PCR-based analysis

A third type of polymorphism is due to tandem repeats of short sequences that can be detected by PCR-based analysis. These are known variously as microsatellites, short tandem repeats (STRs), STR polymorphisms (STRPs), or short sequence length polymorphisms (SSLPs). These repeat sequences usually consist of two, three, or four nucleotides and are plentiful in most organisms. All PCR-converted STR markers (those for which a pair of oligonucleotides flanking the polymorphic site suitable for PCR amplification of the locus has been designed) are considered to be STSs. The advent of PCR-based analysis quickly made microsatellites the markers of choice for mapping. 

With this chip, DNA can be concentrated by a factor of up to two orders of magnitude. Khandurina et al. also reported an integrated system for polymerase chain reaction (PCR)-based analysis on a microchip with this preconcentration technique. The chip layout was similar to that depicted in Figure 50.30, with an additional Peltier thermoelectric element integrated for the DNA amplification. With this chip, a 25-fold preconcentration of the DNA sample due to the semipermeable silicate membrane was observed. 

The second NIST human DNA SRM is a PCR-based DNA Profiling Standard. The PCR was first described by Saiki et al. (1985,1989). Since then it has developed into a highly versatile and widely used detection, identification, manipulation and analysis tool in molecular biology, including DNA profiling. In brief, two short synthetic oligonucleotides, or primers, are used to define an intervening DNA sequence... 

Newton, L.A., Chilton, N.B., Beveridge, I., Hoste, H., Nansen, P. and Gasser, R.B. (1998a) Genetic markers for strongylid nematodes of livestock defined by PCR-based restriction analysis of spacer rDNA. Acta Tropica 69,1-15. 

J. Khandurina, T.E. McKnight, S.C. Jacobson, L.C. Waters, R.S. Foote, and J.M. Ramsey, Integrated system for rapid PCR-based DNA analysis in microfluidic devices. Anal. Chem. 72, 2995-3000 (2000). 

With the currently available systems for PCR-based detection and identification, however, qualitative information about the presence or absence of a certain fimgus can be obtained and this should be used to advantage in food and feed quality control because the technology has the power to provide insights into the mycotoxigenic potential of analyzed samples. This information can then be used in order to decide whether samples should proceed down the process of production or should be retained for further analysis of mycotoxins. PCR-based multiplex systems... 

Demeke, T., Clear, R. M., Patrick, S. K., and Gaba, D. (2005). Species specific PCR-based assays for the detection of Fusarium species and a comparison with the whole seed agar plate method and trichothecene analysis. