DNA size a crucial factor in genetic mutations, study finds

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DNA size a crucial factor in genetic mutations, study finds

http://www.medicalnewstoday.com/medicalnews.php?newsid=32704

Researchers at Stanford University have created a larger-than-normal

DNA molecule that is copied almost as efficiently as natural DNA. The

findings, reported in the Oct. 25 online edition of the Proceedings

of the National Academy of Sciences (PNAS), may reveal new insights

into how genetic mutations-tiny mistakes that occur during DNA

replication-arise. The discovery was made in the laboratory of

Kool, a professor of chemistry at Stanford and co-author of the PNAS

study.

DNA, the genetic encoder of life, comes in two parallel strands that

form a double helix. It's like a long, twisted ladder where each rung

consists of two molecules that form a base pair. DNA has four bases:

adenosine (A), thymine (T), guanine (G) and cytosine ©. A always

pairs with T, and G with C. To copy itself, the DNA molecule unwinds

and splits. Either strand is now a template to build a new DNA

molecule. An enzyme-a protein that speeds the reaction, in this case

the bacteria E. coli's DNA polymerase I-moves along the template and

selects the corresponding base to create a new base pair.

DNA bases fit into a specialized site on the enzyme before they are

bonded to the template. Kool wanted to see how the enzyme reacts if

the bases are not the usual size. ''The idea was to see how DNA

replication depends on size,'' Kool says.

The researchers investigated it by offering bases of different sizes

to the DNA polymerase I enzyme and measuring how accurately the

enzyme made new DNA copies. About once every 10,000 to 100,000 times

the enzyme will put in the wrong base, choosing for instance a G

instead of a T to pair with an A. The rate that the enzyme accurately

copies DNA is known as its efficiency.

These rare and random mistakes can cause genetic mutations. While we

tend to heap negative connotations onto the term, some mutations

create new traits that actually benefit the organism or yield no

effect. These small-scale changes, collectively called genetic drift,

play an important role in evolution, as does natural selection.

To make their DNA bases, Kool started with a molecule similar to

thymine-called an analog-and made five different sizes by adding

increasingly larger atoms. The first analog was smaller than natural

thymine, the second about the same size and the last three were

increasingly larger. The difference between the smallest and largest

analogs was only one angstrom, or a tenth of a nanometer.

Bigger is better

When the researchers offered the analog bases to DNA polymerase I,

the enzyme not only recognized the synthetic molecules as it would

natural DNA but also copied one of the slightly larger analogs at a

rate 22 times more efficiently than the natural-sized analog. In

fact, DNA polymerase I incorporated the slightly larger analog almost

as efficiently as it did natural thymine, both in the test tube and

in live E. coli bacteria. In contrast to this, the smallest and

largest analogs in the set were rejected by the enzyme and the

bacteria.

According to Kool, these results indicate that size is a strong

factor determining enzyme efficiency-and a mechanism for allowing

mutations into the DNA molecule.

''It's a way the organism can evolve,'' Kool says. ''If the protein

that copies DNA prefers a molecule that's slightly bigger than

natural DNA, then it can accept mistakes more readily.'' For example,

although T is supposed to match up with A, it might be inclined to

pair with G, which has a slightly larger configuration.

The sheer fact that a living system readily used a base-or nucleotide-

that was artificially created is itself groundbreaking. ''Here we

have, I think, the first example of an efficient, human-designed

nucleotide working in a live cell,'' he says.

Kool and the gang are now exploring ''the funny finding that the bugs

prefer DNA that's larger than natural DNA'' by making larger

nucleotides. ''Size and shape are related issues, so we're interested

now in keeping the size constant and changing the shape,'' Kool adds.

The PNAS study was co-written by Stanford postdoctoral fellow Tae Woo

Kim (lead author) and C. Delaney and M. Essigmann at the

Massachusetts Institute of Technology. The work was supported by the

National Institutes of Health.

By Krista Zala

Krista Zala is a science-writing intern at the Stanford News Service.

The paper, ''Probing the Active Site Tightness of DNA Polymerase in

Subangstrom Increments,'' is available online at the PNAS website,

http://www.pnas.org.

RELEVANT WEB URLS:

http://www.stanford.edu/group/kool

http://syntheticbiology.org

http://www.pnas.org

News Service website:

http://www.stanford.edu/news