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

In previous work, the functional importance of the 31 nt comprising Stem 3 and Loop 2 in the SARS-CoV pseudoknot (C36 through A67) were investigated and no obvious determinants for efficient frameshift stimulation for this specific element could be identified. Deletion analysis characterizing variants with 5(6) and 11 nt (2) crossing the minor groove side of Stem 1 yielded 35 and 52% of wild-type frameshifting levels. However, because of the common lack of precise structural information for pseudoknot varaints, determining the exact contribution of specific nucleotides of the pseudoknot to frameshifting is often difficult. There is a potential pitfall in the mutational methods because longer-range distortions that are difficult to predict using e.g. Mfold especially in complicated three-stemmed architectures of Group II CoV could lead to false hypotheses regarding the physical mechanism of frameshifting.