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. 2008 Jul 15;36(14):4680–4688. doi: 10.1093/nar/gkn438

Figure 1.

Figure 1.

Plasmid substrates. (A) Map of the parental plasmid substrate, pTFOLK. pTFOLK contains tandemly arranged supF genes each containing a different deletion at a different location, separated by 60 bp and a TFO1 binding site adjacent to a psoralen crosslinking site. The black bars indicate the deletions. The 8 bp deletion in the upstream supF gene is located at the BstBI site, and the 24 bp deletion in the downstream supF gene spans the XhoI to BsrBI sites. The binding site for the psoralen-conjugated TFO (pTFO1) was either centrally located between the supF copies (A), was nearer to the downstream supF gene (B) or was placed nearer to the upstream supF gene (C). (D and E) Plasmid substrates used to confirm that the distance between the supF promoter and the supF genes did not affect the function of the genes. The plasmid in 1D (p24BstB-TFOLK) is similar to pTFOLK plasmid, except that the upstream supF gene contains a larger deletion (24 bp) at the BstBI site, and the downstream supF gene is wild-type. The plasmid in 1E (p24BstB–1.4K) is similar to plasmid p24BstB–TFOLK, the only difference being the distance between the supF genes is 1.4 kb rather than 60 bp. (F) Plasmid p24BstB/TFOLK/BsrB was designed to determine the effect of deletion size on gene conversion events. This plasmid is similar to pTFOLK, except that the deletion positions were inverted; the larger 24 bp deletion at the BstBI site is in the upstream supF gene, while the smaller 8 bp deletion at the BsrBI site is in the downstream supF gene.