Figure 2.

Hydroxyl radical footprinting profiles of 148.1-38m and its delU6 variant in the presence (magenta) or absence (blue) of RT. (A) Cleavage patterns from hydroxyl radical digestions are shown for 148.1-38m (45) and the delU6 variant (18). When in complex with RT, 148.1-38m was subjected to hyper-sensitive cleavage (‘exposed’) at position A30 of the UCAA bulge. Positions A19, U22, A31 and C29, were also sensitive to cleavage but not to the same level as A30. In contrast, C9 to C13 and G25-U27 experienced decrease in level of cleavage (‘protected’) when RT was present. (B) Protected (green) and exposed (orange) positions are mapped onto predicted structure of 148.1-38m.