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.