FIGURE 5.

Solution structure probing. (A) 5′-end labeled A6U and A6P3 alone or hybridized to gA6-14 (+14), gA6-14sU (+sU), and gA6-14-C6 (+C6). (B) 5′-end labeled gA6-14, gA6-14sU, and gA6-14-C6 alone and hybridized to A6U and A6P3. (Anchor) sequence complementary to A6U-ABS. (Extension) anchor sequence extended, complementary to A6P3-ABS. Figures are representative of denaturing polyacrylamide gels from partial digestions of RNAs with RNases T2 (single-stranded A specific) and V1 (specific to double-stranded or stacked nucleotides) or DEPC (chemical specific to nonstacked nucleotides). (T1) ladder lane produced by partial digestion under denaturing conditions with RNase T1. (NE, NC) no enzyme or chemical controls. (Numbers above each lane) digestion time in minutes. (Numbers next to bands) nucleotide position according to Figure 1.