Torque measurements reveal sequence-specific cooperative transitions in supercoiled DNA

B-DNA becomes unstable under superhelical stress and is able to adopt a wide range of alternative conformations including strand-separated DNA and Z-DNA. Localized sequence-dependent structural transitions are important for the regulation of biological processes such as DNA replication and transcription. To directly probe the effect of sequence on structural transitions driven by torque, we have measured the torsional response of a panel of DNA sequences using single molecule assays that employ nanosphere rotational probes to achieve high torque resolution. The responses of Z-forming d(pGpC)(n) sequences match our predictions based on a theoretical treatment of cooperative transitions in helical polymers. Bubble templates containing 50-100 bp mismatch regions show cooperative structural transitions similar to B-DNA, although less torque is required to disrupt strand-strand interactions. Our mechanical measurements, including direct characterization of the torsional rigidity of strand-separated DNA, establish a framework for quantitative predictions of the complex torsional response of arbitrary sequences in their biological context.