pH modulation methods and systems for detecting binding events

A method of detecting binding between a protein nucleic acid (PNA) and a deoxyribonucleic acid (DNA), comprising:

• obtaining a first fluorescence measurement of a first solution comprising a PNA;
• introducing a second solution comprising a DNA to the first solution to form a third solution,
• wherein the PNA or the DNA, but not both, is labeled with a pH-sensitive fluorophore, wherein the pH-sensitive fluorophore is ortho-sulforhodamine 101;
• and
• obtaining a second fluorescence measurement of the third solution, wherein a change in fluorescence between the first and second fluorescence measurements is indicative of binding of the PNA and the DNA to form a PNA/DNA complex.

A method of detecting binding between a first molecule and a second molecule, comprising:

• obtaining a first fluorescence measurement of a pH-sensitive fluorophore-labeled substrate and a first non-fluorescently-labeled molecule, wherein the pH-sensitive fluorophore-labeled substrate is an ortho-sulforhodamine 101-labeled substrate;
• contacting the pH-sensitive fluorophore-labeled substrate with a second non-fluorescently-labeled molecule in the presence of the first molecule;
• and
• obtaining a second fluorescence measurement of the pH-sensitive fluorophore-labeled substrate, wherein a change in fluorescence between the first and second measurements is indicative of binding of the first molecule to the second molecule.