As PCR progresses, the DNA generated is itself used as a template for replication, setting in motion a chain reaction in which the original DNA template is exponentially amplified. Almost all PCR applications employ a heat-stable DNA polymerase, such as Taq polymerase , an enzyme originally isolated from the thermophilic bacterium Thermus aquaticus. If the polymerase used was heat-susceptible, it would denature under the high temperatures of the denaturation step. Before the use of Taq polymerase, DNA polymerase had to be manually added every cycle, which was a tedious and costly process.
Applications of the technique include DNA cloning for sequencing , gene cloning and manipulation, gene mutagenesis; construction of DNA-based phylogenies , or functional analysis of genes ; diagnosis and monitoring of hereditary diseases ; amplification of ancient DNA;  analysis of genetic fingerprints for DNA profiling for example, in forensic science and parentage testing ; and detection of pathogens in nucleic acid tests for the diagnosis of infectious diseases.
The thermal cycler heats and cools the reaction tubes to achieve the temperatures required at each step of the reaction see below. Many modern thermal cyclers make use of the Peltier effect , which permits both heating and cooling of the block holding the PCR tubes simply by reversing the electric current. Thin-walled reaction tubes permit favorable thermal conductivity to allow for rapid thermal equilibration. Most thermal cyclers have heated lids to prevent condensation at the top of the reaction tube. Older thermal cyclers lacking a heated lid require a layer of oil on top of the reaction mixture or a ball of wax inside the tube.
Typically, PCR consists of a series of 20—40 repeated temperature changes, called thermal cycles, with each cycle commonly consisting of two or three discrete temperature steps see figure below. The temperatures used and the length of time they are applied in each cycle depend on a variety of parameters, including the enzyme used for DNA synthesis, the concentration of bivalent ions and dNTPs in the reaction, and the melting temperature T m of the primers.
To check whether the PCR successfully generated the anticipated DNA target region also sometimes referred to as the amplimer or amplicon , agarose gel electrophoresis may be employed for size separation of the PCR products. As with other chemical reactions, the reaction rate and efficiency of PCR are affected by limiting factors. Thus, the entire PCR process can further be divided into three stages based on reaction progress:. In practice, PCR can fail for various reasons, in part due to its sensitivity to contamination causing amplification of spurious DNA products.
Because of this, a number of techniques and procedures have been developed for optimizing PCR conditions. Primer-design techniques are important in improving PCR product yield and in avoiding the formation of spurious products, and the usage of alternate buffer components or polymerase enzymes can help with amplification of long or otherwise problematic regions of DNA. Addition of reagents, such as formamide , in buffer systems may increase the specificity and yield of PCR. Other applications of PCR include DNA sequencing to determine unknown PCR-amplified sequences in which one of the amplification primers may be used in Sanger sequencing , isolation of a DNA sequence to expedite recombinant DNA technologies involving the insertion of a DNA sequence into a plasmid , phage , or cosmid depending on size or the genetic material of another organism.
Bacterial colonies such as E. Some PCR 'fingerprints' methods have high discriminative power and can be used to identify genetic relationships between individuals, such as parent-child or between siblings, and are used in paternity testing Fig. This technique may also be used to determine evolutionary relationships among organisms when certain molecular clocks are used i.
This is often critical for forensic analysis , when only a trace amount of DNA is available as evidence. These PCR-based techniques have been successfully used on animals, such as a forty-thousand-year-old mammoth , and also on human DNA, in applications ranging from the analysis of Egyptian mummies to the identification of a Russian tsar and the body of English king Richard III. There are two methods for simultaneous detection and quantification.
The first method consists of using fluorescent dyes that are retained nonspecifically in between the double strands. The second method involves probes that code for specific sequences and are fluorescently labeled. Detection of DNA using these methods can only be seen after the hybridization of probes with its complementary DNA takes place. An interesting technique combination is real-time PCR and reverse transcription.
This technique lowers the possibility of error at the end point of PCR,  increasing chances for detection of genes associated with genetic diseases such as cancer. Prospective parents can be tested for being genetic carriers , or their children might be tested for actually being affected by a disease.
