Do kinks and twists denote DNA damage?

Radiation and chemicals often damage a cell's DNA. Fortunately, there is a natural repair mechanism to undo most of that damage. But what is it that these enzymes must repair? And how do dispatched repair squads find the damage? Using computers to model the most likely stable structure of two types of photochemically induced damage, chemists in Berkeley, Calif., think they may have spotted the answers--bends and a partial unwinding of the DNA's characteristic double helix in the damaged cells. A report of their work appears in the March 15 SCIENCE.

Creation of certain dimers, bound pairs of identical subunits, is the most widely studied radiation-induced DNA change. Upon irradiation with ultraviolet (UV) light, two adjacent structures--thymines--along a strand of DNA may fuse into a thymine dimer. These dimers present roadblocks to normal DNA synthesis and are likely to spawn mutations if they are not repaired before the cell's DNA undergoes replication.

Another well-studied DNA lesion occurs when cells exposed to the drug psoralen (often used for treating the skin disease psoriasis) are subsequently irradiated with long-wavelength UV light. Here the psoralen molecule chemically binds to a nucleic-acid base on each of two strands of DNA. If this psoralen cross-link is not repaired, the affected cell will die.

Scientists believe that the DNA repair mechanism must recognize the structural changes these damaging chemical bonds cause. "Our goal was to see what kinds of changes in the overall DNA structure are induced by this photo-damage," says Stephen R. Holbrook, a staff scientist at Lawrence Berkeley Laboratory, "and our results are that the DNA becomes bent [at the site of damage] by a moderate angle in the thymine dimer formation, and by a very large angle in the psoralen cross-link." David Pearlman at the University of California at Berkeley computed the helical kinks, or bend angle, induced in the DNA as 27[deg.] for the dimer and 46.5[deg.] for the psoralen cross-link (shown in the illustration as b and c, respectively).

The researchers also noted a characteristic alternation in the helical coiling of the double-strand DNA at the point of damage. Normal DNA has 10 base pairs per full turn, meaning that DNA turns 36 degrees for every base pair. In the damaged DNA, the chemists' models showed a change in that winding angle. For dimers, instead of winding 36[deg.], affected base pairs coiled only 16.3[deg.]. In the psoralen cross-link, the 87.7[deg.] twist in the opposite direction actually causes the affected portion of the helix to completely unwind (structure c).

"I should emphasize," Holbrook says, "that this is a proposal." Although the contortions were suggested by computer models based on the best available X-ray crystallographic data on dimer and cross-link DNA damage, he notes that they have not yet been visually observed. Milan Tomic, a student now working with the team, is attempting to isolate enough psoralen-linked base pairs to make that possible.