Linkage specific poly-ubiquitin chains are used to investigate mechanisms of chain recognition, binding and hydrolysis by the proteasome, deubiquitinating enzymes, E3 ligases or other proteins that contain ubiquitin-associated domains (UBAs) or ubiquitin-interacting motifs (UIMs). Lys63- linked poly-ubiquitin has been implicated in several non-degradative processes such as receptor endocytosis and sorting, translation, DNA damage repair, the stress response and signaling in the NFκB pathway. This product is formed with wild-type ubiquitin and linkage-specific enzymes. This mixture of poly-ubiquitin chains contains tri-ubiquitin and higher MW species, mono- and di-ubiquitin have been removed.