Fig. 1: NS5 binding analysis of tRNA-fused stem-loop A (tRNA-SLA).
From: Structures of flavivirus RNA promoters suggest two binding modes with NS5 polymerase
a Interaction between DENV NS5 and SLA. Interactions between NS5 and various SLAs (tRNA-SLADENV and in vitro transcribed SLA70 and SLA80) were examined by electrophoretic mobility shift assay (EMSA). SLA70 and SLA80 contain the first 70 and 80 nucleotides of DENV2 RNA genome, respectively. The tRNA-SLADENV, SLA70 and SLA80 (1 μM) were titrated with increasing concentrations of NS5 from 1 μM to 4 μM. NS5 binds tRNA-SLA, SLA70, and SLA80 similarly. EMSA was performed twice with similar results. b Competition assay between tRNA-SLADENV and other nucleic acids for DENV NS5. The tRNA-SLADENV (1 μM) was titrated with increasing concentrations of DENV NS5 in the presence of tRNAphe, ssDNA (43 nt), and ssRNA (8 nt) (1 μM each). The nucleic acids were stained with ethidium bromide and visualized under UV at 302 nm. The competition assay was repeated twice with similar results. c Interaction between ZIKV NS5 and SLA. Interactions between NS5 and various SLAs (tRNA-SLAZIKV and in vitro transcribed SLA71 and SLA81) were analyzed by EMSA. EMSA was carried out similarly as in a. EMSA was performed twice with similar results. d Competition assay between tRNA-SLAZIKV and other nucleic acids for ZIKV NS5. Competition assay with tRNAphe, ssDNA, and ssRNA was carried out as described above, and repeated twice with similar results. Source data for figures a-d are provided as a Source Data file.
