Development of an RNA–protein crosslinker to capture protein interactions with diverse RNA structures in cells

AMT–NHS and UV have different sequence and structure preferences in crosslinking of Cbf5 and H/ACA snoRNAs. (A) Histogram of 1-mer, 2-mer (NX and XN), and 3-mer (NXN) motifs around mut/del sites (X). (B) Fraction of crosslinked nucleotides in double-stranded regions. (C) Percentage of crosslinked nucleotides in double- and single-stranded regions. Yeast H/ACA snoRNAs have 3621 and 3268 nt in double- and single-stranded regions, respectively.