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Materials

Twist and Stretch

When small stretching forces are applied, DNA winds up more tightly rather than lengthening

by Celia Henry Arnaud
August 14, 2006 | A version of this story appeared in Volume 84, Issue 33

Stretch
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Credit: Adapted from Nature ©2006
Pulling on a DNA strand (left) makes it wind up tighter, as measured by the movement of the rotor bead attached to a nick in one of the DNA strands. In a second type of experiment without the rotor bead, winding the DNA makes the molecule lengthen. In both sets of experiments, one end of the DNA is attached to a glass slide and the other end to a magnetic bead that can be manipulated with magnets.
Credit: Adapted from Nature ©2006
Pulling on a DNA strand (left) makes it wind up tighter, as measured by the movement of the rotor bead attached to a nick in one of the DNA strands. In a second type of experiment without the rotor bead, winding the DNA makes the molecule lengthen. In both sets of experiments, one end of the DNA is attached to a glass slide and the other end to a magnetic bead that can be manipulated with magnets.

What happens to a DNA molecule when you pull on it? A simple picture of DNA envisions it as a twisted or braided rope. Just as a rope lengthens when it unwinds, you might also expect that untwisted DNA would stretch. Independent teams in France and California have shown that this simplistic model isn't right at physiologically relevant forces.

In fact, they have shown that DNA actually winds up tighter and shortens when small forces are applied. Vincent Croquette and coworkers at Ecole Normale Sup érieure, Paris, published their results in May in Physical Review Letters (2006, 96, 178102). Carlos Bustamante and coworkers at the University of California, Berkeley, reported their findings in July in Nature (DOI: 10.1038/nature04974).

"The basic result−that pulling on DNA initially causes the double helix to increase its rate of twist-is certainly surprising given the prejudice many of us have that strong pulling untwists the double helix," says John F. Marko, a physics professor at the University of Illinois, Chicago. "I hasten to point out that this result does not violate any laws of symmetry."

This image of DNA lengthening as it unwinds depends on the length of the backbones and the diameter of the double helix being constant, says Timothée Lionnet, a member of Croquette's group and the lead author on the paper, but that image turns out not to be the case. Instead, the diameter shrinks and the molecule lengthens as the DNA twists, he says.

The coupling of twisting and stretching had been predicted because of DNA's chirality. What was not expected was the inverse relationship between the two at small forces. Researchers tried to observe these effects earlier, but the available methods didn't offer enough resolution, Lionnet says.

Both groups discovered DNA's counterintuitive behavior by investigating the mechanical properties of individual molecules. "Methods of single-molecule manipulation are providing scientists with unique views of how to study these molecules and how to study biochemistry," Bustamante says. "This is a very powerful approach, and I think we are only scratching the surface. Many questions in biology can be better approached and answered by using single-molecule manipulation and single-molecule detection methods."

The two teams performed similar experiments in which they anchored one end of a DNA molecule to a glass surface and the other end to a magnetic bead. They then moved and rotated magnets to stretch or twist the DNA molecule.

In one experiment, they applied a constant force and used the magnets to rotate the DNA. By measuring the position of the magnetic bead, they determined the length of the DNA as a function of the induced twist. Contrary to expectations, the DNA lengthened as it was wound more tightly.

"At first, we were puzzled by this effect," Lionnet says. They enlisted their colleague Richard Lavery to carry out a numerical simulation of the DNA structure under such conditions. The model was in accord with the experimental data.

Bustamante's group performed an additional experiment in which they approached the problem from the other perspective. They stretched the DNA to see how the pulling affects the twisting. They engineered a nick in the DNA strand, creating a freely rotating single-stranded region, and attached a fluorescent reporter bead to the nick. Changes in the angle of this "rotor bead" reflect changes in the twist of the lower portion of the DNA molecule. Stretching the DNA increased the angle of the rotor bead, indicating that the DNA was becoming more tightly wound.

Both groups see this odd behavior only at small forces less than 30 piconewtons. When greater force is applied, the DNA begins to unwind, as expected. The small forces, however, are physiologically relevant and more closely resemble what the DNA probably experiences in the cell. "The types of tensions and forces that are likely to be applied to the DNA molecule are in the low regime," Bustamante says. "We are studying the regime where things are actually likely to happen."

Both groups hypothesize that the effect will depend on the sequence of the DNA, but they don't yet have the experimental data to back up that hunch. Both groups plan to investigate the effect of the DNA sequence on the phenomenon.

Scientists may want to revisit earlier DNA crystal structures, Bustamante says. In some structures, the DNA appeared to be overwound but also lengthened. Investigators thought they were seeing a crystallization artifact. Bustamante and Croquette's studies "suggest that we can actually go back to those kinds of studies and crystallize pieces with specific sequences and establish a correlation between twist and stretch for different sequences," Bustamante says.

The findings could have significant consequences for the understanding of DNA biology. Mechanical properties introduce another mechanism through which DNA and proteins can interact, in addition to hydrogen bonds. "People are starting to think that proteins could recognize sequences just by 'feeling' deformability of a DNA double helix that changes [according to] sequence," Lionnet says. "The majority of this language of deformation remains to be deciphered."

Studies such as the recently described ones are now possible because single-molecule methods are becoming ever more powerful. "Scientists are now moving to the point where they can look at the mechanics of a single molecule," Bustamante says. "We really are following the molecular dynamics at the level of a single molecule."

Bustamante suspects that single-molecule techniques still have much to reveal about DNA. "These studies are showing that there are still discoveries to be made about the molecule we thought we knew very well," he says.

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