FIGURE 2.

Enzymatic probing of the human (A) and chimpanzee (B) HAR1 RNAs. Samples were incubated for 3 min (lanes 2,10) and 10 min (lanes 3,11) with RNase V1, 1 min (lanes 4,12) and 3 min (lanes 5,13) with RNase T2, and 1 min (lanes 6,14) and 3 min (lanes 7,15) with RNase T1. L: alkaline ladder (lanes 8,16). Lanes 1,9: controls without enzyme. Digests were run on 10% denaturing polyacrylamide gels. Guanine positions and the structural features shown in Figure 3 are indicated. In chimpanzee HAR1 RNA (panel B), band doublets occurred (marked, e.g., by an asterisk at C31), arising from 5′ addition of untemplated residues by T7 RNA polymerase (Pleiss et al. 1998). However, this event did not prohibit reliable assignment of the cleaved positions. H, helix; IL, internal loop; L, loop, referring to the 2D structures in Figure 3.