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PCR additives

- PCR additives, including formamide, DMSO, glycerol, betaine, and PCRx Enhancer Solution can enhance amplification. Their proposed mechanism is to lower the melting temperature, thereby aiding primer annealing and helping the DNA polymerase extend through regions of secondary structure.
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- Amplification of a DNA target by the polymerase chain reaction (PCR) often requires laborious optimization efforts. In this regard, the use of certain organic chemicals such as dimethyl sulfoxide, polyethylene glycol, betaine and formamide as cosolvents has been found to be very helpful. Unfortunately, very little is known about the precise structural features that make these additives effective and, accordingly, the number of such chemicals currently known to enhance PCR is limited
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The enhancement of PCR amplification by low molecular weight amides
Raj Chakrabarti and Clarence E. Schutt, 2001

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- A capture assay for nucleic acids that mimic enzyme linked immunosorbant assays. In this assay, PCR products hybridized to an immobilized capture probe.
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PCR-ELISA is PCR that is followed by capture and hybridization in microtiter plates to labeled probes and detection similar to ELISA.
Plum Pox Potyvirus Disease of Stone Fruits
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Laurene Levy
et al., 2000

PCR-RFLP (Polymerase Chain Reaction - Restriction Fragment Length Polymorphism).

Alternative denomination: cleaved amplified polymorphic sequence
-Following PCR amplification of a locus, the amplicon is treated with a restriction endonuclease. If the recognition site for this enzyme is present in the amplicon, two or more restriction fragments are generated. Thus sequence variation between individuals at the recognition site(s) can be detected by electrophoresis.
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PCR-SSCP (Polymerase chain reaction single-strand conformation polymorphism)

PCR-SSCP is a simple procedure where denatured PCR products are electrophoresed through a non-denaturing polyacrylamide gel. The single strands adopt primary conformations that are dependent on their nucleotide sequence and this determines the rate at which they migrate through the gel matrix. Each PCR product with a different sequence therefore, will be theoretically represented by two bands corresponding to the two strands of the amplified molecule
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Pfu DNA polymerase

Pfu DNA polymerase is an enzyme found in the hyperthermophilic archaeon Pyrococcus furiosus, where it functions in vivo to replicate the organism's DNA. In vitro, Pfu is used to quickly amplify DNA in the Polymerase Chain Reaction, where the enzyme serves the central function of copying a new strand of DNA during each extension step.The main difference between Pfu and alternative enzymes is Pfu's superior thermostability and 'proofreading' properties compared to other thermostable polymerases.
Pfu DNA polymerase , Wikipedia, The Free Encyclopedia

Point mutation

- A mutation that can be mapped to one specific site within a locus. A small mutation that consists of the replacement (transition or transversion); addition; or deletion ( frameshift) of one or a few bases.
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- An alteration in DNA sequence caused by a single nucleotide base change, insertion, or deletion
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- A change in a single base pair of DNA.
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Polyacrylamide gel electrophoresis (PAGE)

- Separation of molecules through a polyacrylamide gel matrix in an electric field. Separation may depend upon size and charge of the molecules.
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Electrophoresis of nucleic acids and proteins through polyacrylamide gels.


An enzyme which assembles nucleic acid residues into DNA or RNA polymers. Polymerases work from the DNA complement of the sequence to be built. DNA polymerases copy DNA to DNA to replicate the genome before mitosis, while RNA polymerases copy DNA to RNA as the first step in gene transcription
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Glossary of Biotechnology Terms

- General term for enzymes that carry out the synthesis of nucleic acid, using a pre-existing nucleic acid template and appropriate nucleotides (viz. ribonucleotides for RNA and deoxyribonucleotides for DNA).
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- A polymerase is a naturally occurring enzyme, a biological macromolecule that catalyzes the formation and repair of DNA (and RNA). The accurate replication of all living matter depends on this activity
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Polymerase Chain Reaction : See PCR


- A polymorphism is a DNA sequence variation that is common in the population...The arbitrary cut-off point between a mutation and a polymorphism is 1 per cent. That is, to be classed as a polymorphism, the least common allele must have a frequency of 1per cent or more in the population. If the frequency is lower that this, the allele is regarded as a mutation. ...
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Mutation or polymorphism?
Richard Twyman, 2003

- Differences in DNA sequences that occur naturally in a population. Single nucleotide substitutions, insertions and deletions of nucleotides and repetitive sequences (microsatellites) are all examples of a polymorphism. The position at which such a sequence difference is found is a polymorphic site.
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PCR primers are short fragments of single stranded DNA (15-30 nucleotides in length) that are complementary to DNA sequences that flank the target region of interest. The purpose of PCR primers is to provide a “free” 3’-OH group to which the DNA polymerase can add dNTPs.
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- A primer is a short segment of nucleotides which is complementary to a section of the DNA which is to be amplified in the PCR reaction. Primers are annealed to the denatured DNA template to provide an initiation site for the elongation of the new DNA molecule
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- A short piece of DNA, usually synthetic, that defines the specific site on a DNA molecule for a DNA polymerase to start making new DNA. An essential ingredient in the PCR reaction mix.
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- Single-stranded DNA or RNA molecules of specific base sequence, labeled either radioactively or immunologically, that are used to detect the complementary base sequence by hybridization.
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- Defined nucleic acid (DNA or RNA) that can be used to identify, usually through autoradiography, specific DNA or RNA molecules bearing the complementary sequence. A labeled (radioactive; antigen; enzyme; fluorescent) nucleic acid complementary to the sequence being searched for in a restriction digest, genome library, northern blot or in situ hybridization.
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- A finite nucleic acid piece that can be used to identify specific DNA segments bearing its complementary sequence.
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- In DNA synthesis, the process of recognizing a basepair error during the polymerization events and correcting it.
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- Fidelity of DNA replication in vivo is achieved, in part, by the proof-reading activity of the DNA polymerase. When an errant nucleotide is incorporated and forms a mismatch with the template, it is removed by a 3´ to 5´ exonuclease proof-reading activity associated with the polymerase. Some thermostable DNA polymerases have proof-reading activity, a characteristic desirable for accurate DNA amplification and for PCR amplification of long DNA sequences. The thermostable DNA polymerase most widely used for PCR is Taq polymerase, which lacks proof-reading activity.
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Detection of known mutation by proof-reading PCR
Wanli Bi and  Peter J. Stambrook, 1998


- Laboratory procedures manual.
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