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This technology uses self-labeling mini-proteins to attach functional labels or small molecules to a protein-of-interest. Self-labeling proteins work by first making a fusion protein that combines the protein-of-interest with the self-labeling protein. The self-labeling portion of the fusion protein is then reacted with a substrate that contains a label such as a fluorophore, pull-down-tag, or small molecule. The self-labeling nature of the fusion protein means that molecular biology investigators can easily interchange the label to perform many different kinds of assays. Previous self-labeling protein technologies, such as CLIP or Halo tags, are bulky (>100 amino acids) and therefore frequently disrupt the functionality of the target protein. In contrast, the self-labeling mini-proteins of this invention are small (<30 amino acids), which minimizes their impact on the structure and function of the target protein. Additionally, the mini-protein reaction with the substrate is highly specific, so only proteins containing the tag are labeled.