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. 2004 Oct 8;383(Pt 2):371–382. doi: 10.1042/BJ20040792

Figure 5. A DNA distortion is present in the core gapA P1 promoter.

Figure 5

(a) Plasmid pBS::EcogapA and its derivatives were used as the templates for PCR amplifications with oligonucleotides 1 (5′-ATTGCCCTTTAAAATTCGGGG-3′) and 2 (5′-TATTTCAGCACATATGCCATG-3′) of fragments (+155 to −140) that carry the WT or mutated promoter sequences (see the Experimental section). (b) The amplified fragments, generated from the promoter DNA indicated above the lanes, were fractionated on a 6% polyacrylamide non-denaturing gel. The molecular-mass standard (lane M) was produced by Sau3AI digestion of plasmid pBR322. It was used to determine the apparent lengths of the amplified DNA fragments. (c) Models of the DNA bending of the variant gapA P1 promoters generated by using the plot.it server [30]. Upper panel: differential bending between WT and variant mt-18T to G gapA P1 promoters; lower panel: effect of a mutation at positions −18 and −19 on DNA bending.