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Open survey. In: Facts Methods and Technology. What is PCR? He was awarded the Nobel Prize in Chemistry in for his pioneering work. PCR is a common tool used in medical and biological research labs. It is used in the early stages of processing DNA for sequencing , for detecting the presence or absence of a gene to help identify pathogens during infection, and when generating forensic DNA profiles from tiny samples of DNA.
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Your Cart. Current Items 0. Traditional methods of cloning a DNA sequence into a vector and replicating it in a living cell often require days or weeks of work, but amplification of DNA sequences by PCR requires only hours. While most biochemical analyses, including nucleic acid detection with radioisotopes, require the input of significant amounts of biological material, the PCR process requires very little.
Thus, PCR can achieve more sensitive detection and higher levels of amplification of specific sequences in less time than previously used methods. These features make the technique extremely useful, not only in basic research, but also in commercial uses, including genetic identity testing, forensics, industrial quality control and in vitro diagnostics.
However, PCR has evolved far beyond simple amplification and detection, and many extensions of the original PCR method have been described. This chapter provides an overview of different types of PCR methods, applications and optimization. A typical amplification reaction includes target DNA, a thermostable DNA polymerase, two oligonucleotide primers, deoxynucleotide triphosphates dNTPs , reaction buffer and magnesium.
Once assembled, the reaction is placed in a thermal cycler, an instrument that subjects the reaction to a series of different temperatures for set amounts of time. This series of temperature and time adjustments is referred to as one cycle of amplification. Each PCR cycle theoretically doubles the amount of targeted sequence amplicon in the reaction. Ten cycles theoretically multiply the amplicon by a factor of about one thousand; 20 cycles, by a factor of more than a million in a matter of hours.
Each cycle of PCR includes steps for template denaturation, primer annealing and primer extension. In the denaturation process, the two intertwined strands of DNA separate from one another, producing the necessary single-stranded DNA template for replication by the thermostable DNA polymerase.
At this temperature, the oligonucleotide primers can form stable associations anneal with the denatured target DNA and serve as primers for the DNA polymerase. This step lasts approximately 15—60 seconds.
The extension step lasts approximately 1—2 minutes. Each step of the cycle should be optimized for each template and primer pair combination. If the temperature during the annealing and extension steps are similar, these two steps can be combined into a single step in which both primer annealing and extension take place.
After 20—40 cycles, the amplified product may be analyzed for size, quantity, sequence, etc. Yet numerous instances exist in which amplification of RNA would be preferred. The ideal reverse transcriptase is robust highly active under a variety of conditions and converts all primed RNA within a sample to cDNA, regardless of its abundance, length or secondary structure. Genetic engineering and development of proprietary RT-enhancing buffers have led to the commercial availability of new enzymes that offer superior performance over these naturally occurring RTs.
Some thermostable DNA polymerases e. After this initial reverse transcription step to produce the cDNA template, basic PCR is carried out to amplify the target sequence. The efficiency of the first-strand synthesis reaction, which can be related to the RNA quality, also will significantly affect amplification results. GoScript is available in convenient mixes with either Oligo dT primers or random primers, as part of a complete kit, and as a stand-alone enzyme. Hot-start PCR is a common technique to reduce nonspecific amplification due to assembly of amplification reactions at room temperature.
At room temperature, PCR primers can anneal to template sequences that are not perfectly complementary. This newly synthesized region then acts as a template for primer extension and synthesis of undesired amplification products. Hot-start PCR also can reduce the amount of primer-dimer synthesized by increasing the stringency of primer annealing. At lower temperatures, PCR primers can anneal to each other via regions of complementarity, and the DNA polymerase can extend the annealed primers to produce primer dimer, which often appears as a diffuse band of approximately 50—bp on an ethidium bromide-stained gel.
The formation of nonspecific products and primer-dimer can compete for reagent availability with amplification of the desired product. This omission prevents the polymerase from extending primers until the critical component is added at the higher temperature where primer annealing is more stringent.
However, this method is tedious and increases the risk of contamination. A second, less labor-intensive approach involves the reversible inactivation or physical separation of one or more critical components in the reaction.
