Flexible elements in the structure of promoter DNA as probed by cationic surfactant binding

A susceptibility of promoter DNA for adaptive conformational transitions has been studied using a cationic surfactant dodecyltrimethylammonium bromide (C(12)TAB) as a model DNA-binding ligand. DNAse 1 and KMnO(4) were utilized as structure-specific reagents. Both reagents revealed ligand-induced perturbations in the double helix of promoters T7A1 and T7D. These conformational transitions appeared to be strongly associated with pyrimidine-purine steps, which have non-random distribution within RNA polymerase contact region of the promoter DNA and are present in the binding sites for a majority of transcription regulation proteins. Potential flexibility of these elements creates therefore a specific media for transcription complex formation. Molecular mechanism of DNA interaction with C(12)TAB is discussed.