Polymerase chain reaction primer selection

Cuypers, H. T. M etal. (1992). Storage conditions of blood samples and primer selection affect the yield of cDNA polymerase chain reaction products of hepatitis C virus. J. Clin. Microbiol 30, 3220-3224. 

A set of sense and antisense primers should be selected to synthesize specific cDNAs and also to detect the amplified messages of the genes, complementary to their specific gene sequences. It is important to consider the following points while designing the primers for reverse transcriptase and polymerase chain reaction ... 

The polymerase chain reaction utilizes a thermostable DNA polymerase to amplify DNA through a series of temperature cycle steps. The key to the specificity of the reaction is the selection of oligonucleotide primers that hybridize to the opposite strands of the DNA being tested, about 400-2000 bp apart. If the sequence of the primers is unique within the genome, and the primers hybridize to the target DNA at a high enough temperature to avoid close matches (various... 

Figure 9.4. Request form for primer selection. The nucleotide sequence of a target DNA for polymerase chain reaction can be submitted for primer selection at Primer3 server.

Segal GH, Jorgensen T, Masih AS, Braylan RC. Optimal primer selection for clonahty assessment by polymerase chain reaction analysis I. Low grade B-ceU lymphoprohferative disorders of nonfolUcular center cell type. Hum Pathol 1994 25 1269-75. 

After both selective regimes, microbes were isolated as single colonies, DNA isolated and primers for 16S rRNA genes were used to amplify, fragments with polymerase chain reactions as previously described" Comparisons of the DNA sequence from the various colonies with those in DNA sequence data bases allowed the identification of the recovered microbes. 

Rychlik, W. 1993. Selection of primers for polymerase chain reaction. In Methods in molecular biology, Vol. 15 PCR protocols Current methods and applications, ed. B. A. White, 31 40. Totowa, NJ Humana. 

More sensitive is the polymerase chain reaction (PCR). Using two PCR primers, even small amounts of DNA can be detected, due to selective amplification (Newton and Graham, 1997). Thus, PCR allows the unambiguous identification of animal and plant species in food or feedstuffs. Moreover, the unique specificity, selectivity, and sensitivity of PCR affords the analysis of complex matrices (Meyer et al., 1993). In addition, primers (in contrast to antibodies) as starting points for PCR are independent of commercial sources and easily accessible to everyone. 

Segal, S., Do, D., Jorgensen, J. et al. (1994) Optimal primer selection for clonality assessment by polymerase chain reaction analysis 1 low grade B-cell lymphoproliferative disorders of nonfollicular type. Hum Pathol, 25, 1269-1275. 

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