Fig. 3.

In-line probing analyses of poly(A) RNAs complexed with dENE variants. (A) Sequence and secondary structure model for the wild-type and mutant (M1 to M3) dENEs used in the experiment. (B) In-line probing analyses of ³²P 5ʹ end-labeled poly(A)₃₀ or poly(A)₃₆ in free form (—) or complexed with the wild-type (WT) or M1 dENE. The dotted line indicates the directionality of poly(A) hydrolysis products. (C) In-line probing analyses of poly(A)₃₀ complexed with the WT, M2, and M3 dENEs. NR and OH ^– designate no reaction and partial digestion with alkali, respectively. The 7-nt 3ʹ-end protected region of the dENE-bound poly(A) is marked by brackets. The 5ʹ-end region of poly(A), whose cleavage pattern responds to the upper stem mutations, is boxed in blue.