HARVARD GAZETTE ARCHIVES

Professor Gregory Verdine (standing) and graduate student Anirban Banerjee watch computer images (top) of an enzyme that locates hard-to-find damage in DNA, then makes the necessary repairs. (Staff photo Justin Ide/Harvard News Office)

For the first time, researchers at Harvard University have taken snapshots of one of these protective "mechanics" at work. It's a protein that checks out parts known as "bases," the building blocks of DNA, which makes up our genes and carries the blueprints for our biology and behavior.

"Every second of every hour of every lifetime, such proteins search through millions of bases looking for errors," notes Gregory Verdine, Erving Professor of Chemistry. "These proteins work like a jukebox, removing bases (disks) from a stack one at a time to check their labels. It's quite a task to check through a couple hundred disks, so imagine what it would be like to inspect 10 million of them to find a particular one. That's what DNA repair enzymes have to do. Their search-and-rescue mission is a marvel of nature's design." (Enzymes are proteins that make chemical changes without undergoing changes in themselves.)

The enzyme boasts a long technical name that scientists shorten to "OGG1."

After three years of difficult laboratory experiments, Verdine and his colleagues Anirban Banerjee, Wei Yang, and Martin Karplus managed to capture a series of pictures showing one of the enzymes at work. The enzyme boasts a long technical name that scientists shorten to "OGG1."

As described in the April 1 issue of the scientific journal Nature, OGG1 moves up and down long segments of DNA looking for aberrations in a base known as guanine. If everything is normal, the enzyme moves on. But if it detects an abnormal mutation, or change, it removes the damaged part. Other enzymes then follow up and install a replacement.

"Accumulations of such mutations may eventually lead to cancer," Verdine points out. Also, some evidence exists that they are involved in premature aging.

In the pocket

The tools used by OGG1 are as fascinating as its work.

Guanine is one of four bases that make up DNA. Most people are familiar with the appearance of DNA as two long strands twisted together to make up a double helix. These strands are held together by adjacent pairs of bases, which resemble steps on a winding staircase.

Guanine is the base that OGG1 checks out on its rounds. During these searches, OGG1 finds millions of normal guanines for every aberrant one. It must be able to detect very subtle differences between good and bad, and the molecular snapshots taken by Verdine's group reveal how it does that.

OGG1 boasts a tiny pocket in its structure that acts as a trap. Normal guanine won't fit into the pocket. Mutated guanine, carrying an extra oxygen atom, fits smoothly.

That oxygen atom can cause problems. It may come from radiation received for treatment of cancer, breathing polluted air, or normal breakdown of food we eat. In the last case, the oxygen is usually converted to water, releasing life-giving energy in the process. But occasionally, a highly reactive form of oxygen escapes into the body, as can also happen when someone breathes polluted air or receives treatment with radiation.

Called "free radicals," these oxygen atoms react ferociously with anything nearby. Most of the molecules they attack are constantly being replenished, so no harm is done. But if they react with a base like guanine, problems occur. "They can attack your genetic heritage," is the way Verdine puts it. Over time, these kinds of attacks may eventually lead to lung, colorectal, or other cancers, and they also may speed up aging.

Installing replacements

Once an oxygen-damaged guanine is removed, it needs to be replaced. Details of how replacements are made and installed are less clear. "Other enzymes in the cell are always searching for baseless sites," Verdine explains. "Some evidence exists that OGG1 may hand off the damaged guanine to these other enzymes, and that starts the replacement process going."

Verdine and his team are looking into exactly how this happens, using a technique he pioneered. "We first used it successfully in 1998 to determine how HIV, the AIDS virus, makes copies of itself inside a human cell. The technique is now being utilized by a number of pharmaceutical companies in designing new drugs."

OGG1 moves at a rapid pace because it has so many bases to check out, so it's very difficult to get a clear picture of it. The enzyme stops momentarily when it finds and grabs a damaged guanine base. That helps things a bit, but a whole series of snapshots is needed to see what is actually going on. To take such snapshots, the researchers faced years of exacting labor without any assurance of success.

Verdine calls it "an ugly duckling project. Others thought of it as risky, if not crazy. But Anirban Banerjee agreed to take it on. He's the project hero."

Banerjee, a graduate student, says, "It was well worth the effort. We got more out of it than we thought, because we not only found the structure but were able to describe the process with numbers. That's due to the help from Martin Karplus (Theodore William Richards Research Professor of Chemistry Emeritus) and Wei Yang, a postdoctoral associate in his lab."

Verdine agrees. "To get a complete understanding of what's going on, you need to answer questions like how much energy is needed to get the damaged base out of the DNA. When the job involves searching for one bad needle in a good haystack, you want to know how much energy it will take to find it. That kind of information is vital to obtaining fundamental knowledge of how this marvelously efficient process works to preserve the integrity of our genes."