Even when biophysicist Paul Wiggins pursues his favorite sport, rock climbing, he doesn’t leave his work behind. While struggling to untangle ropes—”one of the most frustrating aspects of climbing,” he says—Wiggins envisions great lengths of DNA tangled inside cells. The mechanical properties, particularly the flexibility, of that biomolecule fascinate him.
In cells, random thermal motion makes DNA and other long biomolecules wriggle. Experimenters have observed that the distance between bends in DNA tends to be around 50 nanometers. The stiffness of stretches shorter than that seems to overcome the thermal-bending forces. However, scientists have long known that short segments of DNA nonetheless become tightly curved in some cellular DNA-protein complexes, and researchers assumed that proteins muscle the DNA into those configurations. Until recently, however, researchers hadn’t looked directly at such short sections of DNA to see what they were actually doing.
Two years ago, biologists examining DNA in solution reported that short segments can bend more sharply than scientists had expected. Another team challenged that finding. New experimental results from a team of scientists, including Wiggins, now support the bendability of small pieces of DNA.
How easily DNA bends affects crucial functions such as the tight packing of DNA inside cellular nuclei and viral shells and a cell’s use of genetic information to make proteins. For instance, DNA molecules wrap tightly around proteins to form complexes called nucleosomes that must partially unwind at the right moment to make sections of the genetic code accessible to a cell’s molecular machinery.
A revised understanding of DNA bending could also influence designs of nanotechnologists who incorporate DNA into structures such as nanoscale building blocks (SN: 12/10/05, p. 372: Instant Nano Blocks: One-step process makes trillions of DNA pyramids) and devices such as robots (SN: 6/12/04, p. 382: Available to subscribers at DNA puts its best foot forward).
“We are at the very beginning of what may be a paradigm shift in our understanding of how protein-DNA complexes form and function,” says Alexey Onufriev of the Virginia Polytechnic Institute and State University (Virginia Tech) in Blacksburg.
Not all specialists in DNA physics find the new findings so compelling. “I do not see any reliable data proving that DNA is more flexible for [sharp] bends,” says Alexander Vologodskii of New York University.
U-turn
Like a climbing rope, DNA is a floppy filament when considered at lengths that are long compared with its thickness. Yet imagine a piece of heavy rope that’s only a little longer than with its own diameter: The stubby strand would resist sharp bending.
For decades, scientists calculated DNA’s resistance to bending with a formula that took into account the length of DNA segments. Then, in 2004, experiments on DNA in solution at room temperature indicated that a double-helical DNA segment only 30 nm long was thousands of times as likely to spontaneously curl to join its ends as the formula had predicted, reported Timothy E. Cloutier, now of Abbott Laboratories in Abbott Park, Ill., and Jonathan Widom of Northwestern University in Evanston, Ill.
The short DNA pieces in those tests bent to a radius of curvature of 5 nm. Their bends were as tight as those that occur when DNA entwines with proteins in cells. The finding implies that the tight curves seen in DNA-protein complexes can occur without protein.
Vologodskii and his coworkers challenged that result. They pointed out an error in the experimental procedure. Widom and his colleagues are now repeating the experiment with a revised protocol. In the results so far, DNA looping is still 100 times as prevalent as had been originally expected, Widom told Science News.
However, when Vologodskii’s team performed the test, the researchers reported no excess loops.
Despite the disagreement over the results of that experiment, it inspired further tests on the bendability of DNA. Wiggins and his colleagues at five universities in the United States and the Netherlands next took a different tack. Instead of examining dissolved DNA, the team used positive ions to lightly adhere double-helical DNA strands about 1 micrometer long to mica. The researchers then dried the samples and imaged the molecules with an atomic-force microscope.
The scientists, who include Widom and Philip C. Nelson of the University of Pennsylvania in Philadelphia, viewed bends having curvatures as high as those detected by Cloutier and Widom. Those curves were 30 times as prevalent as expected from the standard formula, Wiggins and his colleagues report in the November 2006 Nature Nanotechnology.
Other scientists question whether the drying and other treatment of the DNA examined by Wiggins and his colleagues might have boosted the molecules’ flexibility.
“I’d sure like to see [such measurements] done in free solution,” says biophysicist John F. Marko of Northwestern University.
Around the bend
An examination of DNA in even finer detail also suggests that the molecule is highly bendable. No experimental method is currently available to directly probe DNA’s atomic-level behavior, but Onufriev and Jory Z. Ruscio, also of Virginia Tech, have used computer simulations of every atom in short lengths of DNA in solution and under conditions similar to those of the earlier experiments.
In the simulations, reported in the December 2006 Biophysical Journal, jiggling DNA in solution tended to shorten its length in a way that indicated that it was bending more tightly than predicted by the conventional view of DNA flexibility. Further analysis indicated that the energy needed to make the DNA bend sharply is less than expected in the traditional model.
The team simulated strands 50 nm long—the same length as those that wrap around nucleosomes. At that length, “everyone thought of DNA as similar to an uncooked spaghetti noodle,” which could bend only a little, says Ruscio. “But what we’re seeing is as if you cooked that noodle al dente so it’s much more flexible.”
Further studies of DNA flexibility are under way by many groups. Like rock climbers on an unfamiliar cliff face, DNA specialists must stay flexible themselves, Wiggins adds, to follow whatever unexpected turns the data might take.
