title: Flexible elements in the structure of promoter DNA as probed by cationic surfactant binding.
abstract: 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.
authors.affiliation: Institute of Cell Biophysics, Russian Academy of Sciences Pushchino, Moscow Region, 142290 Russia.
authors.forename: I S
authors.initials: IS
authors.lastname: Masulis
authors.forename: V A
authors.initials: VA
authors.lastname: Buckin
authors.forename: O N
authors.initials: ON
authors.lastname: Ozoline
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D002412:Cations; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D008024:Ligands; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D000644:Quaternary Ammonium Compounds / Q000737:chemistry*; D013501:Surface-Active Agents / Q000737:chemistry*; D014158:Transcription, Genetic
chemical_list: D002412:Cations; D008024:Ligands; D000644:Quaternary Ammonium Compounds; D013501:Surface-Active Agents; D004247:DNA; C022806:dodecyltrimethylammonium