We have identified two regions of non-random purine/pyrimldine strand asymmetry that were nearly identical in sequence in the 5′ flanking (promoter) regions of the human cystic fibrosis transmembrane conductance regulator (CFTR) gene and the human MUC1 gene. These regions contain perfect mirror repeat elements, a sequence motif previously found to be associated with the formation of H-DNA conformations. In this report we demonstrate that a single-stranded non-B DNA conformation exists at low pH in supercoiled plasmids containing the similar mirror repeat elements, and that S1 nuclease digestion maps the single-stranded region to the position of the mirror repeats. In addition, we identify a nuclear protein of approximately 27 kD that binds to single-stranded oligonucleotides corresponding to the purtne-rlch strand of this region, but not to the pyrlmldlne-rlch strands or to double-stranded oligonucleotides with corresponding purine/pyrimidlne strand asymmetry.
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