The DNA polymerase also can be kept in an inactive state by binding to an oligonucleotide, also known as an aptamer Lin and Jayasena, ; Dang and Jayasena, or an antibody Scalice et al. This bond is disrupted at the higher temperatures, releasing the functional DNA polymerase. Finally, the DNA polymerase can be maintained in an inactive state through chemical modification Moretti, T.
Activity is restored during initial denaturation, allowing hot-start PCR. Amplification of long DNA fragments is desirable for numerous applications such as physical mapping applications Rose, and direct cloning from genomes.
While basic PCR works well when smaller fragments are amplified, amplification efficiency and therefore the yield of amplified fragments decreases significantly as the amplicon size increases over 5kb. This decrease in yield can be attributed to the accumulation of truncated products, which are not suitable substrates for additional cycles of amplification. These products appear as smeared, as opposed to discrete, bands on a gel. In , Wayne Barnes Barnes, and other researchers Cheng et al.
They devised an approach using a mixture of two thermostable polymerases to synthesize longer PCR products. Presumably, when the nonproofreading DNA polymerase e. The proofreading polymerase e. Although the use of two thermostable DNA polymerases can significantly increase yield, other conditions can have a significant impact on the yield of longer PCR products Cheng et al. Logically, longer extension times can increase the yield of longer PCR products because fewer partial products are synthesized.
Extension times depend on the length of the target; times of 10—20 minutes are common. In addition, template quality is crucial. Depurination of the template, which is promoted at elevated temperatures and lower pH, will result in more partial products and decreased overall yield. In long PCR, denaturation time is reduced to 2—10 seconds to decrease depurination of the template.
Additives, such as glycerol and dimethyl sulfoxide DMSO , also help lower the strand-separation and primer-annealing temperatures, alleviating some of the depurination effects of high temperatures. Cheng et al. This optimized enzyme mixture allows efficient amplification of up to 40kb from lambda DNA or 30kb from human genomic DNA.
However, a wide variety of applications, such as determining viral load, measuring responses to therapeutic agents and characterizing gene expression, would be improved by quantitative determination of target abundance. Theoretically, this should be easy to achieve, given the exponential nature of PCR, because a linear relationship exists between the number of amplification cycles and the logarithm of the number of molecules.
In practice, however, amplification efficiency is decreased because of contaminants inhibitors , competitive reactions, substrate exhaustion, polymerase inactivation and target reannealing. As the number of cycles increases, the amplification efficiency decreases, eventually resulting in a plateau effect. Normally, quantitative PCR requires that measurements be taken before the plateau phase so that the relationship between the number of cycles and molecules is relatively linear.
This point must be determined empirically for different reactions because of the numerous factors that can affect amplification efficiency. Because the measurement is taken prior to the reaction plateau, quantitative PCR uses fewer amplification cycles than basic PCR. This can cause problems in detecting the final product because there is less product to detect. To monitor amplification efficiency, many applications are designed to include an internal standard in the PCR.
Amplification of housekeeping genes verifies that the target nucleic acid and reaction components were of acceptable quality but does not account for differences in amplification efficiencies due to differences in product size or primer annealing efficiency between the internal standard and target being quantified.
In competitive PCR, a known amount of a control template is added to the reaction. This template is amplified using the same primer pair as the experimental target molecule but yields a distinguishable product e. The amounts of control and test product are compared after amplification.
While these approaches control for the quality of the target nucleic acid, buffer components and primer annealing efficiencies, they have their own limitations Siebert and Larrick, ; McCulloch et al. Numerous fluorescent and solid-phase assays exist to measure the amount of amplification product generated in each reaction, but they often fail to discriminate amplified DNA of interest from nonspecific amplification products.
Some of these analyses rely on blotting techniques, which introduce another variable due to nucleic acid transfer efficiencies, while other assays were developed to eliminate the need for gel electrophoresis yet provide the requisite specificity. Real-time PCR, which provides the ability to view the results of each amplification cycle, is a popular way of overcoming the need for analysis by electrophoresis.
The use of fluorescently labeled oligonucleotide probes or primers or fluorescent DNA-binding dyes to detect and quantitate a PCR product allows quantitative PCR to be performed in real time. Specially designed instruments perform both thermal cycling to amplify the target and fluorescence detection to monitor PCR product accumulation.
