To test what happens when a DNA molecule is overwound, the DNA was stretched between a glass coverslip and a paramagnetic bead, while a fluorescent avidin-coated rotor bead was attached to the DNA just below a biochemical nick. Tension in the DNA was controlled by raising or lowering the magnets, and changes in winding were observed by tracking the rotation of the fluorescent bead.
A simple toy model shows DNA as an elastic rod (grey) wrapped helically by a stiff wire (red). Stretching generates an overwinding of the helix because the inner rod decreases in diameter as it is stretched. The outer helix is then able to wrap a larger number of times over the length of the molecule
To explain the overwinding, Bustamante and his coauthors have proposed a simple “toy” model in which the radius of the DNA double-helix is allowed to shrink as the molecule is stretched. The model consists of an elastic rod that is wrapped around its outer surface by a stiff wire, analogous to DNA’s sugar-phosphate backbone. The elastic rod is constructed from a material that conserves volume under stress.
“As this system is stretched, the elastic rod decreases in diameter,” said Bustamante. “This enables the outer wire to wrap a larger number of times over the length of the rod.”
The twist-stretch coupling results demonstrated by Bustamante and his collaborators holds important implications for how DNA-binding proteins are able to recognize their target sites along the helix. These proteins are known to bend, wrap, loop and twist DNA. Now it has been shown that they can achieve their goals by simultaneously stretching and overwinding a DNA molecule, or by compressing and underwinding it.