SECONDARY STRUCTURE MODEL OF THE RNA RECOGNIZED BY THE REVERSE-TRANSCRIPTASE FROM THE R2 RETROTRANSPOSABLE ELEMENT

RNA transcripts corresponding to the 250-nt 3' untranslated region of the R2 non-LTR retrotransposable element are recognized by the R2 reve rse transcriptase and are sufficient to serve as templates in the targ et DNA-primed reverse transcription (TPRT) reaction. The R2 protein en coded by the Bombyx mori R2 can recognize this region from both the B. mori and Drosophila melanogaster R2 elements even though these region s show little nucleotide sequence identity. A model for the RNA second ary structure of the 3' untranslated region of the D. melanogaster R2 retrotransposon was developed by sequence comparison of 10 species aid ed 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 o btained by a combination of chemical modification data and free energy minimization. These two secondary structure models, found independent ly, share several common sites. This study shows the utility of combin ing free energy minimization, sequence comparison, and chemical modifi cation to model an RNA secondary structure.