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

To confirm that pk dimerization occurs via Loop 2, full-length pk, ÁS3 pk and S3-2bp-cuug pk were incubated with S3L2 transcripts ( Figure 3C ). Detection of heterodimers was performed by incubation of unlabeled pk with 32 P-labeled S3L2 (S3L2*) transcripts ( Figure 3C , lane 5), where the radioactive-labeled transcripts showed mobility shifts compatible with both homo-and heterodimers. Similarly, ÁS3 pk, a construct that lacks Stem 3 but retains Loop 2, was found to self-associate ( Figure 3C , lane 3) and to form heterodimers when incubated with S3L2 ( Figure 3C , lane 6), albeit weakly. S3L2 was unable to form heterodimers with S3-2bp-cuug pk ( Figure 3C, lane 7) , a variant lacking sequence complementarity in Loop 2.