The retroviral DNA integration reaction. Panel A. The processing and joining steps catalyzed by retroviral integrases produce a gapped recombination intermediate. The shaded region represents an IN multimer, heavy lines the viral DNA, and thin lines host DNA. The position of the conserved CA dinucleotides at the ends of the viral DNA is shown and the position of the processing cleavage sites are marked with straight arrows. The curved arrows indicate the staggered phosphodiester bonds cleaved during the joining reaction. Panel B. Simple in vitro assays for IN activity represent reactions at a single viral DNA end. Viral(donor) or host(target) DNAs are distinguished as in A. Filled circles mark the 5' phosphate ends and open circles the 3' hydroxyl ends.