Figure 3
Differential cleavage of mismatched substrates by P.a . RNase H2. A 30mer oligonucleotide S-rC 14-1-15 having a single RNA base (rC) was paired with its perfect match DNA complement (shown) or oligonucleotides having a single base mismatch at one of the 11 positions identified in bold. Every possible mismatch at these locations was tested. DNA bases are uppercase and RNA bases are lowercase. 32P-labeled duplexes were incubated with RNase H2 at 70°C. Reaction products were separated by PAGE, and the extent of cleavage of the substrate was quantified by phosphorimaging. The percent cleavage of each of the mismatched duplexes relative to the perfect match (= 100%) are plotted. The sequence of the invariant RNA-containing top strand is shown above the plot with each mismatch base aligned above its associated data point in the bar graph. The site of cleavage by RNase H2 is indicated by the arrow.