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.

In the experiments of Bidou et al. (20) studying the HIV-1 gag-pol frameshift hairpin the stem-length was kept at 11 bp, while its stability was varied between À3.4 and À22.1 kcal/mol (recalculated using MFOLD 2.3) by changing the number of AU and GC base pairs in a small set of six hairpins. In the case of the dnaX gene of Escherichia coli 22 variants of the wild-type 11 bp hairpin were tested for their ability to stimulate À1 PRF at the AAAAAAG slippery sequence. Hairpin stabilities varied between À10.4 and À27 kcal/mol and a positive correlation between frameshifting efficiency and calculated stability was observed both in the presence (R 2 = 0.62) and absence (R 2 = 0.72) of upstream enhancer (19) . The dnaX gene with the highly efficient (prokaryotic) AAAAA AG slippery sequence is not directly comparable to our in vitro system; a 6 bp hairpin in the dnaX gene displayed 17% of frameshifting without upstream enhancer, whereas a 6 bp hairpin in our system induced only 3.5% of frameshifting.