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. Author manuscript; available in PMC: 2008 Sep 29.
Published in final edited form as: Biochemistry. 2005 Aug 30;44(34):11315–11322. doi: 10.1021/bi051061i

FIGURE 5.

FIGURE 5

Model of a minimal frameshifting-pseudoknot motif. a, three-dimensional model of a 22-nucleotide pkRNA that triggers frameshifting comparable in extent to that observed with PLRV wt-pkRNA. To build the model, nucleotides C18, A19, A20 and A21 were excised from the crystal structure of PLRV pkRNA, the 3’-OH of U17 was connected to the 5’-PO3- of C22 by manually repositioning the linker nucleotide U17 (gray), and the resulting structure was energy-minimized. b, the trinucleotide C16-U17-C22 (color code for carbon atoms matches that in panel a superpositioned on the linker-loop 2 motif observed in the crystal structure of PLRV pkRNA (green).