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. 2015 Sep;21(9):1591–1605. doi: 10.1261/rna.049007.114

FIGURE 5.

FIGURE 5.

Footprinting assays for RNase MRP RNA, typical gels. 3′-end 32P-labeled RNase MRP RNA alone or in complexes with equimolar amounts of Pop1 and the Pop6/Pop7 heterodimer (as indicated above the gels) was partially digested with RNase V1 (A) and hydroxyl radicals (B). (Lanes 1,19,27) RNase MRP RNA digested with RNase T1 (sequence ladder, identifies positions of guanines, shown on the left); (lanes 2,18) alkali hydrolysis of RNase MRP RNA (ladder); (lanes 3–6,28) digestion of RNase MRP RNA; (lanes 7–9,29) digestion of the complex of RNase MRP RNA with Pop1; (lanes 10–13,30) digestion of the quaternary complex of RNase MRP RNA with proteins Pop1, Pop6, and Pop7; (lanes 14–17,31) digestion of the complex of RNase MRP RNA with the Pop6/Pop7 heterodimer; (lanes 20–22,32–34) controls (RNA incubated with proteins as indicated above the gels). Secondary structure elements are marked on the left of the gels: Helical regions are shown by thick solid lines, terminal loops by thin solid lines. Gel traces are shown on the right of the gels (lanes 23–26,35–38) as marked on top.