Cause Described for Botched DNA Repair

By one count, just breathing every day adds more than 10,000 nicks and dings to a cell’s DNA. That’s not counting other troubles caused by radiation or chemicals. Now, like a routine home repair gone terribly wrong, researchers have discovered that some of those common repairs may be bungled, creating a bigger problem for cells to fix.

“DNA repair itself induces damage,” said Harvard School of Public Health toxicology professor Bruce Demple, senior author of the report in the March 8 issue of the Journal of Biological Chemistry.

The Way It’s Supposed to Be

Led by postdoctoral researcher Michael DeMott, investigators in Demple’s lab studied the process of base excision repair. Normally, a plentiful and robust enzyme known as Ape1 recognizes a missing base in a length of DNA. The enzyme binds briefly to the sugar-phosphate backbone of the gap-toothed DNA strand and makes an incision upstream. Ape1 recruits a second enzyme, polymerase beta, which also binds transiently and makes a downstream cut, neatly excising the damaged section and replacing it with a full base-sugar-phosphate residue. Then the enzymes rush ahead to their next appointment.

The attempted repair skids to a stop if the enzymes will not let go, report Demple and his colleagues. In a model system, polymerase beta hung on to an oxidized carbon on the sugar molecule under repair, a structure called lactone. This molecular sticking point can be formed by radiation–Demple’s interest–as well as by errant oxygen and water molecules careening around the cell in daily life.

The Broken Fix

The clinging, covalently bonded protein poses three immediate problems for the cell. First, the repair of a potential mutagenic missing base has failed. Second, a scarce repair enzyme, polymerase beta, is removed from circulation, where it presumably would be attending to other needed repairs. Third, the permanent protein-DNA bond seems to create a bigger lesion in the DNA. Yet in such an important repair pathway, scientists reason, the cell must have a way of handling the problem, even if no one yet knows how.

“This changes the way we think about how DNA lesions are repaired in cells,” said biochemist Samuel Wilson, deputy director of the National Institute of Environmental Health Sciences in Research Triangle Park, North Carolina, and one of the world’s foremost authorities on polymerase beta. “It suggests a whole new machinery in the cell that’s tailored to process that particular type of abnormal DNA molecule. That’s a very exciting possibility. People around the world are now looking for the repair of the DNA protein cross-link lesion.”

Of the many different kinds of damage ionizing radiation can inflict upon a cell, lactone was one of the first identified, a generation ago. But it was difficult to study until several years ago when organic chemist Marc Greenberg of Colorado State University and his colleagues figured out how to custom-make short, damaged pieces of DNA with a lactone lesion. For this study, the HSPH researchers worked with designer damage created by Greenberg, who showed last year that this kind of cross-link can form in an uncleaved lactone site.

–Carol Cruzan Morton

(Originally published in Focus, the twice monthly newsletter for the Harvard medical community)

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