Scientists Find DNA is Packaged Like a Yoyo

Claire Sturgeon, IGB
3/17/2015

Pictured left to right are Jaya Yodh, research assistant professor and CPLC director of education and outreach, Thuy Ngo, graduate research assistant, and Taekjip Ha, Gutgsell professor of physics
Pictured left to right are Jaya Yodh, research assistant professor and CPLC director of education and outreach, Thuy Ngo, graduate research assistant, and Taekjip Ha, Gutgsell professor of physics
To pack two meters of DNA into a microscopic cell, the string of genetic information must be wound extremely carefully into chromosomes. Surprisingly the DNA’s sequence causes it to be coiled and uncoiled much like a yoyo, scientists reported in Cell.

“We discovered this interesting physics of DNA that its sequence determines the flexibility and thus the stability of the DNA package inside the cell,” said Gutgsell Professor of Physics Taekjip Ha, who is a member of the Carl R. Woese Institute for Genomic Biology. “This is actually very elementary DNA physics. Many people thought we should have known this many decades ago, but there are still surprises in the physics of DNA.”

The DNA is packaged into chromosomes, which resemble beaded bracelets. The string of DNA is coiled around beads, called histones, to create nucleosomes. These nucleosomes are braided together into beaded strings that are intricately woven into chromosomes.

Scientists knew the DNA could be uncoiled from the nucleosome, but it was assumed that the two ends were symmetric, meaning uncoiling the DNA would be like untying a shoe. University of Illinois researchers found that the DNA is actually very asymmetric, like the string wrapped around a yoyo. Pulling on one end of DNA will simply tighten the coil while pulling on the other will cause it to uncoil like a yoyo.

The physics of this nucleosome packaging is determined by the DNA’s sequence, which makes the strand of DNA flexible enough to satisfy two conflicting principles: it has to be stable enough to compact DNA, but dynamic enough so the strand can be uncoiled and read to make proteins.

“There are many good studies that show that if you change the sequence of the gene, then it will affect other things. Different proteins may be created because they require certain sequences for binding and so on,” said Ha. “But no one had really thought about sequence changes having an effect on DNA physics, which in turn cause changes in the biology.”

Ha’s research has shown that it is easier for the cell’s protein-making machinery to read from the “weak” end of the nucleosome that uncoils more easily. They believe that genetic mutations related to diseases, like cancer, alter the stability of the nucleosome.

“This could have a major impact on how the information is read out and how different proteins are produced,” Ha said. “For example, cancer-fighting proteins or cancer-causing proteins may be made differently depending on the changes in DNA flexibility and stability caused by mutations.”

Ha plans to use next generation sequencing to determine the flexibility of an entire genome. He hopes to create the first genome-wide map of physical properties. He also wants to find out if mutations can make the DNA easier or more difficult to read.

This work was supported by the National Science Foundation, the National Institutes for Health, and the Howard Hughes Medical Institute. Ha’s research team included Thuy Ngo, a graduate research assistant; Jaya Yodh, Research Assistant Professor and CPLC Director of Education and Outreach; Qiucen Zhang, a postdoctoral research associate; and graduate student Ruobo Zhou.

The paper, “Asymmetric Unwrapping of Nucleosomes under Tension Directed by DNA Local Flexibility,” is available online (http://dx.doi.org/10.1016/j.cell.2015.02.001).

Recent News

Innovative materials are the foundation of countless breakthrough technologies, and the Illinois Materials Research Science and Engineering Center will develop them. The new center is supported by a six-year, $15.6 million award from the National Science Foundation’s Materials Research Science and Engineering Centers program. It is led by Professor Nadya Mason of Engineering at Illinois’ Department of Physics and its Frederick Seitz Materials Research Laboratory

By building highly interdisciplinary teams of researchers and students, the Illinois Materials Research Center will focus on two types of materials. One group will study new magnetic materials, where ultra-fast magnetic variations could form the basis of smaller, more robust magnetic memory storage. The second group will design materials that can withstand bending and crumpling that typically destroys the properties of those materials and even create materials where crumpling enhances performance.

  • In the Media
  • Condensed Matter Physics
  • Biological Physics

Quanta Magazine recently spoke with Goldenfeld about collective phenomena, expanding the Modern Synthesis model of evolution, and using quantitative and theoretical tools from physics to gain insights into mysteries surrounding early life on Earth and the interactions between cyanobacteria and predatory viruses. A condensed and edited version of that conversation follows.

Assistant Professors Jessie Shelton and Benjamin Hooberman of the Department of Physics at the University of Illinois Urbana-Champaign have been selected for 2017 DOE Early Career Awards. They are among 65 early-career scientists nationwide to receive the five-year awards through the Department of Energy Office of Science’s Early Career Research Program, now in its second year. According to the DOE, this year’s awardees were selected from a pool of about 1,150 applicants, working in research areas identified by the DOE as high priorities for the nation.

  • Outreach

The most intriguing and relevant science happens at the highest levels of scientific pursuit-at major research universities and laboratories, far above and beyond typical high-school science curriculum. But this summer, 12 rising high school sophomores, juniors, and seniors-eight from Centennial and four from Central High Schools, both in Champaign-had the rare opportunity to partake in cutting-edge scientific research at a leading research institution.

The six-week summer-research Young Scholars Program (YSP) at the University of Illinois at Urbana-Champaign was initiated by members of the Nuclear Physics Laboratory (NPL) group, who soon joined forces with other faculty members in the Department of Physics and with faculty members of the POETS Engineering Research Center.