DNA Flips out! Enzymes Repair and Modify DNA in a Surprising Way
Travis, John, Science News
Like cars, an organism's genes require frequent tuning and maintenance to function properly and avoid breakdowns. The mechanics responsible for this servicing are certain specialized proteins--enzymes that bind directly to DNA. Some of these enzymes tack atoms onto DNA, signaling whether a gene is turned on or off. Others scan the genome, searching for DNA in need of repair or removal.
Working on cars or genes can be awkward, however. To get at a broken part, auto mechanics may have to elevate the car on a lift or move undamaged parts out of the way. Similarly, to perform their biochemical maintenance, enzymes often must dramatically distort the normal helical shape of DNA.
The corkscrew structure of DNA consists of two linked strands, each a necklace of molecules called nucleotides, the fundamental building blocks of DNA. On each strand, a nucleotide bonds chemically to the nucleotide above and below it. In addition, creating ladderlike rungs between the strands, every nucleotide forms a weaker connection with a counterpart on the other DNA strand. This joining occurs between bases, a cluster of atoms each nucleotide possesses.
In DNA, bases come in four flavors--adenine, thymine, cytosine, and guanine. (RNA, a single-stranded molecule similar to DNA, substitutes the base uracil for thymine.) Since each base has a regular partner that it pairs with--adenine with thymine and cytosine with guanine--the sequence of nucleotide bases on one DNA strand determines the sequence on the other.
The attraction between bases on opposite strands and the bonds between the nucleotides that make up each strand confer a certain rigidity on DNA's double helix. That stiffness can make it difficult for an enzyme to position itself properly against a nucleotide or its base. As a result, when enzymes bind to DNA, they sometimes bend the DNA or throw a kink into its double helix--temporary distortions that provide greater access to specific parts of a strand. In some cases, an enzyme completely unzips the double helix, splitting it into two distinct strands.
According to recent research, however, enzymes have another way of tackling DNA. Some apparently pry apart a base pair, then rotate one of the freed nucleotides, bringing its base out of the confines of the double helix and into the enzyme's active site, a pocket within the protein's structure. The enzyme can then remove this pocketed base from its nucleotide or modify the base and sling it back into its proper position.
Until last year, scientists had never caught an enzyme performing this kind of remarkable maneuver, which they call base flipping. It's as if an automobile mechanic lifted the engine out of car, conducted repairs, and then casually dropped the engine back into place.
"It came as a total surprise to us. In retrospect, of course, it looks like the obvious thing to do. It's a simple and elegant way to do chemistry on a base," says Nobel laureate Richard J. Roberts of New England Biolabs, a biotech firm in Beverly, Mass. Roberts, along with three investigators from Cold Spring Harbor Laboratory in New York, published the first description of a base-flipping enzyme in the January 28, 1994 Cell.
Since that initial report, researchers have confirmed a second case of base flipping and have interpreted the shapes of other enzymes as suggesting that this unusual mechanism occurs in many DNA-protein encounters, including the essential ones by which enzymes repair damaged DNA. Enzymes used by humans, viruses, and bacteria all appear to employ this base-flipping ability.
Indeed, investigators believe they have belatedly discovered one of life's more basic genetic tricks. "Anything that's preserved so completely between [the bacterium] Escherichia coli and humans is very fundamental. We think this is a very ancient paradigm for DNA-protein interaction," says John Tainer of the Scripps Research Institute in La Jolla, Calif. …