Figure 7.

Structure probing of 5′domain and 5WJ RNAs with S4. (a) Representative sequencing gel showing DMS modification of 5WJ•S4 complex. The gel is labeled as in Figure 6, and symbols are as described in the key. (b,c) Summary of hydroxyl radical footprinting and chemical base modification on (b) 5′domain and (c) 5WJ RNA. Colored circles indicate backbone protections in HKM4. Colored circles with black outlines indicate riboses that are in direct contact with S4 [1j5e, (18); 2i2p, (42)]. Gray symbols, undetermined. Moderate-to-strong protection (squares) or enhanced base modification (triangles) is represented by closed red symbols. Open red symbols indicate Gs weakly or inconsistently modified by kethoxal.