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Figure 4 | Mobile DNA

Figure 4

From: R2 and R2/R1 hybrid non-autonomous retrotransposons derived by internal deletions of full-length elements

Figure 4

The 5' ends of D. willistoni (Dwi) elements function as ribozymes. (A) RNA sequences from the 5' end of R2Dwi folded into the secondary structure previously determined for the ribozymes encoded by other Drosophila R2 (left). J = nucleotides joining paired regions; L = loop; P = base paired region [25]. Similar structures are presented for R2Dwi_SIDE (‘Short Internally Deleted Element’) (center) and R2/R1Dwi_SIDE (right) with nucleotide differences relative to the R2 element circled in blue. J1/2 sequences for each element type are presented below with nucleotide differences relative to R2Dwi boxed in blue. Nucleotides boxed in pink correspond to a stop codon found in most Drosophila R2 elements. Nucleotide circled in pink corresponds to a ‘U’ residue conserved in Drosophila R2 elements and the R2 SIDE but not the hybrid SIDEs. (B) A 5% polyacrylamide denaturing gel showing the in vitro generated RNAs from 5' junction templates starting 95 bp upstream of the R2 site (lanes 1 and 2) or 74 bp upstream of the R1 site (lane 3) and extending 5 to 10 bp downstream of the ribozyme structure. Lane numbers correspond to ribozyme structure in (A). The uncleaved RNA (solid circle) and self-cleaved products (open circles) are indicated for each ribozyme. The fraction of synthesized RNA undergoing self-cleavage (fc) is under each lane. Lane M, RNA length markers with sizes indicated.

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