Photodamage's 'perfect storm'

The chemical structure has been known for more than four decades, "but the holy grail of DNA photodamage has been to understand exactly how these are formed," Bern Kohler, Ph.D., says.

The associate professor of chemistry and his research group at Ohio State University, Columbus, Ohio, together with collaborators from the University of Munich, Germany, finally have the answer to that question. They have found that the change is fast - very fast: about 1 picosecond. Furthermore, structure and position of the DNA thymine pairs are key to the reaction occurring.

DNA absorbs photons, and these excited electronic states possess significant amounts of energy, posing a real danger for further reactions, Dr. Kohler tells Dermatology Times.

"But most of the time they do not get a reaction. DNA has a number of mechanisms for dissipating energy that is deposited there by light. Much of that is nonradiative decay, where DNA simply returns back to its original starting state.

"The challenge in studying DNA photodamage is that you have to have a photon excite a TT sequence and, even then, it doesn't cause damage most of the time," he says.

To increase the odds of capturing a dimerization event, Dr. Kohler and collaborators used a repeat sequence of DNA that only contained thymine and found that dimerization occurred just 3 percent of the time.

"The reaction is fast enough that the DNA is essentially frozen; conformationally, there is not a lot of change that can take place." He says that it takes tens to hundreds of picoseconds for a base to move in and out of the double helix.

"Because the motions are slow on the time scale of the reaction, it means that what really decides whether two thymines can react or not is what orientations they already have when the light is absorbed. That is a great simplification in our thinking about photodamage."

Dr. Kohler says the way that DNA is packaged around histone proteins, to help it fit inside the cell nucleus, alters the orientation of sequential bases from what researchers are used to seeing in unwound helical DNA. That packaging creates fragile points where the DNA is more vulnerable to photodamage. This finding reinforces the importance of structure as to whether photodamage occurs.

The paper suggests that "The twist angle between successive base pairs in DNA may be a little too high for TT dimerization to occur" in many instances. The implication for Dr. Kohler is that the strand must either be unwinding, or kinked just so, for the two thymines to be positioned next to one another in a manner that will allow dimerization to occur.

A matter of degree

While damage to DNA occurs in less than an instant, "What really matters biologically is how much damage you accumulate."

Dr. Kohler says cell repair mechanisms are usually capable of handling this photodamage, and it becomes a numbers game of damage and repair before the balance is tipped to mutagenesis.

Dr. Kohler explains, "Our study opens up a new way of looking at damage. I think that, ultimately, we are going to be able to make progress in understanding and rationalizing why damage occurs in particular parts of the genome."

Some of the things researchers learn about photodamage may lead to new insights into repair, particularly with regard to structure and how proteins control the conformational structure of DNA.