Secondary structure models of the 3' untranslated regions of diverse R2 RNAs.
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.
Ruschak
Amy M
AM
Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, USA.
Mathews
David H
DH
Bibillo
Arkadiusz
A
Spinelli
Sherry L
SL
Childs
Jessica L
JL
Eickbush
Thomas H
TH
Turner
Douglas H
DH
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
D020413:3' Untranslated Regions; D018626:Retroelements; D012313:RNA; D012194:RNA-Directed DNA Polymerase