title: Secondary structures for 5' regions of R2 retrotransposon RNAs reveal a novel conserved pseudoknot and regions that evolve under different constraints.
abstract: Sequences from the 5' region of R2 retrotransposons of four species of silk moth are reported. In Bombyx mori, this region of the R2 messenger RNA contains a binding site for R2 protein and mediates interactions critical to R2 element insertion into the host genome. A model of secondary structure for a segment of this RNA is proposed on the basis of binding to oligonucleotide microarrays, chemical mapping, and comparative sequence analysis. Five conserved secondary structures are identified, including a novel pseudoknot. There is an apparent transition from an entirely RNA structure coding function in most of the 5' segment to a protein coding function near the 3' end. This suggests that local regions evolved under separate functional constraints (structural, coding, or both).
authors.affiliation: Department of Chemistry, University of Rochester, NY 14627-0216, USA.
authors.forename: Elzbieta
authors.initials: E
authors.lastname: Kierzek
authors.forename: Shawn M
authors.initials: SM
authors.lastname: Christensen
authors.forename: Thomas H
authors.initials: TH
authors.lastname: Eickbush
authors.forename: Ryszard
authors.initials: R
authors.lastname: Kierzek
authors.forename: Douglas H
authors.initials: DH
authors.lastname: Turner
authors.forename: Walter N
authors.initials: WN
authors.lastname: Moss
mesh_terms: D020121:5' Untranslated Regions; D000818:Animals; D001483:Base Sequence; D012831:Bombyx / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012333:RNA, Messenger / Q000737:chemistry* / Q000235:genetics; D018626:Retroelements / Q000235:genetics*; D016415:Sequence Alignment
chemical_list: D020121:5' Untranslated Regions; D012333:RNA, Messenger; D018626:Retroelements