Scientists uncover DNA repair mechanism

Scientists at the American Johns Hopkins University have now uncovered the mechanism the body uses to identify and remove errors in the genetic code, according to the prestigious scientific journal Nature.

Appearing online at www.nature.com, the Hopkins team describes how the UDG enzyme (for uracil DNA glycosylase) scrutinises the shape of DNA building blocks by holding on to them and testing their fit into a specially sized pocket. The UDG pocket holds onto mistakes only — the enzyme loses its grip on the right building blocks, which fall back in line with the rest of the DNA.

"Locating damage in DNA is critical for a cell's survival. So much can go wrong if damage goes unrepaired, cells can't tolerate any of this going on," said author James Stivers, professor of pharmacology and molecular sciences at Hopkins.

"But the question is how these enzymes find the few mistakes among the billions of correct building blocks in DNA."

One typical error that occurs in DNA is the chemical conversion of the base cytosine to a similar looking base (but one that does not belong in DNA): uracil (U).

"Even water can cause DNA damage," Stivers said. "It's not a fast reaction, but water does convert the occasional cytosine into an unwanted uracil."

The team figured out how the enzyme works by examining the phenomenon called "DNA breathing'.

"Although the bases in the DNA double helix resemble the rungs of a ladder, the rungs are not that sturdy," said Stivers. "They actually pop in and out of the helix a bit, randomly."

Each time a base pops out of the helix, it exposes itself to water. The team magnetically labeled water, allowing them to analyse which bases pop out — and for how long — using a strong magnet.

When the researchers added UDG into the mix, they saw that UDG holds onto the normal DNA building block thymine (T) after it pops out of the DNA on its own, before letting it fall back into DNA helix.

But when the DNA contains an unwanted U, the UDG enzyme actually grabs on and pulls it all the way out and holds it in the enzyme's pocket. The enzyme then clips out the U, leaving a gap in the DNA for other repair machinery to fill in with the correct base, cytosine (C).

"This is the first time we've been able to actually see how an enzyme discriminates between right and wrong bases in DNA," says Stivers. "Our discovery helps us appreciate what properties of DNA itself might lead to errors that are not repaired. The finding may help address how and where diseases like cancer arise in the genome."