title: The UAA/GAN internal loop motif: a new RNA structural element that forms a cross-strand AAA stack and long-range tertiary interactions.
abstract: 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.
authors.affiliation: The Institute for Cellular and Molecular Biology, The University of Texas at Austin, 1 University Station A4800, Austin, TX 78712-0159, USA.
authors.forename: Jung C
authors.initials: JC
authors.lastname: Lee
authors.forename: Robin R
authors.initials: RR
authors.lastname: Gutell
authors.forename: Rick
authors.initials: R
authors.lastname: Russell
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry*; D020029:Base Pairing; D001483:Base Sequence; D007438:Introns; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000737:chemistry*; D012338:RNA, Ribosomal, 23S / Q000737:chemistry*; D043262:Ribonuclease P / Q000737:chemistry*
chemical_list: D001426:Bacterial Proteins; D012329:RNA, Bacterial; D012338:RNA, Ribosomal, 23S; D043262:Ribonuclease P