Polymerase chain reaction

The polymerase chain reaction (PCR) is a scientific technique in molecular biology to amplify a single or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence.

PCR principles and procedure

PCR is used to amplify a specific region of a DNA strand (the DNA target). Most PCR methods typically amplify DNA fragments of up to ~10 kilo base pairs (kb), although some techniques allow for amplification of fragments up to 40 kb in size.

A basic PCR set up requires several components and reagents. These components include:

- DNA template that contains the DNA region (target) to be amplified.

- Two primers that are complementary to the 3 (three prime) ends of each of the sense and anti-sense strand of the DNA target.

- Taq polymerase or another DNA polymerase with a temperature optimum at around 70 °C.

- Deoxynucleoside triphosphates (dNTPs; nucleotides containing triphosphate groups), the building-blocks from which the DNA polymerase synthesizes a new DNA strand.

- Buffer solution, providing a suitable chemical environment for optimum activity and stability of the DNA polymerase.

- Divalent cations, magnesium or manganese ions; generally Mg²⁺ is used, but Mn²⁺ can be utilized for PCR-mediated DNA mutagenesis, as higher Mn²+ concentration increases the error rate during DNA synthesis.

- Monovalent cation potassium ions.

The PCR is commonly carried out in a reaction volume of 10-200 pl in small reaction tubes (0.2-0.5 ml volumes) in a thermal cycler. The thermal cycler heats and cools the reaction tubes to achieve the temperatures required at each step of the reaction .

Procedure

Typically, PCR consists of a series of 20-40 repeated temperature changes, called cycles, with each cycle commonly consisting of 2-3 discrete temperature steps, usually three. The cycling is often preceded by a single temperature step (called hold) at a high temperature (>90°C), and followed by one hold at the end for final product extension or brief storage. The temperatures used and the length of time they are applied in each cycle depend on a variety of parameters. These include the enzyme used for DNA synthesis, the concentration of divalent ions and dNTPs in the reaction, and the melting temperature (Tm) of the primers.

- Initialization step: This step consists of heating the reaction to a temperature of 94- 96 °C (or 98 °C if extremely thermostable polymerases are used), which is held for 1 - 9 minutes. It is only required for DNA polymerases that require heat activation by hot-start PCR.

- Denaturation step: This step is the first regular cycling event and consists of heating the reaction to 94-98 °C for 20-30 seconds. It causes DNA melting of the DNA template by disrupting the hydrogen bonds between complementary bases, yielding single-stranded DNA molecules.

- Annealing step: The reaction temperature is lowered to 50-65 °C for 20-40 seconds

allowing annealing of the primers to the single-stranded DNA template. Typically the annealing temperature is about 3-5 degrees Celsius below the Tm of the primers used. Stable DNA-DNA hydrogen bonds are only formed when the primer sequence very closely matches the template sequence. The polymerase binds to the primer-template hybrid and begins DNA synthesis.

• Extension/elongation step: The temperature at this step depends on the DNA polymerase used; Taq polymerase has its optimum activity temperature at 75-80 °C, and commonly a temperature of 72 °C is used with this enzyme. At this step the DNA polymerase synthesizes a new DNA strand complementary to the DNA template strand by adding dNTPs that are complementary to the template in 5' to 3' direction, condensing the 5'-phosphate group of the dNTPs with the 3'-hydroxyl group at the end of the nascent (extending) DNA strand. The extension time depends both on the DNA polymerase used and on the length of the DNA fragment to be amplified.

- Final elongation: This single step is occasionally performed at a temperature of 70- 74 °C for 5-15 minutes after the last PCR cycle to ensure that any remaining stranded DNA is fully extended.

- Final hold: This step at 4-15 °C for an indefinite time may be employed for short­term storage of the reaction.