Methods for Determining Bound and Unbound Regions in Nucleic Acid Molecules and Systems for Practicing Same

A system, comprising:

• a device, comprising:
• a substrate having a nanopore therein, the substrate separating a first fluid chamber from a second fluid chamber;
• a power source electrically coupled to electrodes, wherein the power source and electrodes are adapted to apply a potential difference between the first fluid chamber and the second fluid chamber;
• and
• instructions that cause the system to:
• apply a potential difference between the first fluid chamber and the second fluid chamber such that genomic DNA in the first fluid chamber is drawn toward the second fluid chamber and exposed to the nanopore in a sequential manner, wherein the genomic DNA comprises adducts that mark the locations of linker genomic DNA in the genomic DNA;
• detect electrical signals from the nanopore corresponding to the adducts;
• and
• record the locations of the adducts in the genomic DNA.

A method for determining bound regions in a double-stranded nucleic acid molecule, comprising:

• 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,
• wherein bound regions of the double-stranded nucleic acid molecule are determined based on the absence of adducts.

A system, comprising:

• a device, comprising:
• a substrate having a nanopore therein, the substrate separating a first fluid chamber from a second fluid chamber;
• a power source electrically coupled to electrodes, wherein the power source and electrodes are adapted to apply a potential difference between the first fluid chamber and the second fluid chamber;
• and
• instructions that cause the system to:
• apply a potential difference between the first fluid chamber and the second fluid chamber such that a double-stranded nucleic acid molecule in the first fluid chamber is drawn toward the second fluid chamber and exposed to the nanopore in a sequential manner, wherein the double-stranded nucleic acid molecule comprises adducts that mark the locations of unbound regions of the double-stranded nucleic acid molecule;
• detect electrical signals from the nanopore corresponding to the adducts;
• and
• record the locations of the adducts in the double-stranded nucleic acid molecule.