What is the purpose of pull down assays in protein interaction studies?

Pull down assays are specifically designed to assess the interactions between proteins. The primary purpose of these assays is to determine if one protein (often referred to as protein X) interacts with another protein (protein Y). This is achieved by using a bait protein that is attached to a solid substrate, allowing researchers to capture any binding partners from a mixture, usually a cell lysate.

In the context of protein interaction studies, a typical pull down assay will involve tagging protein X with a specific affinity tag (like a His-tag or GST-tag), incubating it with a lysate that might contain protein Y, and then isolating the tagged protein along with any bound proteins. After the wash steps, researchers can analyze the isolated proteins, often via techniques such as SDS-PAGE followed by Western blotting, to confirm the presence of protein Y, thus providing evidence of their interaction.

The other options—isolating DNA fragments, visualizing protein structures, or quantifying protein concentration—do not capture the aim of pull down assays. Those techniques serve different purposes in molecular biology and biochemistry, underscoring the specificity of pull down assays for studying protein-protein interactions.