Fig. 3: Loop 3 interactions with DNA are requisite for gap filling.
From: Molecular basis for DNA repair synthesis on short gaps by mycobacterial Primase-Polymerase C
a, b Schematic solvent-accessible surface representations of Loop 3 interacting with template strand DNA, shown in two orientations. Residues that interact are highlighted in yellow, and hydrogen bonds are depicted in black (hatched line). See also Supplementary Fig. 2b and c. c Flipping activity of Prim–PolC on different short-gap substrates examined using a 2-aminopurine (2-AP)-based assay. The ability of Prim–PolC to flip the −2 primer base (2-AP) was measured as an increase in 2-AP fluorescence intensity when the −2 base was unpaired. Each reaction contained 0, 0.125, 0.5, 0.75 or 1 µM Prim–PolC (WT), 1 µM substrate, 5 mM Ca2+ ions and 250 µM ATP. d, e Flipping activity of Prim–PolC variants. Quantification of primer −2 base flipping by Prim–PolC variants on 1-nt (d) or 3-nt gap (e) substrates under the same conditions as stated in (c). Data shown (c, d and e) are representative of the mean of at least three individual experiments, and error bars show the standard deviation.
