Enzymatic and chemical probing of an S1 nuclease-sensitive site upstream from the human CFTR gene

Similar purine/pyrimidine mirror repeat ( PMR) DNA sequences have been identified in the 5'-flanking regions of the human cystic fibrosis transmembrane conductance regulator (h CFTR) and mucin (h MUC1) genes, and supercoiled (but not linearized) plasmids containing these promoter regions were previously shown to be sensitive to digestion by SI nuclease. The PMR element derived from the h CFTR promoter region is now sub-cloned and characterized at nucleotide resolution with respect to its reactivity toward nucleases S1 and P1, and toward the chemical probes dimethyl sulfate, chloroacetaldehyde, diethylpyrocarbonate and osmium tetroxide. These probes confirm the presence, at pH 4.5 (but not at pH 7.1), of a non-B-DNA structure. This non-B-DNA structure is distinct from H-DNA, because enzymatic and chemical probing detect single-stranded character in the absence of a stable intramolecular triple helix or extruded purine strand.