Figure 7

Comparison of NCp7 and NCp8 RNA strand exchange activity. (A) A schematic of the RNA/DNA strand exchange reaction. Note that the TAR1 RNA may adopt a stem-loop structure, not shown here. (B) A representative electrophoretic analysis of RNA strand exchange in the R1(−) DNA/TAR1 RNA duplex at increasing concentrations of NCp7 or NCp8. Lane 1: R1(−) DNA only; lane 2: heat-annealed R1(−) DNA/TAR1 RNA; lane 3: heat-annealed R1(−)DNA/R1(+)DNA; lane 4: heat-annealed R1(−) DNA/TAR1 RNA incubated with R1(+)DNA at 37°C; lanes 5 – 9: strand exchange reaction at 0.06, 0.125, 0.25, 0.5 and 1 μM NCp7; lanes 10 – 14: strand exchange reaction at 0.06, 0.125, 0.25, 0.5 and 1 μM NCp8. (C) Percentage of TAR1 RNA exchanged, measured as a ratio of R1(−) DNA/R1(+)DNA to R1(−) DNA/TAR1 RNA duplex. (D) Percentage of TAR1 RNA exchanged, measured as a ratio of TAR1(−) DNA/TAR1(+) DNA to TAR1(−) DNA/TAR1 RNA duplex. The graphs represent averaged data from three independent experiments. The error bars represent standard deviations.