The compaction of DNA helices into either continuous supercoils or folded-fiber rods and toroids

Abstract

We have investigated by electron microscopy the mechanism of DNA compaction and have found that the double helix has the intrinsic potential to direct its own packaging into two distinctly different and mutally exclusive modes. The mode of DNA packaging is determined by the electrostatic charge density and water activity of the immediate microenvironment of the helix. The two basic structures formed by both linear and covalently closed-circular DNA are: a left-handed supercoil characteristic of minimally charge-shielded DNA, and a smooth rod characteristic of fully charge-shielded DNA. We propose that in the supercoil, the double helix is overwound (increased turn-angle), while in the rod, the helix is folded back and forth on itself. Variation of these two basic structures are the beaded fiber of DNA obtained with partially charge-shielded DNA and the toroid formed by the bending of the DNA rod and fusion of its ends in the presence of certain cations. We compare the DNA packaging inside these in vitro generated structures to DNA packaging in chromatin and viral capsids, and conclude that the packaging of DNA brought about by the use of salts and alcohol closely mimics the packaging behavior of the DNA in vivo, where it is usually complexed with histones or polyamines.