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.

Substituting UUCG by another stable tetraloop sequence (GAAA) resulted in a 2-fold decrease in frameshifting ( Figure 5A , lanes 1 and 2) either with GC ( Figure 4 , bar 10) or CG cbp (Figure 4 , bar 9). We designed another five loop mutants to try to explain the low efficiency of the GAAA tetraloop constructs. Constructs AAAA and CAAA induced 5.2% and 4.7% frameshifting, respectively (Figure 4, bars 2 and 3) , which is close to that of the GAAA constructs. The efficiency of two other A-rich loop mutants, ACAA and AAAU, was 7.5% and 7.1%, respectively (Figure 4 , bars 4 and 5), thereby closely matching that of the UUCG constructs. Finally, the GGGA tetraloop construct, belonging to the stable GNRA tetraloop family, induced 1.7-times more frameshifting than its GAAA sibling (Figure 4, bar 11) . These data suggest that the presence of 3 or 4 adenines at the 3 0 side of a tetraloop is unfavorable for frameshifting.