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 addition to stem size, loop composition is another determinant of hairpin stability. An important subgroup of hairpin loops is the tetraloop, which is the most common loop size in 16S and 23S ribosomal RNAs (37) . The tetraloops with consensus UNCG, GNRA, or CUUG loop sequence form stable loop conformations (38, 39) . As opposed to the mentioned stable tetraloops, purine-rich (32) and larger loops (40) are considered to be less favorable for hairpin formation. Our results showed that the GGGC loop is indeed less efficient in inducing frameshifting but the larger loop construct (9 bp/9 nt), although having a lower thermodynamic stability, showed comparable frameshifting efficiency to the stable UUCG tetraloop hairpin. This is consistent with previous studies that showed that increasing the size of the loop in a hairpin or pseudoknot can increase frameshift-inducing ability to a certain extent (21, 41) . Although larger loops seem efficient in inducing frameshifting, in known examples of frameshifter hairpins, there are no loop sizes of more than 5 nt. This could relate to hairpin folding kinetics (40) or to nuclease sensitivity.