PCR analysis is also essential to preimplantation genetic diagnosis , where individual cells of a developing embryo are tested for mutations. PCR allows for rapid and highly specific diagnosis of infectious diseases, including those caused by bacteria or viruses. The basis for PCR diagnostic applications in microbiology is the detection of infectious agents and the discrimination of non-pathogenic from pathogenic strains by virtue of specific genes.
Characterization and detection of infectious disease organisms have been revolutionized by PCR in the following ways:. PCR has a number of advantages. It is fairly simple to understand and to use, and produces results rapidly. The technique is highly sensitive with the potential to produce millions to billions of copies of a specific product for sequencing, cloning, and analysis. Therefore, it has its uses to analyze alterations of gene expression levels in tumors, microbes, or other disease states. PCR is a very powerful and practical research tool. The sequencing of unknown etiologies of many diseases are being figured out by the PCR.
The technique can help identify the sequence of previously unknown viruses related to those already known and thus give us a better understanding of the disease itself.
Although there are several different challenges e. Testing methods, DNA targets used and result interpretation criteria vary, and laboratories do not use the same cutoffs for determining a positive result. Primer concentration: Begin PCR with a primer concentration of 0. Analytical Biochemistry. Initialization cycle Denaturation Annealing elongation Final elongation Final hold. Before the use of Taq polymerase, DNA polymerase had to be manually added every cycle, which was a tedious and costly process. Transcription 3.
If the procedure can be further simplified and sensitive non radiometric detection systems can be developed, the PCR will assume a prominent place in the clinical laboratory for years to come. One major limitation of PCR is that prior information about the target sequence is necessary in order to generate the primers that will allow its selective amplification.
Like all enzymes, DNA polymerases are also prone to error, which in turn causes mutations in the PCR fragments that are generated. Another limitation of PCR is that even the smallest amount of contaminating DNA can be amplified, resulting in misleading or ambiguous results. To minimize the chance of contamination, investigators should reserve separate rooms for reagent preparation, the PCR, and analysis of product. Reagents should be dispensed into single-use aliquots.
Pipetters with disposable plungers and extra-long pipette tips should be routinely used. Gobind Khorana first described a method of using an enzymatic assay to replicate a short DNA template with primers in vitro. When Mullis developed the PCR in , he was working in Emeryville , California for Cetus Corporation , one of the first biotechnology companies, where he was responsible for synthesizing short chains of DNA. Mullis has written that he first conceived the idea for PCR while cruising along the Pacific Coast Highway one night in his car.
In Scientific American , Mullis summarized the procedure: "Beginning with a single molecule of the genetic material DNA, the PCR can generate billion similar molecules in an afternoon. The reaction is easy to execute. It requires no more than a test tube, a few simple reagents, and a source of heat. Mullis was awarded the Nobel Prize in Chemistry in for his invention, seven years after he and his colleagues at Cetus first put his proposal to practice.
Saiki and H. Some controversies have remained about the intellectual and practical contributions of other scientists to Mullis' work, and whether he had been the sole inventor of the PCR principle see below.
The DNA polymerases initially employed for in vitro experiments presaging PCR were unable to withstand these high temperatures. The DNA polymerase isolated from T. The Taq polymerase enzyme was also covered by patents. There have been several high-profile lawsuits related to the technique, including an unsuccessful lawsuit brought by DuPont.
The pharmaceutical company Hoffmann-La Roche purchased the rights to the patents in and currently holds those that are still protected. A related patent battle over the Taq polymerase enzyme is still ongoing in several jurisdictions around the world between Roche and Promega. The legal arguments have extended beyond the lives of the original PCR and Taq polymerase patents, which expired on March 28, From Wikipedia, the free encyclopedia.
For other uses, see PCR disambiguation. This article may be too technical for most readers to understand. Please help improve it to make it understandable to non-experts , without removing the technical details.
October Learn how and when to remove this template message. Main article: PCR optimization. See also: Use of DNA in forensic entomology. Main article: Variants of PCR.
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