In pull-down assays, polyhistidine tag binds to:
Polyhistidine tag, commonly hexahistidine, interacts with immobilized divalent cations through coordination chemistry. Histidine imidazole side chains donate electrons to vacant coordination sites of nickel or cobalt ions chelated by nitrilotriacetic acid resin. This interaction remains stable under physiological pH but reversible by competition with high imidazole or low pH. In pull-down and affinity chromatography, His-tagged bait is immobilized on Ni-NTA beads to capture prey interactors. The small tag minimally perturbs folding and enables IMAC purification under native or denaturing conditions unlike streptavidin or glutathione systems.
Ref: NCERT Biology Class XII Principles on Klenow fill-in labeling, Lehninger Chapter 9 DNA cloning techniques, and Molecular Cloning by Sambrook Chapter 10 documenting end-labeling of cohesive termini.