Abstract: Provided are methods of determining bound and unbound regions in nucleic acid molecules. In certain aspects, the methods include forming adducts in a double-stranded nucleic acid molecule that mark the locations of unbound regions in the double-stranded nucleic acid, and detecting the locations of the adducts in the double-stranded nucleic acid using a nanopore. Bound regions of the double-stranded nucleic acid molecule are determined based on the absence of adducts. In certain aspects, the double-stranded nucleic acid molecule is genomic DNA and the bound regions are nucleosome positions. As such, encompassed by the methods are methods of determining nucleosome positions in genomic DNA. Systems and kits that find use, e.g., in practicing the methods of the present disclosure are also provided.