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Introduction

The polymerase chain reaction (PCR) devised by Kary Mullis is an in vitro method for producing large amounts of essentially identical copies of a specified DNA sequence. This technique has revolutionized molecular genetics.

PCR exploits certain features of natural DNA replication. DNA polymerase uses single-stranded DNA as a template for the synthesis of a new complementary strand. These single-stranded DNA templates can be produced by heating double-stranded DNA to temperatures near boiling. The initiation of the DNA synthesis requires a small section of double-stranded DNA known as primers. Figure 1 shows the example used in [5]. Hence we can specify the starting point for DNA synthesis by supplying an oligonucleotide primer that anneals to the template at that point. This is the first prominent feature of PCR, that is, we can specify amplification regions by choosing proper primers.

If we supply a primer for each of the two strands, then they can both be used as templates for synthesis. For a PCR, the primers are chosen to flank the region of DNA that is to be amplified. The newly synthesized strands of DNA, starting at each primer, extend beyond the position of the primer on the opposite strand, so that they both contain new primer binding sites for further replication. Then this reaction mixture is heated again to denature both the original and new double-stranded sequences, and form templates for the next cycle of primer hybridization, DNA synthesis, and strand separation. Each cycle consists of three steps: strand separation or DNA denaturing, primer annealing, and DNA synthesis or polymer extension. After n cycles, ideally, the mixture will have double-stranded DNA molecules that identical to the original sequences between the two primers. This is the second prominent feature of PCR---amplification.

  
Figure 1: Primers for DNA polymerase. (a) The target for amplification, a small section covering 110 bp of the --globin, is shown. Two sequences separated by 60 nucleotides are detailed, and the 20 nucleotides underlined are used as oligonucleotide primers for the PCR. (b) When the DNA is heated, the strands separate. (c) The oligonucleotide primers (shown in green) hybridize specifically to their complementary sequences at the 3' ends of each strand of the target sequence. (d) DNA polymerase uses these primers to begin synthesis of new strands (shown in orange and underlined) complementary to the target DNA sequences in the 5'--to--3' directions.

The specificity of PCR is determined by the oligonucleotide primers. This feature allows DNA from a variety of sources to be amplified by PCR. PCR does not require highly purified DNA, and enables the amplification from a very tiny number of DNA molecules.



next up previous
Next: Standard PCR protocol Up: Stat 260: Statistics Previous: Stat 260: Statistics



Simon Cawley
Wed Apr 29 19:50:12 PDT 1998