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A strip of eight PCR tubes, each containing a 100 μL reaction mixture Placing a strip of eight PCR tubes into a thermal cycler. The polymerase chain reaction (PCR) is a method widely used to make millions to billions of copies of a specific DNA sample rapidly, allowing scientists to amplify a very small sample of DNA (or a part of it) sufficiently to enable detailed study.
The free NCBI tool Primer-BLAST integrates primer design and BLAST search into one application, [6] as do commercial software products such as ePrime and Beacon Designer. Computer simulations of theoretical PCR results ( Electronic PCR ) may be performed to assist in primer design by giving melting and annealing temperatures, etc. [ 7 ]
The primer design for all primers pairs has to be optimized so that all primer pairs can work at the same annealing temperature during PCR. Multiplex-PCR was first described in 1988 as a method to detect deletions in the dystrophin gene. [1] It has also been used with the steroid sulfatase gene. [2]
However, dsDNA dyes such as SYBR Green will bind to all dsDNA PCR products, including nonspecific PCR products (such as primer dimer). This can potentially interfere with, or prevent, accurate monitoring of the intended target sequence. In real-time PCR with dsDNA dyes the reaction is prepared as usual, with the addition of fluorescent dsDNA dye.
Random amplified polymorphic DNA (RAPD), pronounced "rapid", [1] is a type of polymerase chain reaction (PCR), but the segments of DNA that are amplified are random. [2] The scientist performing RAPD creates several arbitrary, short primers (10–12 nucleotides), then proceeds with the PCR using a large template of genomic DNA, hoping that fragments will amplify.
Conventional PCR requires primers complementary to the termini of the target DNA. The amount of product from the PCR increases with the number of temperature cycles that the reaction is subjected to. A commonly occurring problem is primers binding to incorrect regions of the DNA, giving unexpected products.
The protocols for 5' or 3' RACES differ slightly. 5' RACE-PCR begins using mRNA as a template for a first round of cDNA synthesis (or reverse transcription) reaction using an anti-sense (reverse) oligonucleotide primer that recognizes a known sequence in the middle of the gene of interest; the primer is called a gene specific primer (GSP). The ...
The last 10-12 bases at the 3' end of a primer are sensitive to initiation of polymerase extension and general primer stability on the template binding site. The effect of a single mismatch at these last 10 bases at the 3' end of the primer depends on its position and local structure, reducing the primer binding, selectivity, and PCR efficiency.
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