FIGURE 5.

A representative set of chemical probing reactions. (A,B) The edited and (C,D) pre-edited forms of RNA B were probed with DMS and CMCT under native and denaturing conditions. Sites of modification result in RT terminations. A RT primer complementary to the 3′ extension illustrated in Figure 3A was used to detect modifications of nucleotides #36–#81 and an internal primer used for nucleotides 3–36. Sites of modification migrate one nucleotide faster than the corresponding position within the RT dideoxy sequencing ladder. The 10 nucleotides that have significantly different chemical reactivity within the edited and pre-edited RNAs are indicated. The three U's that are inserted by editing are not numbered.