Chapter 11, Problem 6EQ

Another technique described in Chapter 21 is polymerase chain reaction (PCR) (see Figures 21.5 and 21.6), which is based on our understanding of DNA replication. In this method, a small amount of double-stranded template DNA is mixed with a high concentration of primers. Nucleotides and DNA polymerase are also added. The template DNA strands are separated by heat treatment, and when the temperature is lowered, the primers bind to the single-stranded DNA, and then DNA polymerase replicates the DNA. This increases the amount of DNA made from the primers. This cycle of steps (i.e., heat treatment, lower temperature, allowing DNA replication to occur) is repeated again and again. Because the cycle is repeated many times, this method is called a chain reaction. It is called polymerase chain reaction because DNA polymerase is the enzyme needed to increase the amount of DNA with each cycle. In a PCR experiment, the template DNA is placed in a tube, and the primers, nucleotides, and DNA polymerase are added to the tube. The tube is then placed in a machine called a thermocycler, which raises and lowers the temperature. During one cycle, the temperature is raised (e.g., to $95°\text{C}$) for a brief period and then lowered (e.g., to $60°\text{C}$) to allow the primers to bind. The sample is then incubated at a slightly higher temperature for a few minutes to allow DNA replication to proceed. In a typical PCR experiment, the tube may be left in the thermocycler for 25–30 cycles. The total time for a PCR experiment is a few hours.

A. Why is DNA helicase not needed in a PCR experiment?

B. How is the sequence of each primer important in a PCR experiment? Do the two primers recognize the same strand or opposite strands?

C. The DNA polymerase used in PCR experiments is isolated from thermophilic bacteria. Why is this kind of polymerase used?

D. If a tube initially contained 10 copies of double-stranded DNA, how many copies of double-stranded DNA (in the region flanked by the two primers) would be obtained after 27 cycles?