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

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

Research output: Contribution to journalArticlepeer-review

30 Citations (Scopus)

Abstract

-1 Programmed ribosomal frameshifting (PRF) in synthesizing the gag-pro precursor polyprotein of Simian retrovirus type-1 (SRV-1) is stimulated by a classical H-type pseudoknot which forms an extended triple helix involving base-base and base-sugar interactions between loop and stem nucleotides. Recently, we showed that mutation of bases involved in triple helix formation affected frameshifting, again emphasizing the role of the triple helix in -1 PRF. Here, we investigated the efficiency of hairpins of similar base pair composition as the SRV-1 gag-pro pseudoknot. Although not capable of triple helix formation they proved worthy stimulators of frameshifting. Subsequent investigation of ∼30 different hairpin constructs revealed that next to thermodynamic stability, loop size and composition and stem irregularities can influence frameshifting. Interestingly, hairpins carrying the stable GAAA tetraloop were significantly less shifty than other hairpins, including those with a UUCG motif. The data are discussed in relation to natural shifty hairpins.

Original languageEnglish
Pages (from-to)8952-8959
Number of pages8
JournalNucleic acids research
Volume39
Issue number20
DOIs
Publication statusPublished - 2011 Nov

All Science Journal Classification (ASJC) codes

  • Genetics

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