Dynamics and energy landscape of DNA plectoneme nucleation

Abstract

DNA buckling is the fundamental step for plectoneme nucleation and supercoil dynamics that are critical in the processing of genetic information. Here we systematically quantify DNA buckling dynamics using high-speed magnetic tweezers. Buckling times are ∼10-100ms and depend exponentially on both applied force and twist. By deconvolving measured time traces with the instrument response, we reconstruct full two-dimensional extension-twist energy landscapes of the buckling transition that reveal an asymmetry between the pre- and postbuckling states and suggest a highly bent transition state conformation.