Using DMS-MaPseq to dissect structural differences of ribosomal RNA in different pre-40S intermediates

Ribosomes are among the largest folded RNAs, whose function depends on their structure. Nonetheless, in vitro studies indicate a propensity of rRNAs to misfold. We use a combination of DMS-MaPseq, structural analyses, biochemical experiments, and yeast genetics to dissect the final RNA folding steps of the small ribosomal subunit head. Pre-40S are purified from WT or S15_YRR or Rio2_Δloop cells are purified via Rio2-TAP. Mature 40S are also tested. Each sample has DMS treated and its untreated control. There are 5 biological replicates for WT pre-40S, 4 biological replicates for Rio2_Δloop pre-40S and 3 biological replicates for S15_YRR and mature 40S.