Figure 5

Analysis of 5e SRP RNA kinking. a. Polynucleotide fragment assemblies to investigate 5e SRP RNA kinking. In assembly 1, the 5e motif was placed in the middle, residues 240-AUC-242 were deleted in assembly 2, and the 5e motif was placed near the end in assembly 3. Gray and black lines indicate DNA and RNA, respectively. The sequences of the fragments are provided as Additional File 1. b. The annealed polynucleotide fragments were separated by electrophoresis on an eight percent native polyacrylamide gel followed by staining with Ethidium bromide as described in Methods. Lane 1, annealed fragments 1 and 2 (1-2) and annealed fragments 3 and 4 (3-4); lane 2, same as lane 2 with added r1 and r2; lane 3, same as lane 1 with added r1 and r3; lane 4, annealed fragments 5, 6, r1 and r4; lane 5, annealed fragments 5 and 6; lane m, 100 base pair DNA ladder as indicated. The migration distances of the three assemblies, the annealed fragments and some intermediates (i) are labeled on the left. c. Base arrangements in the predicted 5e SRP RNA K-turn (top) in comparison with the Kt-7 kink-turn (bottom)[27].