DNA-binding dyes are easy to use but do not differentiate between specific and nonspecific PCR products and are not conducive to multiplex reactions. Fluorescently labeled nucleic acid probes have the advantage that they react with only specific PCR products, but they can be expensive and difficult to design. The dye is simply added to the reaction, and fluorescence is measured at each PCR cycle.
Because fluorescence of these dyes increases dramatically in the presence of double-stranded DNA, DNA synthesis can be monitored as an increase in fluorescent signal. However, preliminary work often must be done to ensure that the PCR conditions yield only specific product.
In subsequent reactions, specific amplification can verified by a melt curve analysis. The product length and sequence affect melting temperature Tm , so the melt curve is used to characterize amplicon homogeneity. Nonspecific amplification can be identified by broad peaks in the melt curve or peaks with unexpected Tm values.
By distinguishing specific and nonspecific amplification products, the melt curve adds a quality control aspect during routine use.
These probes also can be used to detect single nucleotide polymorphisms Lee et al. There are several general categories of real-time PCR probes, including hydrolysis, hairpin and simple hybridization probes. These probes contain a complementary sequence that allows the probe to anneal to the accumulating PCR product, but probes can differ in the number and location of the fluorescent reporters.
During the annealing step, the probe hybridizes to the PCR product generated in previous amplification cycles. The fluor is freed from the effects of the energy-absorbing quencher, and the progress of the reaction and accumulation of PCR product is monitored by the resulting increase in fluorescence.
With this approach, preliminary experiments must be performed prior to the quantitation experiments to show that the signal generated is proportional to the amount of the desired PCR product and that nonspecific amplification does not occur. Hairpin probes, also known as molecular beacons, contain inverted repeats separated by a sequence complementary to the target DNA.
The hairpin probe is designed so that the probe binds preferentially to the target DNA rather than retains the hairpin structure. As the reaction progresses, increasing amounts of the probe anneal to the accumulating PCR product, and as a result, the fluor and quencher become physically separated.
The fluor is no longer quenched, and the level of fluorescence increases. One advantage of this technique is that hairpin probes are less likely to mismatch than hydrolysis probes Tyagi et al. However, preliminary experiments must be performed to show that the signal is specific for the desired PCR product and that nonspecific amplification does not occur.
The use of simple hybridization probes involves two labeled probes or, alternatively, one labeled probe and a labeled PCR primer. In the first approach, the energy emitted by the fluor on one probe is absorbed by a fluor on the second probe, which hybridizes nearby. In the second approach, the emitted energy is absorbed by a second fluor that is incorporated into the PCR product as part of the primer.
Both of these approaches result in increased fluorescence of the energy acceptor and decreased fluorescence of the energy donor. The use of hybridization probes can be simplified even further so that only one labeled probe is required. In this approach, quenching of the fluor by deoxyguanosine is used to bring about a change in fluorescence Crockett and Wittwer, ; Kurata et al. The labeled probe anneals so that the fluor is in close proximity to G residues within the target sequence, and as probe annealing increases, fluorescence decreases due to deoxyguanosine quenching.
With this approach, the location of probe is limited because the probe must hybridize so that the fluorescent dye is very near a G residue. The advantage of simple hybridization probes is their ability to be multiplexed more easily than hydrolysis and hairpin probes through the use of differently colored fluors and probes with different melting temperatures reviewed in Wittwer et al. Many of these suggestions also apply when using other DNA polymerases.
Magnesium is a required cofactor for thermostable DNA polymerases, and magnesium concentration is a crucial factor that can affect amplification success. Template DNA concentration, chelating agents present in the sample e. In the absence of adequate free magnesium, Taq DNA polymerase is inactive. Excess free magnesium reduces enzyme fidelity Eckert and Kunkel, and may increase the level of nonspecific amplification Williams, ; Ellsworth et al. For these reasons, researchers should empirically determine the optimal magnesium concentration for each target.
To do so, set up a series of reactions containing 1. The effect of magnesium concentration and the optimal concentration range can vary with the particular DNA polymerase. For example, the performance of Pfu DNA polymerase seems depend less on magnesium concentration, but when optimization is required, the optimal concentration is usually in the range of 2—6mM.
