DNA Flips out! Enzymes Repair and Modify DNA in a Surprising Way

By Travis, John | Science News, September 16, 1995 | Go to article overview

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. …

The rest of this article is only available to active members of Questia

Sign up now for a free, 1-day trial and receive full access to:

  • Questia's entire collection
  • Automatic bibliography creation
  • More helpful research tools like notes, citations, and highlights
  • Ad-free environment

Already a member? Log in now.

Notes for this article

Add a new note
If you are trying to select text to create highlights or citations, remember that you must now click or tap on the first word, and then click or tap on the last word.
One moment ...
Default project is now your active project.
Project items

Items saved from this article

This article has been saved
Highlights (0)
Some of your highlights are legacy items.

Highlights saved before July 30, 2012 will not be displayed on their respective source pages.

You can easily re-create the highlights by opening the book page or article, selecting the text, and clicking “Highlight.”

Citations (0)
Some of your citations are legacy items.

Any citation created before July 30, 2012 will labeled as a “Cited page.” New citations will be saved as cited passages, pages or articles.

We also added the ability to view new citations from your projects or the book or article where you created them.

Notes (0)
Bookmarks (0)

You have no saved items from this article

Project items include:
  • Saved book/article
  • Highlights
  • Quotes/citations
  • Notes
  • Bookmarks
Notes
Cite this article

Cited article

Style
Citations are available only to our active members.
Sign up now to cite pages or passages in MLA, APA and Chicago citation styles.

(Einhorn, 1992, p. 25)

(Einhorn 25)

1

1. Lois J. Einhorn, Abraham Lincoln, the Orator: Penetrating the Lincoln Legend (Westport, CT: Greenwood Press, 1992), 25, http://www.questia.com/read/27419298.

Cited article

DNA Flips out! Enzymes Repair and Modify DNA in a Surprising Way
Settings

Settings

Typeface
Text size Smaller Larger Reset View mode
Search within

Search within this article

Look up

Look up a word

  • Dictionary
  • Thesaurus
Please submit a word or phrase above.
Print this page

Print this page

Why can't I print more than one page at a time?

Full screen

matching results for page

Cited passage

Style
Citations are available only to our active members.
Sign up now to cite pages or passages in MLA, APA and Chicago citation styles.

"Portraying himself as an honest, ordinary person helped Lincoln identify with his audiences." (Einhorn, 1992, p. 25).

"Portraying himself as an honest, ordinary person helped Lincoln identify with his audiences." (Einhorn 25)

"Portraying himself as an honest, ordinary person helped Lincoln identify with his audiences."1

1. Lois J. Einhorn, Abraham Lincoln, the Orator: Penetrating the Lincoln Legend (Westport, CT: Greenwood Press, 1992), 25, http://www.questia.com/read/27419298.

Cited passage

Thanks for trying Questia!

Please continue trying out our research tools, but please note, full functionality is available only to our active members.

Your work will be lost once you leave this Web page.

For full access in an ad-free environment, sign up now for a FREE, 1-day trial.

Already a member? Log in now.