title: Photocleavage of DNA and photofootprinting of E. coli RNA polymerase bound to promoter DNA by azido-9-acridinylamines.
abstract: The long-wavelength ultraviolet (lambda approximately 420 nm) radiation induced reaction between 6-azido-2-methoxy-9-acridinylamines and supercoiled plasmid DNA results in single strand scissions and formation of covalent adducts (ratio approximately 1:10). By treating azidoacridine-photomodified DNA with piperidine at 90 degrees C, additional strand scissions are observed in a complex sequence dependent manner with an overall preference for T greater than or equal to G greater than C much greater than A. The resulting DNA fragments migrate as 5'-phosphates in polyacrylamide gels. Photofootprinting of the binding site of RNA-polymerase on promoter DNA is demonstrated with an azido-9-acridinylamino-octamethylene-9-aminoacridine. Similar experiments using 9-amino-6-azido-2-methoxyacridine indicate that this reagent recognizes changes in the DNA conformation induced by RNA polymerase binding, in relation to open complex formation.
mesh_terms: D000609:Aminoacridines; D001386:Azides; D001665:Binding Sites; D004269:DNA, Bacterial / Q000378:metabolism*; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D004926:Escherichia coli / Q000201:enzymology*; D010777:Photochemistry; D011401:Promoter Regions, Genetic
chemical_list: D000609:Aminoacridines; D001386:Azides; D004269:DNA, Bacterial; C056683:N-(6-azido-2-methoxy-9-acridinyl)-N'-(9-acridinyl)octane-1,8-diamine; C044658:9-amino-3-azido-7-methoxyacridine; D012321:DNA-Directed RNA Polymerases