Once the viral RNA template has been degraded (dashed line), the minus-strand ssDNA (solid line) is available for A3G binding. Due to the high effective concentration of the few A3G molecules packaged in the small volume of the virion and the strong electrostatic interaction between the NTD and negatively charged ssDNA, free A3G (predominately in a globular conformation) quickly binds available ssDNA and remains bound on the timescale of 100 s. While bound, A3G monomers can spontaneously switch into a dumbbell conformation with the two domains partially decoupled, enabling transitions along three paths. First, the CTD can locally bind the ssDNA in an enzymatically active state, enabling recognition of target CCC motifs and subsequent deamination activity. This binding conformation stabilizes A3G’s dumbbell form and tightly contracts the ssDNA substrate. Quick sampling of the ssDNA by the CTD, along with the ability of the NTD to slide along the ssDNA under physiological salt conditions, allows fast and processive deamination of neighboring target sites before full A3G dissociation. A3G deamination activity displays a strong directional bias, inhibited from accessing sites within ~30 nt of the 3′ end due to the presence of the NTD, and deaminating processively in the 5′ direction. Second, the CTD can bind non-locally to another region of the viral genome due to the high flexibility of ssDNA segments. Due to the stronger ssDNA binding affinity of the NTD versus the CTD, the protein usually remains at the NTD side of the loop, but sometimes relocates when the CTD remains bound longer. This allows for moderately processive deamination even in the presence of barriers such as regions of dsDNA and RNA/DNA hybrid. Third, if an A3G monomer collides with other bound protein(s), an oligomer will form. This path becomes favored at higher A3G concentrations and over longer timescales. Oligomerization reduces deaminase activity due to decreased protein mobility and/or occlusion of the CTD’s active site by other bound A3G subunits. Oligomers can be broken up, however, over long timescales, allowing for additional enzymatic activity at a reduced rate. Alternatively, oligomers that remain bound to the minus-strand ssDNA template block processive polymerization of the complementary plus strand ssDNA (gray line) by RT (green diamond). Slowing RT also extends the window of ssDNA vulnerability, allowing other A3G monomers to fully deaminate the viral genome.