Figure 7.

RNase T2 footprint analysis of H1 RNA bound by Rpp21 and Rpp29. (A) A model of H1 RNA structure. (B) The 5′-end ³²P-labeled H1 RNA was incubated without or with Rpp21 at final concentrations of 0.5, 1 and 2 µM (lane 4 versus 5–7) in a binding buffer for 20 min and then digested with 1 U of RNase T2 for 5 min at 25°C. The specificity (S) domain is indicated. Positions of key nucleotides and RNA size markers (lanes 1 and 2) are shown. Position of A13 protected by Rpp21 is boxed. (C) Digestion of 5′-end-labeled H1 RNA with RNase T2 for the indicated times in the absence (lanes 1–3) or presence of increasing concentrations of Rpp29 (lanes 4–7). In lanes 8–10, identical concentrations of Rpp29 were used but digestion with the nuclease was for the indicated times. Position of A85 protected by Rpp29 is boxed.