in the supernatant.

Cross-linking immunoprecipitation (CLIP) identifies regions of protein binding sites on endogenous RNA by co-precipitating them during active transcription. RNA molecules are cross-linked to proteins to hold them together and prevent degradation. This technique studies RNA interactions with RNA binding proteins and their modifications across various biological systems. Purified samples can be further analyzed using peptide identification using tandem mass spectrometry.