A Versatile Method to Quantify DNA-Protein Interactions on Negatively Supercoiled DNA

Many genomic processes are regulated by torsional stress, resulting in a range of supercoiled DNA structures. In order to understand the effect of such structures on protein binding and activity, several single-molecule techniques are often employed. These include magnetic, micro-pipette and angular optical tweezers. However, two factors can limit the study of DNA-protein interactions on supercoiled DNA. First, it is challenging to combine DNA-torque control with fluorescence microscopy. Second, the DNA substrate is typically tethered to a surface, hindering rapid buffer exchange.