Secondary structure of the 5′ UTR of spe2 RNA. (A) The structure of the crosslinker LC-SDA. (B) Electropherogram of a photoactive DA-Spd and RNA crosslinks. The in vitro transcribed RNA was irradiated with UV light with DA-Spd (blue), compared with the in vitro transcribed RNA irradiated with DA-Spd, and a 10-fold excess of unlabeled Spd (red) and the in vitro transcribed RNA irradiated with inactive DA-Spd (green) as controls. (C) Electropherogram of DMS-modified RNA with DMS ([+] DMS, blue trace), compared with that of unmodified RNA ([−] DMS, gray trace). (D) Predicted secondary structure of the 5′ UTR RNA by Vienna computational folding, covariance modeling, and chemical probing. Black circles filled with green indicate the DMS reactive nucleotides, and red indicates the crosslinking nucleotides.
