Fig. 2: Binding capabilities of various SL3 RNA variants with human TIA1 protein.
a WT SL3 consists of a 7-nt hairpin loop (HP), a 4-base pairs stem, and a 5-nt 3′-terminal loop (TL). The binding curves of human TIA1 protein with various mutated and truncated variants of SL3 RNA element: b SL3-HP3, the 7-nt HP reduced to 3-nt length, c SL3-HP-C7, sequence of 7-nt HP mutated to oligo C, (d) SL3-HP-U7, sequence of 7-nt HP mutated to oligo U, e SL3-TL1, last four nucleotides of 5-nt TL deleted, f SL3-TL-C3, three successive uridines in TL replaced by three cytosines, g SL3-TL-G3, three successive uridines in TL replaced by three guanines, h SL3-GC, two middle A-U base pairs in the stem substituted by G-C base pairs. All the secondary structures for SL3 variants are predicted by RNAStructure36 and mutated nucleotides are colored by red. All the Kd values were calculated from the EMSA image quantification from three independent experiments. Data are presented as mean ± SD. i The yield of the bona fide SARS-CoV-2 virus with designed ASOs targeting SL3 RNA elements (including HP and TL loops and the transcriptional regulatory sequence (TRS)) in Huh7.5.1 cells for 24 h, compared to the “scramble” control treated with a non-targeting ASO. SL2/3 has previously been reported18. Data represent the mean ± SEM; n = 3 biological replicates. ***p = 3.4 × 10−6 (ASO-SL2/3), 4.4 × 10−7 (ASO-HP), 1.2 × 10−5 (ASO-TL), and 1.6 × 10−7 (ASO-TRS) using unpaired two-sample Student’s t test. Source data are provided as a Source Data file.
