title: Bulge-out structures in the single-stranded trimer AUA and in the duplex (CUGGUGCGG).(CCGCCCAG). A model-building and NMR study.
abstract: Model-building studies were carried out on the trimer AUA. Bulge-out structures which allow incorporation into a continuous RNA helix were generated and energy-minimized. All geometrical features obtained by previous NMR studies on purine-pyrimidine-purine sequences are accounted for in these models. One of the models was used to fit into a double helical fragment. Only minor changes were necessary to construct a central bulge-out in an otherwise intact duplex. NMR and model-building studies were performed on the duplex (CUGGUGCGG).(CCGCCCAG) which contains an unpaired uridine residue. NOE data, chemical-shift profiles and imino-proton resonances provided evidence that the extra U is bulged out of the duplex. The relatively small dispersion in 31P chemical shifts (approximately equal to 0.7 ppm) indicate the absence of t/g or g/t combinations for the phosphodiester angles zeta/alpha. An energy-minimized model of the duplex, which fits the present collection of data, is presented.
authors.affiliation: Gorlaeus Laboratories, Leiden University, The Netherlands.
authors.forename: Y T
authors.initials: YT
authors.lastname: van den Hoogen
authors.forename: A A
authors.initials: AA
authors.lastname: van Beuzekom
authors.forename: E
authors.initials: E
authors.lastname: de Vroom
authors.forename: G A
authors.initials: GA
authors.lastname: van der Marel
authors.forename: J H
authors.initials: JH
authors.lastname: van Boom
authors.forename: C
authors.initials: C
authors.lastname: Altona
mesh_terms: D001482:Base Composition; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012330:RNA, Double-Stranded
chemical_list: D012330:RNA, Double-Stranded