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

The common ancestor of the civet and human strains seems to have been a bat virus (9, 41) . Therefore, we attempted to obtain information about the combined conservation of sequential and structural features of Stem 3 from a compilation of 22 sequences from related human [GenBank accession codes AY304495 (42) and NC_004718 (43, 44) ], masked palm civet [GenBank accession code AY304488 (42) ] and bat coronaviruses. For this purpose, Mfold (30) was used to predict lowest energy structures of aligned CoV S3 sequences. While 22 out of 24 nt of the S3L2 region are absolutely invariant between the 22 viral species (Supplementary Figure S6) , the variation that does occur most frequently disrupts the hexanucleotide palindromic sequence at its 3 0 -end exhibiting a U51C substitution (Supplementary Figure S6) . The U51C substitution stabilizes the hairpin and lowers the calculated ÁG from À4.8 kcal/mol to À7.5 kcal/mol (Supplementary Table S1 ). We previously showed that this 'ancestor' S3L2-AGUAGc 51 variant was dimerization incompetent (lanes 2, Figure 3A, D) .