Errors in the genetic code can give rise to cancer and
a host of other diseases, but finding
these errors can be more difficult than looking for the
proverbial needle in the haystack. Now,
scientists at Johns Hopkins have uncovered how the tiny
protein machines in cells tasked to search
for potentially life-threatening genetic damage actually
recognize DNA errors.
Appearing on-line this week in Nature, the Johns
Hopkins team describes how the UDG enzyme
(for uracil DNA glycosylase) scrutinizes the shape of DNA
building blocks by holding onto 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 study author James Stivers, professor of
pharmacology and molecular sciences in the School of
Medicine. "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 is the DNA building
block cytosine being chemically converted to
uracil, a similar-looking building block not normally found
in DNA. "Even water can cause DNA damage,"
Stivers said. "It's not a fast reaction, but water does
convert the occasional cytosine into an unwanted
To figure out how the enzyme responsible for cutting
unwanted uracils out of DNA works,
Stivers and colleagues studied a tiny segment of DNA,
asking whether the "breathing" properties of
DNA played a role in the search process of UDG. "Although
the bases in the DNA double helix
resemble the rungs of a ladder, the rungs are not that
sturdy," Stivers said. "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. So, using a special chemical
trick, the researchers magnetically labeled water to allow
them to follow its interaction with bases
that had randomly popped out of the DNA helix. The team
could follow which bases popped out, and
for how long, using a strong magnet.
After studying DNA breathing by itself, the
researchers added UDG into the mix. They then
saw that UDG holds onto the normal DNA building block
thymine (T) after it pops out of the DNA on
its own. However, because T is not identical to U, UDG then
lets it fall back into the DNA helix.
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. Once sitting
in this pocket, the enzyme clips out the U,
leaving a gap in the DNA for other repair machinery to fill
in with the correct building block.
"This is the first time we've been able to actually
see how an enzyme discrimin- ates between
right and wrong bases in DNA," Stivers said. "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."
The research was funded by the National Institutes of
Health and the National Science
Authors on the paper are Jared Parker, Mario Bianchet,
Daniel Krosky, Joshua Friedman, L.
Mario Amzel and Stivers, all of Johns Hopkins.