A Genome-Wide Analysis of RNA Pseudoknots That Stimulate Efficient −1 Ribosomal Frameshifting or Readthrough in Animal Viruses
Figure 1
Schematic diagrams of the sequence elements for forming an H-type RNA pseudoknot. Abbreviations used are: S1, stem1; S2, stem2; S1-5′ and S1-3′, the 5′ and 3′ strands of stem1; S2-5′ and S2-3′, the 5′ and 3′ strands of stem2; L1, loop1; L2, loop2; L3, loop3. (a): Linear sequential arrangement of the pseudoknot-forming sequence elements. Residues involved in the formation of S1 and S2 are represented as black and gray squares, respectively. Residues in the single-stranded loop region are represented as unfilled circles. (b): Schematic representations of folded pseudoknots. Left: with a nonzero L3 sequence; right: with the absence of L3, S1 and S2 can stack coaxially to form a quasicontinuous double helix. L1 and L2 locate on the same side of the double helix, with L1 crossing the major groove of S2 and L2 crossing the minor groove of S1.
