MOHCA-seq: RNA 3D models from single multiplexed proximity-mapping experiments

Large RNAs control myriad biological processes but challenge tertiary structure determination. We report that integrating Multiplexed •OH Cleavage Analysis with tabletop deep sequencing (MOHCA-seq) gives nucleotide-resolution proximity maps of RNA structure from single straightforward experiments. After achieving 1-nm resolution models for RNAs of known structure, MOHCA-seq reveals previously unattainable 3D information for ligand-induced conformational changes in a double glycine riboswitch and the sixth community-wide RNA puzzle, an adenosylcobalamin riboswitch.