title: Diversity of base-pair conformations and their occurrence in rRNA structure and RNA structural motifs.
abstract: In addition to the canonical base-pairs comprising the standard Watson-Crick (C:G and U:A) and wobble U:G conformations, an analysis of the base-pair types and conformations in the rRNAs in the high-resolution crystal structures of the Thermus thermophilus 30S and Haloarcula marismortui 50S ribosomal subunits has identified a wide variety of non-canonical base-pair types and conformations. However, the existing nomenclatures do not describe all of the observed non-canonical conformations or describe them with some ambiguity. Thus, a standardized system is required to classify all of these non-canonical conformations appropriately. Here, we propose a new, simple and systematic nomenclature that unambiguously classifies base-pair conformations occurring in base-pairs, base-triples and base-quadruples that are associated with secondary and tertiary interactions. This system is based on the topological arrangement of the two bases and glycosidic bonds in a given base-pair. Base-pairs in the internal positions of regular secondary structure helices usually form with canonical base-pair groups (C:G, U:A, and U:G) and canonical conformations (C:G WC, U:A WC, and U:G Wb). In contrast, non-helical base-pairs outside of regular structure helices usually have non-canonical base-pair groups and conformations. In addition, many non-helical base-pairs are involved in RNA motifs that form a defined set of non-canonical conformations. Thus, each rare non-canonical conformation may be functionally and structurally important. Finally, the topology-based isostericity of base-pair conformations can rationalize base-pair exchanges in the evolution of RNA molecules.
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
mesh_terms: D020029:Base Pairing; D002241:Carbohydrates / Q000737:chemistry; D018360:Crystallography, X-Ray; D019614:Haloarcula marismortui / Q000235:genetics; D006860:Hydrogen Bonding; D015394:Molecular Structure; D011522:Protons; D012335:RNA, Ribosomal / Q000737:chemistry*; D016963:Thermus thermophilus / Q000235:genetics
chemical_list: D002241:Carbohydrates; D011522:Protons; D012335:RNA, Ribosomal