Copy Shop

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he technique called PCR, or Polymerase Chain Reaction, has been applied to every branch of DNA research, from sequencing to forensics.

To run PCR to find or copy a gene, you need to know the "flanking sequences," the 15 or 20 pairs of nucleotides that lie on either side of it. Flanking sequences are stored in DNA libraries in, for example, the Penn State Nucleic Acid Facility. Programming the sequence into a DNA synthesizing machine, you make millions of single-stranded primers, one for each strand. These you put into a solution along with your target DNA, millions of free nucleotides (A,T,G, and C), and the patented taq polymerase, a variety of DNA polymerase from a bacterium first found in a hotspring at Yellowstone National Park.

PCR has three basic steps: First the DNA is heated, causing the double helix to unzip into two single strands. As the mixture cools, the short primers quickly seek out and stick to their complements on the longer strands before the original DNA can zip back up. Now the taq polymerase goes to work: If it reads an "A" on a target strand, it will insert a "T" on the incomplete strand. A copy of the target strand region is quickly made.

Taq polymerase can withstand high temperatures, so the solution can be reheated, causing new copies to separate into individual strands. A chain reaction begins: from four copies to eight copies to millions of copies in a few hours.

PCR has been credited with making the Human Genome Project possible — but it may soon be obsolete. Penn State chemist Stephen Benkovic and post-doctoral scholar Frank Salinas filed a patent disclosure last April on a "PCR replacement" that will be both faster and cheaper to use.

—Daniel DeJoseph

Stephen J. Benkovic, Ph.D., is Evan Pugh Professor of Chemistry in the Eberly College of Science, 414 Wartik Lab, University Park, PA 16802; 814-865-2882; sjb1@psu.edu