The first chemical step of integration involves a single step transesterification, in which the recessed 3' hydroxyl of the viral DNA becomes covalently joined to a protruding 5' end in the target DNA. This step at the same time cleaves the target DNA.
Varmus, HE, Hughes, SH, Coffin, JM
Bushman, FD, Farnet, CM
Setlow, JK
integrase activity of IN:viral DNA bound to host genomic DNA with staggered ends [nucleoplasm]
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