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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.
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