RNA secondary structome of different retrotransposons with DNA/protein binding

We determined the RNA secondary structure of different retrotransposon by icSHAPE. The retrotransposon has differnet states including protein bound, DNA and protein bound. RNA was prepared as in the cryo-EM studies in three conditions: apo RNA, RNA-protein complex, and RNA-DNA-protein ternary complex. In each condition, the RNA sequence has three types: 5’ORF, 3UTR, and 5’ORF-linker-3’UTR chimeric. We design reverse transcription primers for the nine RNA samples with specific barcodes. Then, all samples were performed by icSHAPE.