Structure of an RNA Interacting with the Stem-loop Sequence at the Gag-pol Junction

Enzymatic probing of RNA aptamer 13-1-15 labeled at the 5’-end. The RNA was partially digested with RNase T1 (A), RNase V1 (B) and nuclease S1 (C). The cleaved nucleotides are indicated by arrows. Region A7UA9 was protected from RNase V1 digestion by the hairpin RNA. Lane C, control; lane T, the denatured RNA treated with RNase T1; lane OH, partial alkaline ladder; lanes R and R+S-l, enzymatic cleavages in the absence of and the presence of stem-loop RNA, respectively.