Counterintuitive findings could shed light on how proteins bind to DNA
By Charles Q. Choi | July 12, 2006
When DNA is gently stretched, it appears to wind itself more tightly, a counterintuitive finding that may eventually help explain how proteins bind to DNA, researchers reported this week in Nature.
"This is a very intellectually interesting result that is very fundamental to understanding the properties of DNA," Wilma Olson at Rutgers University in Piscataway, N.J., not a coauthor, told The Scientist.
Scientists have studied DNA's mechanical properties on a single molecular level for more than a decade. A previous study did not see DNA unwinding when gently stretched, but relatively noisy data may have obscured the miniscule effect, according to the authors of the latest paper, led by Carlos Bustamante at the University of California at Berkeley.
To stretch the DNA, Bustamante and his team attached a magnetic bead to one end of a DNA molecule and attached the other end of the DNA molecule to glass, then pulled the bead and the DNA back and forth using magnetic tweezers. To measure DNA twisting, Bustamante and his colleagues attached a fluorescent bead to the middle of a double-stranded DNA molecule, just below a single-strand nick that served as a swivel for the bead to spin in like a rotor. Changes in the angle of the rotor bead, spotted using an inverted epifluorescence microscope, reflected any shift in the twist of the DNA.
Bustamante and his colleagues found that under gentle stretching, DNA molecules actually overwind (instead of unwinding as expected), reaching maximum twist when pulled at a tension of 30 piconewtons. Once DNA is stretched beyond this level, it begins to unfurl. Likewise, overwinding the DNA by rotating the magnets caused the DNA to stretch. The researchers designed a mathematical model of DNA that showed that when the molecule was stretched, the radius of the double helix shrunk, possibly explaining the overwinding.
These findings could explain why previous studies have found that DNA appears unusually resistant against twisting. The outer helix of the double-stranded molecule could compress when twisted, stiffening it, according to the researchers. "It's amazing that 53 years after the discovery of the structure of DNA, there are mysteries there still awaiting discovery," Bustamante told The Scientist.
Timothée Lionnet at École Normale Supérieure in Paris has found similar results, but did not participate in the study. "This work has important implications for the modeling DNA-protein interactions -- for example, the understanding of how proteins recognize specific sequences," he told The Scientist. The findings suggest DNA-binding proteins must induce changes in stretching or winding of DNA molecules in order to recognize binding sites that vary in length -- due, for instance, to base pair insertions or deletions, Bustamante said.
"It would be interesting to test how DNA sequence affects the response to twist. This could be performed by comparing the single-molecule behavior of several DNA sequences," Lionnet added.
"We can also go back and reexamine results from past crystallography experiments to look for this relationship between sequence and length and torsion that might have been discounted before," Bustamante noted.
Additional studies could also investigate the stretching and twisting properties of other geometries the DNA double helix can assume, beside the B-form that may predominate in cells. "In RNA, the double helix is an A-form also, which of course we'd like to know the behavior of as well. And hybrids of DNA and RNA happen in transcription, which we're planning on investigating ourselves," Bustamante said.
Charles Q. Choi
Links within this article
J. Gore et al. "DNA overwinds when stretched." Nature, published online July 12, 2006.
J.D. Moroz, P. Nelson. "Entropic elasticity of twist-storing polymers." Macromolecules, August 19, 1998.
Illustration of how the DNA was stretched and how DNA twisting was measured
C.G. Baumann et al. "Ionic effects on the elasticity of single DNA molecules." PNAS, June 10, 1997.
T. Lionnet et al. "Wringing out DNA." Physical Review Letters, May 5, 2006.