title: The right angle (RA) motif: a prevalent ribosomal RNA structural pattern found in group I introns.
abstract: The right angle (RA) motif, previously identified in the ribosome and used as a structural module for nano-construction, is a recurrent structural motif of 13 nucleotides that establishes a 90° bend between two adjacent helices. Comparative sequence analysis was used to explore the sequence space of the RA motif within ribosomal RNAs in order to define its canonical sequence space signature. We investigated the sequence constraints associated with the RA signature using several artificial self-assembly systems. Thermodynamic and topological investigations of sequence variants associated with the RA motif in both minimal and expanded structural contexts reveal that the presence of a helix at the 3' end of the RA motif increases the thermodynamic stability and rigidity of the resulting three-helix junction domain. A search for the RA in naturally occurring RNAs as well as its experimental characterization led to the identification of the RA in groups IC1 and ID intron ribozymes, where it is suggested to play an integral role in stabilizing peripheral structural domains. The present study exemplifies the need of empirical analysis of RNA structural motifs for facilitating the rational design and structure prediction of RNAs.
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA.
authors.forename: Wade W
authors.initials: WW
authors.lastname: Grabow
authors.forename: Zhuoyun
authors.initials: Z
authors.lastname: Zhuang
authors.forename: Zoe N
authors.initials: ZN
authors.lastname: Swank
authors.forename: Joan-Emma
authors.initials: JE
authors.lastname: Shea
authors.forename: Luc
authors.initials: L
authors.lastname: Jaeger
mesh_terms: D001483:Base Sequence; D007438:Introns; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012335:RNA, Ribosomal / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D012335:RNA, Ribosomal