Fig. 4: Rev and RRE SLII binding assays.

A Schematics of Rev domains. Arginine-rich motif (ARM, beige) required for RNA interaction and oligomerization domains (OD, brown), facilitating oligomerization of Rev molecules are indicated. Rev_ARM was used to test RNA recognition and Rev₇₀ was used to assess dimer formation. B Interaction of SLII, SLII–tRNA, and tRNA with Rev proteins. Binding assays were performed with 500 nM RNA and increasing molar excess of Rev proteins. A schematic of the RNA used in the binding assay is shown to the left of the gel. SLII–tRNA is colored as in Fig. 1. The sequences of RNAs are listed in Fig. S4. SLII or SLII–tRNA contains two Rev_ARM binding sites, M1 and M2, representing a high-affinity and a low-affinity site. The two sites individually accommodate Rev₇₀ dimers, indicated as D1 and D2. Unbound RNA is denoted by F and higher-order oligomers are denoted with an asterisk (*). C Interaction of SLII three-way junction mutants with Rev proteins. SLII_DS–tRNA mimics the closed conformation by double-stranded C–G base pairs (left) and SLII_SS–tRNA mimics the ssRNA three-way junction structure (right). D Interaction of SLII stem deletion mutants with Rev proteins. SLII_delA–tRNA, SLII_delB–tRNA, and SLII_delC–tRNA mutants lack stems IIA, IIB, and IIC, respectively. The deleted stems are indicated with gray dotted lines in the RNA schematics. Each binding assay was performed three times with similar results. Uncropped gel images are provided in the Source Data file.