The UAA/GAN internal loop motif: a new RNA structural element that forms a cross-strand AAA stack and long-range tertiary interactions

J Mol Biol. 2006 Jul 28;360(5):978-88. doi: 10.1016/j.jmb.2006.05.066. Epub 2006 Jun 16.


Analysis of aligned RNA sequences and high-resolution crystal structures has revealed a new RNA structural element, termed the UAA/GAN motif. Found in internal loops of the 23 S rRNA, as well as in RNase P RNA and group I and II introns, this six-nucleotide motif adopts a distinctive local structure that includes two base-pairs with non-canonical conformations and three conserved adenine bases, which form a cross-strand AAA stack in the minor groove. Most importantly, the motif invariably forms long-range tertiary contacts, as the AAA stack typically forms A-minor interactions and the flipped-out N nucleotide forms additional contacts that are specific to the structural context of each loop. The widespread presence of this motif and its propensity to form long-range contacts suggest that it plays a critical role in defining the architectures of structured RNAs.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / chemistry*
  • Base Pairing
  • Base Sequence
  • Introns
  • Models, Molecular*
  • Molecular Sequence Data
  • Nucleic Acid Conformation*
  • RNA, Bacterial / chemistry*
  • RNA, Ribosomal, 23S / chemistry*
  • Ribonuclease P / chemistry*


  • Bacterial Proteins
  • RNA, Bacterial
  • RNA, Ribosomal, 23S
  • Ribonuclease P