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. Overall design: 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.