FIGURE 3.

Analysis of RNase J1 endonuclease activity on trp leader RNA bearing a triphosphate 5′-end (A) or a monophosphate 5′-end (C). Times of incubation (min) are indicated on top of each lane. Lanes M, substrate incubated with H76A mutant RNase J1 protein. The general locations of cleavage sites are indicated by arrowheads on the trp leader RNA schematics below each gel. ppp, triphosphate; p, monophosphate; *, labeled phosphate. B, sequencing gel to determine precise sizes of endonuclease cleavage fragments generated from trp leader RNA bearing a 5′-triphosphate end. Range of sizes of RNA fragments is indicated at the right. D, quantitation of accumulation of endonuclease fragments generated for 5′-triphosphorylated substrate (filled squares) and 5′-monophosphorylated substrate (open triangles) in the presence or absence of TRAP. Data are the average of three experiments ± S.D. FL, full length.