Experience is one thing you can't get for nothing.
    Oscar Wilde



Lab Resources
Pre-lab Preparation

Additional Resources

Polymerase Chain Reaction (PCR®)

Polymerase chain reaction (PCR®) produces many copies of segments of DNA. The reproduction relies on the ability of DNA polymerase to make double stranded DNA. If a shorter, complementary segment of single stranded DNA (primer) is annealed to a longer single strand of DNA (template), the polymerase will extend the 3' end of the shorter segment to create double stranded DNA. Using two primers that are complementary to opposite strands, the DNA between and including the two primers is amplified. One cycle of amplification of DNA consists of three steps:

  1. Denature the double strands by melting (90-94°C)
  2. Anneal the primers to the template DNA at a reduced temperature (55-70°C)
  3. Synthesize (extend) the complementary DNA (70-75°C) with a DNA polymerase

Usually, 30 cycles are run yielding a near doubling of the number of DNA copies in each cycle. Actual efficiencies approach 1.8 fold increase in copy number/cycle.

Originally, DNA polymerase had to be added after each denaturation step but a thermal stable polymerase isolated from Thermus aquaticus (Taq) eliminated this tedious and expensive step. DNA fragments of fewer than 10,000 base pairs can be amplified with Taq. Longer fragments tend to fail due to mismatch errors that stall the enzyme. Several other thermal stable enzymes have been isolated that can survive the heating cycles. Each has varying efficiencies of proofreading and exonuclease activity for the correction of mismatch errors. A combination of two enzymes achieves amplification of longer lengths of DNA, up to 30-40 kb.

The efficiency of the PCR reaction necessitates scrupulous attention to keeping solutions clean and free from contamination. Some laboratories devote separate areas and equipment as PCR positive and PCR negative to prevent possible cross contamination. The preparation of target DNA should never occur in the same space as the preparation of the PCR reaction. (This guideline is not possible in the teaching lab making the negative control very important in our experiment.) Positive displacement pipettes or special filtered pipette tips are used to prevent contamination. For diagnostic and very sensitive procedures, reactions are set up in a laminar flow hood and all non-DNA solutions and containers are exposed to UV light to destroy errant DNA. Care must be taken to prevent contamination of the stock solutions. PCR on 1 µl of a 1:100 dilution of the plasmid preparation in this experiment can produce a visible band on the agarose gel.

The manufacturer's protocol recommends that 1 x 10(5)-1 x 10(6) target molecules be placed in the reaction mix. Consider the following relationships as a guideline for amplification of single copy genes:

    DNA source = # molecules

  • 1 µg human genomic DNA = 3 x 10(5)
  • 10 ng yeast DNA = 3 x 10(5)
  • 1 ng E. coli DNA = 3 x 10(5)
  • 1 pg plasmid = 3 x 10(5) [p=pico=10(-12)]

Primer design is a critical component of PCR -- ideally, a primer pair will anneal specifically to the target sequence and amplify just that region. Online tools, such as Primer3 (Center for Genome Research, Whitehead Institute for Biomedical Research), and software packages, such as the Wisconsin Package from Genetics Computer Group (GCG), help you design effective primers for PCR. However, there are several simple guidelines you can follow to design good primers "by hand."

  • Choose a sequence 18-24 nucleotides (nt's) in length
  • Choose a sequence that is 40-60% G/C content
  • Include G's and C's in the 5' and central regions to increase hybridization stability
  • Avoid complementary sequences at the 3' ends to minimize formation of primer-dimers
  • Include 3 A's or T's within the last 5 nt's
  • Avoid mismatches at the 3' end -- add sequences not present on the target, such as restriction sites, to the 5' end
  • Choose sequences that do not form stable internal secondary structure (loops or hairpins)
  • Design primer pairs with melting temperatures (Tm's) within 5°C of each other
PCR® was developed by Cetus Corporation scientists in 1984-1985. The discovery of a thermostable DNA polymerase from Thermus aquaticus (Taq) in 1988 revolutionized the PCR process. Numerous applications of PCR, such as DNA sequencing, RT-PCR, and site-directed mutagenesis, have been developed. PCR has had and continues to have a tremendous impact on molecular and evolutionary biology, disease diagnosis, forensic science, and human genetics.

For some useful information, see these guides from Invitrogen and Promega.
***Just for fun, check out Bio-Rad's Scientists for Better PCR***

Selected References

Eckert, K.A. and T.A. Kunkel. (1990) High fidelity DNA synthesis by the Thermus aquaticus DNA polymerase. Nucl. Acids Res.18: 3739.

Innis, M.A., K.B. Myambo, D.H. Gelfand, and M.A. Brow. (1988) DNA sequencing with Thermus aquaticus DNA polymerase and direct sequencing of polymerase chain reaction-amplified DNA. Proc. Natl. Acad. Sci. USA 85: 9436.

Kawasaki, E.S., and A.M. Wang. (1989) Detection of gene expression. In: Erlich, H.A., ed., PCR Technology: Principles and Applications of DNA Amplification. Stockton Press, Inc., New York, NY, pp. 89-97.

Landt, O., H.P. Grunert, and U. Hahn. (1990) A general method for rapid site-directed mutagenesis using the polymerase chain reaction. Gene 96: 125.

Lee, J.S. (1991) Alternative dideoxy sequencing of double-stranded DNA by cyclic reactions using Taq polymerase. DNA Cell Biol.10: 67.

Liang, Q., L. Chen, and A.J. Fulco. (1995) An efficient and optimized PCR method with high fidelity for site-directed mutagenesis. PCR Methods Appl.4: 269.

Mullis, K., F. Faloona, S. Scharf, R. Saki, G. Horn, and H. Erlich. (1986) Specific enzymatic amplication of DNA in vitro: The Polymerase Chain Reaction. Cold Spring Harbor Symposia on Quantitative Biology 51: 263.

Saiki, R.K., D.H. Gelfand, S. Stoffel, S.J. Scharf, R. Higuchi, G.T. Horn, K.B. Mullis, and H.A. Erlich. (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239: 487.

***The PCR process is covered by U.S. patents owned by Hoffmann-La Roche, Inc. and F. Hoffmann-La Roche Ltd.***

We would like to thank New England Biolabs for their generous support of our laboratory program

New England Biolabs

Copyright and Intended Use
Visitors: to ensure that your message is not mistaken for SPAM, please include the acronym "Bios211" in the subject line of e-mail communications
Created by David R. Caprette (caprette@rice.edu), Rice University 14 Jul 08
Author: Beth Beason Abmayr, Ph.D., Rice University
Updated 2 July 2014