RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus

Ishimaru, Daniella; Plant, Ewan P.; Sims, Amy C.; Yount, Boyd L.; Roth, Braden M.; Eldho, Nadukkudy V.; Pérez-Alvarado, Gabriela C.; Armbruster, David W.; Baric, Ralph S.; Dinman, Jonathan D.; Taylor, Deborah R.; Hennig, Mirko

When the palindromic sequence was mutated from 5 0 -A CUAGU-3 0 to ACUAGc or ACUucc, the resulting S3L2-A CUAGc and -ACUucc transcripts migrated as single species, indicating that dimer formation was abolished ( Figure 3A , lanes 2 and 3). Unexpectedly, replacement of the entire Loop 2 (5 0 -GCACUAGUA-3 0 ) with the stable tetraloop 5 0 -cuug-3 0 generated a transcript migrating as a dimeric species ( Figure 3A , lane 4). This could be explained by the formation of an extended duplex featuring two central U-U wobble mismatches and was further investigated using NMR methods. In contrast, a 5 0gaaa-3 0 tetraloop containing transcript, S3-gaaa, efficiently prevented dimer formation in vitro ( Figure 3A , lane 5).