A universal mode of helix packing in RNA

RNA molecules fold into specific three-dimensional shapes to perform struct ural and catalytic functions. Large RNAs can form compact globular structur es, but the chemical basis for close helical packing within these molecules has been unclear. Analysis of transfer, catalysis, in vitro-selected and r ibosomal RNAs reveal that helical packing predominantly involves the intera ction of single-stranded adenosines with a helix minor groove. Using the Te trahymena thermophila group I ribozyme, we show here that the near-perfect shape complementarity between the adenine base and the minor groove allows for optimal van der Waals contacts, extensive hydrogen bonding and hydropho bic surface burial, creating a highly energetically favorable interaction. Adenosine is recognized in a chemically similar fashion by a combination of protein and RNA C components in the ribonucleoprotein core of the signal r ecognition particle. These results provide a thermodynamic explanation for the noted abundance of conserved adenosines within the unpaired regions of RNA secondary structures.