Skip to main content
. 2012 Jun;18(6):1230–1243. doi: 10.1261/rna.032177.111

FIGURE 4.

FIGURE 4.

(A) The ratio of the number of counts in chamber b to chamber a in equilibrium dialysis assay for the B. subtilis yitJ aptamer, and other hybrid constructs. SAM binding observed for the 3P1_10AT hybrid is reduced dramatically when the possibility for optimal coaxial stacking with the AT helix is disrupted in 3P1_Only and in 3P1_9AT. The error bars represent standard deviation for at least three replicates of each experiment. (B–D) In-line probing data for 3P1_10AT, 3P1_10AT_5′GCC, and 3P1_9AT hybrid constructs: (B) Densitometry traces showing intensity of the base catalyzed cleavage on 8% denaturing acrylamide gel for 3P1_10AT, 3P1_9AT, and 3P1_10AT_5′GCC. The red arrows indicate sites of enhanced cleavage in the presence of SAM and the blue arrows indicate sites of protection in the presence of SAM. (C) Cleavage pattern with and without SAM for 3P1_10AT mapped onto the secondary structure schematic, with color coding as in B. (D) Sample of raw in-line probing data for 3P1_10AT with the lanes representing no reaction (1), alkaline hydrolysis (2), RNase T1 (3), RNA without SAM in in-line probing buffer (4), and RNA with SAM in in-line probing buffer (5).