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D. tyrosine (Y) intermediate of topoisomerase enzyme. Activated intermediates. DNA polymerase I, DNA ligase, and topoisomerase I catalyze the formation of phosphodiester bonds. What is the activated intermediate in the linkage reactions.. DNA polymerase I uses deoxyribonucleoside triphosphates; pyrophosphate is the leaving group. DNA ligase uses a DNA-adenylate (AMP joined to the 5′-phosphate) as a reaction partner; AMP is the leaving group. Topoisomerase I uses a DNA-tyrosyl intermediate (5′-phosphate linked to the phenolic OH group); the tyrosine residue of the enzyme is the leaving group.