Cryo-EM reveals mechanisms of natural RNA multivalency

Homo-oligomerization of biological macromolecules leads to functional assemblies that are critical to understanding various cellular processes. However, RNA quaternary structures have been rarely reported. Comparative genomics analysis has identified RNA families containing hundreds of sequences that adopt conserved secondary structures and likely fold into complex three-dimensional (3D) structures. We use cryo-electron microscopy (cryo-EM) to determine structures from four RNA families, including ARRPOF and OLE forming dimers, and ROOL and GOLLD forming hexameric, octameric and dodecameric nanostructures, at 2.6 to 4.6 Å resolutions. These homo-oligomeric assemblies reveal a plethora of structural motifs that contribute to RNA multivalency, including kissing loop, palindromic base-pairing, A-stacking, metal ion coordination, pseudoknot and minor-groove interactions. These results provide the molecular basis of intermolecular interactions driving RNA multivalency with potential functional relevance.