Helical correlations in curved DNA condensates

Abstract DNA–DNA interactions at work in chromosome shaping and sequence recognition take place in dense and confined environments. Theory and simulation have predicted that, at small separation, interactions between double helices are helically modulated, leading to correlations, a phenomenon poorly documented experimentally. In particular, helical correlations are not compatible with curvature, a general feature of DNA dense states in vitro and in vivo. Using cryo electron microscopy of DNA toroids obtained in vitro in the presence of a condensing agent, we analyze helical correlations in curved condensates. We show that in-phase helix alignments are preferred over a wide range of ionic concentrations. Optimization of helical correlations in a curved assembly is achieved through rearrangements within the toroid as it grows: the nucleation of radial alignments is followed by a circumferential propagation leading to a polygonal shaping of the object. Extended phased flat domains alternate with localized, highly curved, frustrated regions. In addition, the combination of bending and helical correlations results in a local decrease in the DNA helical pitch in highest curvature regions. Overall, this work shows how helical correlations tune both the shape of DNA condensates at the mesoscale and the conformation of the double helix at the nanoscale.