The apical region of the central domain contains the main cleavage site in the FMDV IRES. The uniformly labeled transcripts, schematically represented in the top panel, were subjected to RNase P digestion parallel to the entire IRES. The reaction products were fractionated in 6% denaturing gels parallel to known markers. The nucleotide composition and RNA structure organization of the indicated transcripts are depicted in Figure 2. Products detected in RNA kept on ice (lanes 1,4,7,10,13,16), or incubated in buffer for the entire duration of the reaction (lanes 2,5,8,11,14,17) were used as negative reaction controls, and not considered as Rz products. Thick arrows in the left and right of each panel depict the reaction products characterized in this study, while thin lines depict reaction products not characterized.
