title: A three-dimensional working model for a guide RNA from Trypanosoma brucei.
abstract: RNA editing in protozoan parasites is a mitochondrial RNA processing reaction in which exclusively uridylate residues are inserted into, and less frequently deleted from, pre-mRNAs. Molecules central to the process are so-called guide RNAs (gRNAs) which function as templates in the reaction. For a detailed molecular understanding of the mechanism of the editing process knowledge of structural features of gRNAs will be essential. Here we report on a computer-assisted molecular modelling approach to construct the first three-dimensional gRNA model for gND7-506, a ND7-specific gRNA from Trypanosoma brucei. The modelling process relied on chemical modification and enzymatic probing data and was validated by in vitro mutagenesis experiments. The model predicts a reasonably compact structure, where two stem/loop secondary structure elements are brought into close proximity by a triple A tertiary interaction, forming a core element within the centre of the molecule. The model further suggests that the surface of the gRNA is primarily made up of the sugar-phoshate backbone. On the basis of the model, footprinting experiments of gND7-506 in a complex with the gRNA binding protein gBP21 could successfully be interpreted and provide a first picture for the assembly of gRNAs within a ribonucleoprotein complex.
authors.affiliation: Laboratorium für Molekulare Biologie, Genzentrum der Ludwig Maximillians Universität München, 82152 Martinsried, Germany.
authors.forename: T
authors.initials: T
authors.lastname: Hermann
authors.forename: B
authors.initials: B
authors.lastname: Schmid
authors.forename: H
authors.initials: H
authors.lastname: Heumann
authors.forename: H U
authors.initials: HU
authors.lastname: Göringer
mesh_terms: D000818:Animals; D001483:Base Sequence; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D009690:Nucleic Acid Conformation; D017394:RNA, Guide, Kinetoplastida / Q000737:chemistry* / Q000378:metabolism; D016053:RNA, Protozoan / Q000737:chemistry* / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D015203:Reproducibility of Results; D014346:Trypanosoma brucei brucei / Q000235:genetics*
chemical_list: D016053:RNA, Protozoan; D016601:RNA-Binding Proteins; D017394:RNA, Guide, Kinetoplastida