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. 2003 Aug;9(8):937–948. doi: 10.1261/rna.2172103

FIGURE 4.

FIGURE 4.

FIGURE 4.

Quantitation of RRE IIB footprinting studies. Lanes 2,3,5,7,9,11 of lead acetate (Fig. 3A ▶) and RNase A (Fig. 3B ▶) footprinting gels were used for the analysis. Band intensities of each lane were normalized to G61 band intensity in lead acetate footprinting gel (Fig. 3A ▶) and to G42 in RNase A footprinting gel (Fig. 3B ▶). The ratio of intensities of each band to the intensities of the corresponding band in the control lane (lane 2) were calculated. When the difference in the band intensities compared with the control exceeded 10%, they were plotted. Positive bars indicate the protection observed at the particular nucleotide, whereas negative bars stand for increase of cleavage at the corresponded nucleotide, due to a conformational change in the RNA molecule induced by ligand binding. The sites on RRE IIB, which appear protected in both lead acetate and RNase A footprinting patterns are assumed to be the binding sites for the ligands.