Conformational change of DNA bound to transcription factor response to environmental change

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The [2Fe-2S] transcriptional factor SoxR functions as a sensor of oxidative stress in Escherichia coli. In the oxidized state, transcription is activated by distorting the target DNA promoter region to initiate transcription by RNA polymerase, while the inactive reduced state of the protein remains uncharacterized. The redox-dependent conformational change of the promoter DNA was directly observed by site-specifically replacing the adenine and cytosine bases of the promoter oligonucleotide with the fluorescent probes 2-aminopurine (2Ap) and pyrrolo-dC, respectively. Reduction of the [2Fe-2S] cluster in SoxR-DNA complex dramatically weakened the fluorescence intensity of the 2Ap moieties incorporated into the central part of the DNA. These results strongly suggested that the redox change caused a large conformational change within the region confined to the central A-T base pairs in the promoter region of the DNA.