Polymerase Chain Reaction (PCR)
PCR is a laboratory method used for making a very large number of copies of short sections of DNA from a very small sample of genetic material. This process is called "amplifying" the DNA and it enables specific genes of interest to be detected or measured.
DNA is made up of repeating sequences of four bases – adenine, thymine, guanine, and cytosine. These sequences form two strands that are bound together in a double helix structure by hydrogen bonds (like a spiral staircase). Each half of the helix is a complement of the other. In humans, it is the difference in the sequence of these bases on each strand of DNA that leads to the uniqueness of each person's genetic makeup. The arrangement of the bases in each gene is used to produce RNA, which in turn produces a protein. There are about 25,000 genes in a human genome, and expression of these genes leads to the production of a large number of proteins that make up our bodies. The DNA of other organisms such as bacteria and viruses is also composed of thousands of different genes that code for their proteins.
How is the method performed?
PCR is carried out in several steps or "cycles" in an instrument called a thermocycler. This instrument increases and decreases the temperature of the specimen at defined intervals during the procedure.
- The first step or cycle of PCR is to separate the strands of DNA into two single strands by increasing the temperature of the sample that contains the DNA of interest. This is called "denaturing" the DNA.
- Once the strands separate, the sample is cooled slightly and forward and reverse primers are added and allowed to bind to the single DNA strands. Primers are short sequences of bases made specifically to recognize and bind to the section of DNA to be amplified, which are the very specific sequence of bases that are part of the gene or genes of interest. Primers are called "forward" and "reverse" in reference to the direction that the bases within the section of DNA are copied.
- After the two primers attach to each strand of the DNA, a DNA enzyme (frequently Taq polymerase) then copies the DNA sequence on each half of the helix from the forward to the reverse primer, forming two double stranded sections of DNA, each with one original half and one new half. Taq polymerase is an enzyme found in a bacterium (Thermues aquaticus) that grows in very hot water, such as in geysers or hot springs. Polymerases copy DNA (or RNA) to make new strands. The Taq polymerase is especially helpful for laboratory testing because (unlike many other enzymes) it does not break down at very high temperatures needed to do PCR.
- When heat is applied again, each of the two double strands separate to make four single strands and, when cooled, the primers and polymerase act to make four double strand sections. The four strands becomes eight in the next cycle, eight become sixteen, and so on.
- Within 30 to 40 cycles, as many as a billion copies of the original DNA section can be produced and are then available to be used in numerous molecular diagnostic tests. This process has been automated so that a billion copies of the original DNA can be produced within a few hours.
How is it used?
This method can be used, for example, to detect certain genes in a person's DNA, such as those associated with cancer or genetic disorders, or it may be used to detect genetic material of bacteria or viruses that are causing an infection.
These are just a few examples of laboratory tests that use PCR:
- Lyme disease
- DNA fingerprinting
- Transplant monitoring
Real-time PCR is similar to PCR except that data are obtained as the amplification process is taking place (i.e., "real time") rather than at a prescribed endpoint and shortens the time for the test from overnight to a few hours. This method is used to measure the amount of DNA that is present in a sample.
RT-PCR (Reverse Transcriptase PCR)
This method uses PCR to amplify RNA. RNA is a single stranded nucleic acid molecule and needs to be made into DNA before it can be amplified. The addition of a new strand that is the complement of RNA is achieved by the enzyme called Reverse Transcriptase (RT) and an antisense (reverse) primer. The primer binds to the single stranded RNA and the enzyme RT copies the RNA strand to make a single stranded DNA, which it then copies to make a double stranded DNA molecule. The double stranded molecule can now be amplified by PCR. Detection can also be by real-time methods.
Here are two examples of laboratory tests that use RT-PCR:
(February 27, 2012). Polymerase Chain Reaction (PCR). National Human Genome Research Institute [On-line information]. Available online at http://www.genome.gov/10000207 through http://www.genome.gov. Accessed August 2012.
Tietz Textbook of Clinical Chemistry and Molecular Diagnostics. Burtis CA, Ashwood ER, Bruns DE, eds. St. Louis: Elsevier Saunders; Fifth edition, 2011, Pp 1412-1413.
Clarke, W. and Dufour, D. R., Editors (2006). Contemporary Practice in Clinical Chemistry, AACC Press, Washington, DC. Pp 135-137.