Compaction of Plasmid DNA by Macromolecular Crowding

Abstract

With a view to understand compaction of DNA in crowded conditions, we have measured the radius of gyration of pHSG298 plasmid (2675 bp) in its supercoiled and linear forms and in the presence of dextran nanoparticles with light scattering. It was observed that the supercoil initially expands and subsequently compacts with increasing volume fraction of the crowder. The extent of the expansion depends on the size of the nanoparticle, with the smallest particles exhibiting the largest effect. In the case of the linear plasmid, monotonous compaction and no apex in the radius of gyration were observed. The plasmid does not collapse into a condensed state. In crowded conditions, the size of the supercoiled molecule exceeds the one of its linear variant. Supercoiling hence restrains rather than facilitates compaction of crowded DNA. Our results show two different, but closely related, aspects of the crowding phenomenon. First, the supercoil expands through a modification of its geometrical properties by the depl...