Fig. 10: AA/GA-facilitated DNA editing by rA3G. rA3G binds the exposed AA/GA motifs on DNA and edits multiple CCCs that are located (1) 5′ upstream and (2) within its editing window required for linear or for hairpin DNA.

a Cartoon depicts the domain organization of rA3G. Location of the zinc-catalytic residue E259 is marked by a pink star in the schematic diagram. b Cartoon depicts how rA3G predominantly uses its CD1 domain to capture the AA/GA dinucleotide on linear ssDNA and presents the editing motif CCC, located at the 5′-side (or upstream) of AA/GA, to its CD2 active site within a 9–20 nt window, with an optimal linear distance of 12−16 nt, for deamination. The editing motif CCC located at the 5′-side of AA/GA within 1–7 nt distance or at the 3′-side of the AA/GA cannot reach to the CD2 active site efficiently. c Diagram depicts that editing efficiency of CCC on hairpin loop DNA is affected by both stem length (h) and 3′ overhang distance (m) to the AA/GA on the 3′-side (downstream). The fate of the editing sites, CCC, whether located on a hairpin loop or on linear ssDNA, will be as follows: the CCC located right next to the 5′-side of AA/GA within 1–7 nt linear distance remains unedited, whereas both the middle CCC on the hairpin loop and the CCC on the 5′-side of the hairpin loop are within the editing distance from the AA/GA for efficient deamination.