title: Analysis of RNA motifs.
abstract: RNA motifs are directed and ordered stacked arrays of non-Watson-Crick base pairs forming distinctive foldings of the phosphodiester backbones of the interacting RNA strands. They correspond to the 'loops' - hairpin, internal and junction - that intersperse the Watson-Crick two-dimensional helices as seen in two-dimensional representations of RNA structure. RNA motifs mediate the specific interactions that induce the compact folding of complex RNAs. RNA motifs also constitute specific protein or ligand binding sites. A given motif is characterized by all the sequences that fold into essentially identical three-dimensional structures with the same ordered array of isosteric non-Watson-Crick base pairs. It is therefore crucial, when analyzing a three-dimensional RNA structure in order to identify and compare motifs, to first classify its non-Watson-Crick base pairs geometrically.
authors.affiliation: Department of Chemistry and Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, Ohio 43403, USA. leontis@bgnet.bgsu.edu
authors.forename: Neocles B
authors.initials: NB
authors.lastname: Leontis
authors.forename: Eric
authors.initials: E
authors.lastname: Westhof
mesh_terms: D020029:Base Pairing; D001665:Binding Sites; D008279:Magnetic Resonance Imaging; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D018747:RNA, Chloroplast / Q000737:chemistry
chemical_list: D018747:RNA, Chloroplast; D012313:RNA