Stem–loop structures can effectively substitute for an RNA pseudoknot in -1 ribosomal frameshifting

Yu, Chien-Hung; Noteborn, Mathieu H.; Pleij, Cornelis W. A.; Olsthoorn, René C. L.

Here, we have carried out a systematic analysis of the frameshift-inducing efficiency of hairpins derived from the SRV-1 gag-pro frameshifter pseudoknot. Investigation of about 30 different hairpin constructs revealed that next to thermodynamic stability, also loop size and composition, and stem irregularities can significantly influence frameshifting. Our data showed that there exists no base specific contacts between the hairpin and the ribosome during frameshifting and suggests that the hairpin primarily serves as a barrier to allow repositioning of tRNAs at the slippery site.