title: Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element.
abstract: RNA transcripts corresponding to the 250-nt 3' untranslated region of the R2 non-LTR retrotransposable element are recognized by the R2 reverse transcriptase and are sufficient to serve as templates in the target DNA-primed reverse transcription (TPRT) reaction. The R2 protein encoded by the Bombyx mori R2 can recognize this region from both the B. mori and Drosophila melanogaster R2 elements even though these regions show little nucleotide sequence identity. A model for the RNA secondary structure of the 3' untranslated region of the D. melanogaster R2 retrotransposon was developed by sequence comparison of 10 species aided by free energy minimization. Chemical modification experiments are consistent with this prediction. A secondary structure model for the 3' untranslated region of R2 RNA from the R2 element from B. mori was obtained by a combination of chemical modification data and free energy minimization. These two secondary structure models, found independently, share several common sites. This study shows the utility of combining free energy minimization, sequence comparison, and chemical modification to model an RNA secondary structure.
authors.affiliation: Department of Chemistry, University of Rochester, New York 14627-0216, USA.
authors.forename: D H
authors.initials: DH
authors.lastname: Mathews
authors.forename: A R
authors.initials: AR
authors.lastname: Banerjee
authors.forename: D D
authors.initials: DD
authors.lastname: Luan
authors.forename: T H
authors.initials: TH
authors.lastname: Eickbush
authors.forename: D H
authors.initials: DH
authors.lastname: Turner
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D012831:Bombyx / Q000235:genetics; D003198:Computer Simulation; D004330:Drosophila / Q000145:classification / Q000235:genetics; D008745:Methylation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D011485:Protein Binding; D012313:RNA / Q000737:chemistry* / Q000187:drug effects / Q000378:metabolism; D012194:RNA-Directed DNA Polymerase / Q000378:metabolism*; D018626:Retroelements / Q000235:genetics*; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D013379:Substrate Specificity; D013696:Temperature; D013698:Templates, Genetic; D013816:Thermodynamics
chemical_list: D018626:Retroelements; D012313:RNA; D012194:RNA-Directed DNA Polymerase