A major new discovery could inspire improved treatments for cancer and genetic diseases.

Coiled within our cells are fragile threads of DNA that contain the codes of life— determining when each of our 30 trillion cells must grow, divide, sit tight — or simply die. This arrangement is precarious. Billions of times per day, our DNA is severed by stray chemical reactions. Our cells must rebuild the broken DNA without making mistakes – or the consequences can be dire.

A team including three UC Davis scientists has now mapped the structure of the tiny machine that repairs these dangerous breaks. Their discovery was published March 2 in the journal Nature.

“We experience DNA damage every day and every minute,” said Wolf-Dietrich Heyer, a distinguished professor and chair of microbiology and molecular genetics. “The proteins that repair these breaks have to be unbelievably reliable — this is central to human health.” Defects in DNA repair can trigger cancer, infertility, and genetic diseases.

The team’s discovery reconstructs the step-by-step movements of a protein called RAD51 and its five helper proteins – called paralogs – that perform this delicate task.

“It was a very difficult but important problem to solve,” said Stanislau Yatskevich, a postdoctoral fellow at South San Francisco-based Genentech, whose team led the effort, collaborating with Heyer at UC Davis. 

Hundreds of mutations in RAD51 helper proteins have been found in people with cancer. Without understanding these proteins, people couldn’t determine how the mutations promote cancer. “But now we can map all of those mutations onto the protein structure, and predict how they disrupt normal function,” said Yatskevich.

Seeking a perfect match

The most serious type of DNA damage is a “double-stranded break,” in which both strands of the double helix are severed, leaving a sequence that comes to an abrupt end — like a thick instruction manual that’s been ripped in half mid-sentence.

The cell must fix this by determining what sequence is missing on the other side of the break, and rebuilding that sequence onto the DNA’s broken end.

Most human cells have two complete copies of our DNA. So the cell can take the DNA sequence immediately preceding the break, and search for a matching sequence in an unbroken DNA from its other set. The cell uses that matching, intact DNA as a template to recreate the same sequence on the broken DNA.

It’s a massive job – equivalent to a proofreader scanning two million pages of instruction manuals to find a single matching paragraph. A cell must often repair several dozens of these breaks at once. Across your body, this happens billions of times per day.

“DNA repair is fundamental to life,” said Heyer. “It works surprisingly well. And without it, there could be no life as we know it.”

Life’s molecular movie

Scientists knew that RAD51 and its paralogs were necessary for DNA repair, but didn’t understand how they worked together. 

“This was a longstanding problem in our field,” said Heyer, who has studied DNA repair for three decades.

So, in 2024 Yatskevich started a project to clarify this picture with several of his Genentech colleagues, including Claudio Ciferri, vice president of protein science, and Christopher Koo, also a postdoc.

Yatskevich and Koo purified the delicate RAD51 and paralog proteins, and gently coaxed them into more complex structures. Cryo-electron microscopy (CryoEM) images showed the proteins assembling into a few different combinations – including one very large structure, containing all six proteins, that hadn’t been seen before.

At this point, they reached out to Heyer, who had spent years developing methods of measuring how well these proteins repair DNA.

Testing Yatskevich’s protein complexes, Heyer found that the big, newly discovered complex repaired DNA better than anything else did.

Yatskevich and Koo altered the proteins — mirroring mutations seen in cancer. Experiments showed that these tiny mutations prevented the proteins from assembling. Heyer confirmed that they also inhibited DNA repair.

All of this suggested that the newly discovered complex is the natural form that these proteins assume in living cells. And by analyzing hundreds of CryoEM images of the proteins and DNA, Yatskevich and Koo captured many individual steps of the DNA repair process.

Heyer compares Yatskevich and Koo’s effort to assembling the plot line of an entire movie, from a random pile of still images. “You have just 10 percent of the frames, but you can still recreate the whole movie,” he said.

Understanding how RAD51 and its helper proteins interact could help researchers create molecules that either correct them — preventing people from developing cancer — or disrupt them, sensitizing cancer cells to radiation or chemotherapy. Scientists could also confirm which mutations inhibit DNA repair. People with these mutations might then benefit from trying existing medications designed to attack tumors with defective DNA repair.

Whatever the future, Heyer is glad to reach this point. “It’s a huge achievement to solve these structures,” he said. “We’re extremely happy to be part of it.”

Heyer’s contributions to this research were funded by the National Institutes of Health.

Additional authors of the newly published Nature paper include: Jie Liu and Steven Gore (UC Davis College of Biological Sciences); Jiaqi Xiao, Christine Yu, Caleigh Azumaya, and Bobby Brillantes (Genentech Inc, Protein Sciences); Sebastien Coassolo (Genentech Inc, Discovery Oncology); Tommy Cheung and Chris Rose (Genentech Inc, Proteomic & Genomic Technologies).