Figure 1.

(A) Schematic diagram of scRNA with nucleotide sequence of 5′ and 3′ ends. The large internal loop of 255 nt is not drawn to scale. Solid arrows show location of Bs-RNase III cleavage sites A and b. Proposed cleavage site X is indicated by dashed arrow. Asterisk denotes 3′ end of mature scRNA. The bold C and A nucleotides are at the 3′ end of the 279- and 283-nt products, respectively. Boxed nucleotides mark the ends of the sequence that is complementary to the 3′-proximal oligonucleotide probe (shown schematically in Figure 6B). Circled nucleotides mark the ends of the sequence that is complementary to the 3′-terminal oligonucleotide probe (shown schematically in Figure 6C and D). (B) Line diagrams of RNA products detected by various probes. Arrowheads above full-length line indicate sites of Bs-RNase III cleavage. Diamond below full-length line indicates site X. Numbers at each end of the line indicate 5′ and 3′ ends of RNAs. Above each line is the likely origin of the RNA species, with the size of the RNA in parentheses. (The sizes of the RNAs are those predicted from earlier data and calculated from the data shown in Figures 2, 3 and 6. The degree of precision from these data is ±2 nt, as mentioned in the text.) For clarity, the 314- and 310-nt RNAs, as well as the 283- and 279-nt RNAs, are grouped.