DNA Supercoiling Enhances Cooperativity and Efficiency of an Epigenetic Switch

Upon infection by bacteriophage λ the λ repressor protein, CI, interacts with the λ operator DNA, thereby regulating protein expression and deciding between the lysogenic and lytic state. This λ switch is a model on the basis of which epigenetic switch regulation is understood. In order to study the interaction between naturally supercoiled DNA and the DNA associating protein CI, we invented a novel assay where supercoiled circular DNA plasmids were individually tethered by peptide nucleic acid (PNA) handles [1]. We used this tethered plasmid assay for a single molecule investigation of the dynamics of supercoiled DNA and studied both the dynamics of the molecule itself and its interactions with the regulatory CI protein. The dynamics of the construct was analyzed by tracking the tethered bead. This revealed that compared with relaxed DNA, the presence of supercoils greatly enhances juxtaposition probability [2]. When CI was added to the supercoiled assay, the protein would attach to the operator sites thereby looping DNA. Our studies reveal that the efficiency and cooperativity of the epigenetic λ switch are significantly increased in the supercoiled system compared with a linear assay, thus increasing the Hill coefficient [2,3]. In contrast to other single molecule assays, the current methodology allows for studying DNA dynamics and DNA-protein interactions of DNA in its naturally supercoiled state.