Close packing of helices 3 and 12 of 16 S rRNA is required for the normal ribosome function

Matthieu G. Gagnon, Alka Mukhopadhyayd, Sergey V. Steinberg

Research output: Contribution to journalArticlepeer-review

12 Scopus citations


The along-groove packing motif is a quasi-reciprocal arrangement of two RNA double helices in which a backbone of each helix is closely packed within the minor groove of the other helix. At the center of the inter-helix contact, a GU base pair in one helix packs against a Watson-Crick base pair in the other helix. Here, based on in vivo selection from a combinatorial gene library of 16 S rRNA and on functional characterization of the selected clones, we demonstrate that the normal ribosome performance requires that helices 3 and 12 be closely packed. In some clones the Watson-Crick and GU base pairs exchange in their positions between the two helices, which affects neither the quality of the helix packing, nor the ribosome function. On the other hand, perturbations in the close packing usually lead to a substantial drop in the ribosome activity. The functionality of the clones containing such perturbations may depend on the presence of particular elements in the vicinity of the area of contact between helices 3 and 12. Such cases do not exist in natural 16 S rRNA, and their selection enriches our knowledge of the constraints imposed on the structure of ribosomal RNA in functional ribosomes.

Original languageEnglish (US)
Pages (from-to)39349-39357
Number of pages9
JournalJournal of Biological Chemistry
Issue number51
StatePublished - Dec 22 2006
Externally publishedYes

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology


Dive into the research topics of 'Close packing of helices 3 and 12 of 16 S rRNA is required for the normal ribosome function'. Together they form a unique fingerprint.

Cite this