Comparison of methods for quantification of ribozyme cleavage. Ribozyme GUC7 was incubated for various lengths of time from 0 to 60 min, as indicated, and substrate cleavage activity was analyzed by agarose gel electrophoresis and real-time RT-PCR as described in Methods. After electrophoresis (right panel), the gel was stained with ethidium bromide, and the bands were quantified by densitometry. Relative band intensity was then graphed against time (left panel). Target (◆), remaining substrate; product 1 (■) and 2 (▲), relative amounts of each of the two cleavage products. Separately, the substrate was quantified by real-time RT-PCR, and the relative amount of remaining substrate (●) was graphed against time.