title: Secondary structure models of the 3' untranslated regions of diverse R2 RNAs.
abstract: The RNA structure of the 3' untranslated region (UTR) of the R2 retrotransposable element is recognized by the R2-encoded reverse transcriptase in a reaction called target primed reverse transcription (TPRT). To provide insight into structure-function relationships important for TPRT, we have created alignments that reveal the secondary structure for 22 Drosophila and five silkmoth 3' UTR R2 sequences. In addition, free energy minimization has been used to predict the secondary structure for the 3' UTR R2 RNA of Forficula auricularia. The predicted structures for Bombyx mori and F. auricularia are consistent with chemical modification data obtained with beta-ethoxy-alpha-ketobutyraldehyde (kethoxal), dimethyl sulfate, and 1-cyclohexyl-3-(2-morpholinoethyl)carbodiimide metho-p-toluene sulfonate. The structures appear to have common helices that are likely important for function.
authors.affiliation: Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, USA.
authors.forename: Amy M
authors.initials: AM
authors.lastname: Ruschak
authors.forename: David H
authors.initials: DH
authors.lastname: Mathews
authors.forename: Arkadiusz
authors.initials: A
authors.lastname: Bibillo
authors.forename: Sherry L
authors.initials: SL
authors.lastname: Spinelli
authors.forename: Jessica L
authors.initials: JL
authors.lastname: Childs
authors.forename: Thomas H
authors.initials: TH
authors.lastname: Eickbush
authors.forename: Douglas H
authors.initials: DH
authors.lastname: Turner
mesh_terms: D020413:3' Untranslated Regions; D000818:Animals; D001483:Base Sequence; D012831:Bombyx / Q000235:genetics; D004330:Drosophila / Q000235:genetics; D007313:Insecta / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics*; D012194:RNA-Directed DNA Polymerase / Q000235:genetics; D018626:Retroelements / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid; D014158:Transcription, Genetic
chemical_list: D020413:3' Untranslated Regions; D018626:Retroelements; D012313:RNA; D012194:RNA-Directed DNA Polymerase