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Genetic mechanics

Article / Review by on February 25, 2012 – 8:17 pmNo Comments

Genetic mechanics
First-ever 3-D images of DNA damage sensor created at Harvard

Everything — from noxious chemicals found in cigarette smoke or car exhaust, to ultraviolet radiation from the sun, to even something as benign as oxygen — is working overtime to damage DNA. Fortunately, all living things have a defense: an intracellular mechanic that patrols DNA, searching for errors and repairing them, thousands of times a day.

Using X-ray crystallography, Harvard scientists produced 3-D images of the protein machinery that detects damaged parts of the genome in bacteria, thus enabling them to be repaired. The Harvard group used the images they obtained to gain a new understanding of how the DNA repair process works.

As reported in the online version of Nature Structural & Molecular Biologyon Feb. 5, the images reveal that the proteins can actually alter their shape. Researchers believe that the alteration is part of a process best described as a genetic “pat-down,” or a way for the mechanism to identify areas of the genetic code that need repair.

“What we think is that the sensor detects regions that require repair by subjecting DNA to a stress test,” David Jeruzalmi of Harvard’s Department of Molecular and Cellular Biology and lead author of the paper, said. “As it patrols, one form of the sensor can interact with both native and damaged DNA, but only normal DNA is able to pass the stress test. The sensor performs these stress tests over and over; regions of the genetic code that pass the test are quickly released. However, once a region of DNA is found that fails the “pat-down,” or stress test, the sensor gets stuck and signals for other biochemical processes to take over and repair the DNA.

“We were really excited to see the 3-D image of the sensor, because this amazing insight is something that could never emerge from studying these proteins biochemically,” Jeruzalmi added. “You needed to have seen the two views. This is totally unprecedented — there was nothing in any previous study that suggested that something like this was occurring.”

The DNA repair machinery is made up of two pairs of proteins: UvrA and UvrB. Although earlier work had shown that the proteins could be arranged into an open, almost butterflylike form, Jeruzalmi’s recent paper found them arranged in a tighter, sleevelike pattern, which cradled the DNA.

“When we modeled normal undamaged DNA into the structure, we found that the groove can accommodate it very nicely,” he said. “What we know about damaged DNA is that it is severely distorted in many different ways, so damaged DNA couldn’t fit into this new structure.”

“We believe the ‘open’ form is the sensor, because it can read all forms of DNA, whether damaged or native,” he continued. “As the proteins change shape, the closed form can only accommodate native DNA, so when it encounters damage, it stops, and that’s the signal for repair.”

The challenge now, Jeruzalmi said, is to determine whether the relatively simple DNA repair system of bacteria can be translated into higher organisms or even into humans, who have a similar, though vastly more complicated, system of proteins. Though it may be years before that system is understood, Jeruzalmi believes this work will serve as a foundation for understanding how DNA repair systems work in any number of organisms.

“There’s no question this is the foundation,” he said. “We don’t know how big the building is going to be, but this is the foundation. This is the sort of structural biology that I love, because we learned something that we did not know was actually there. Often, seeing a 3-D structure or image confirms everything you already knew, and that’s fine, but what is really exciting is when you learn something new and unexpected; here we discovered an answer to a question we did not even know to ask.”

By Peter Reuell
Harvard Staff Writer

Image courtesy of David Jeruzalmi

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Harvard School of Public Health is dedicated to advancing the public’s health through learning, discovery and communication. More than 400 faculty members are engaged in teaching and training the 1,000-plus student body in a broad spectrum of disciplines crucial to the health and well being of individuals and populations around the world. Programs and projects range from the molecular biology of AIDS vaccines to the epidemiology of cancer; from risk analysis to violence prevention; from maternal and children’s health to quality of care measurement; from health care management to international health and human rights.

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About Harvard University.

Established in 1636, Harvard is the oldest institution of higher education in the United States. The University, which is based in Cambridge and Boston, Massachusetts, has an enrollment of over 20,000 degree candidates, including undergraduate, graduate, and professional students. Harvard has more than 360,000 alumni around the world.

Harvard University is devoted to excellence in teaching, learning, and research, and to developing leaders in many disciplines who make a difference globally. Harvard faculty are engaged with teaching and research to push the boundaries of human knowledge. For students who are excited to investigate the biggest issues of the 21st century, Harvard offers an unparalleled student experience and a generous financial aid program, with over $160 million awarded to more than 60% of our undergraduate students. The University has twelve degree-granting Schools in addition to the Radcliffe Institute for Advanced Study, offering a truly global education.

‘Universities nurture the hopes of the world: in solving challenges that cross borders; in unlocking and harnessing new knowledge; in building cultural and political understanding; and in modeling environments that promote dialogue and debate… The ideal and breadth of liberal education that embraces the humanities and arts as well as the social and natural sciences is at the core of Harvard’s philosophy. ’/ Drew Gilpin Faust

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* The above story is adapted from materials provided by Harvard University

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