Before assembling the reactions, be sure to thaw the magnesium solution completely prior to use and vortex the magnesium solution for several seconds before pipetting. Magnesium chloride solutions can form concentration gradients as a result of multiple freeze-thaw cycles, and vortex mixing is required to obtain a uniform solution. These two steps, though seemingly simple, eliminate the cause of many failed experiments.
Some scientists prefer to use reaction buffers that already contain MgCl 2 at a final concentration of 1. It should be noted, however, that Hu et al. The free magnesium changes of 0. They postulated that magnesium chloride precipitates as a result of multiple freeze-thaw cycles. Figure 2. Effects of magnesium concentration on amplification.
Amplifications were performed using various Mg concentrations to demonstrate the effect on the amplification of a 1. The reaction products were analyzed by agarose gel electrophoresis followed by ethidium bromide staining. Most reaction buffers consist of a buffering agent, most often a Tris-based buffer, and salt, commonly KCl.
The buffer regulates the pH of the reaction, which affects DNA polymerase activity and fidelity. The buffer also contains a compound that increases the density of the sample so that it will sink into the well of the agarose gel, allowing reactions to be directly loaded onto an agarose gel without the need for loading dye.
Both buffers are supplied at pH 8. We recommend using 1—1. In most cases, this is an excess of enzyme, and adding more enzyme will not significantly increase product yield.
Pipetting errors are a frequent cause of excessive enzyme levels. PCR primers define the target region to be amplified and generally range in length from 15—30 bases. Also, avoid primers with intra- or intermolecular complementary sequences to minimize the production of primer-dimer.
Intramolecular regions of secondary structure can interfere with primer annealing to the template and should be avoided. Primers can be designed to include sequences that are useful for downstream applications. Successful amplification depends on DNA template quantity and quality. Reagents commonly used to purify nucleic acids salts, guanidine, proteases, organic solvents and SDS are potent inactivators of DNA polymerases.
For example, 0. In some cases, the inhibitor is not introduced into the reaction with the nucleic acid template. A good example of this is an inhibitory substance that can be released from polystyrene or polypropylene upon exposure to ultraviolet light Pao et al.
If an amplification reaction fails and you suspect the DNA template is contaminated with an inhibitor, add the suspect DNA preparation to a control reaction with a DNA template and primer pair that has amplified well in the past. Failure to amplify the control DNA usually indicates the presence of an inhibitor. Additional steps to clean up the DNA preparation, such as phenol:chloroform extraction or ethanol precipitation, may be necessary.
The amount of template required for successful amplification depends upon the complexity of the DNA sample. Conversely, a 1kb target sequence in the human genome 3. Thus, approximately 1,,fold more human genomic DNA is required to maintain the same number of target copies per reaction. Reactions with too little DNA template will have low yields, while reactions with too much DNA template can be plagued by nonspecific amplification.
We recommend diluting the previous amplification reaction to , before reamplification. The two most commonly altered cycling parameters are annealing temperature and extension time.
The lengths and temperatures for the other steps of a PCR cycle do not usually vary significantly. However in some cases, the denaturation cycle can be shortened or a lower denaturation temperature used to reduce the number of depurination events, which can lead to mutations in the PCR products.
Using an annealing temperature slightly higher than the primer Tm will increase annealing stringency and can minimize nonspecific primer annealing and decrease the amount of undesired products synthesized. Using an annealing temperature lower than the primer Tm can result in higher yields, as the primers anneal more efficiently at the lower temperature.
In many cases, nonspecific amplification and primer-dimer formation can be reduced through optimization of annealing temperature, but if undesirable PCR products remain a problem, consider incorporating one of the many hot-start PCR methods. Oligonucleotide synthesis facilities will often provide an estimate of a primer's Tm. The Tm also can be calculated using the Biomath Calculators. Numerous formulas exist to determine the theoretical Tm of nucleic acids Baldino, Jr.
The formula below can be used to estimate the melting temperature for oligonucleotides:. The length of the extension cycle, which may need to be optimized, depends on PCR product size and the DNA polymerase being used. PCR typically involves 25—35 cycles of amplification.
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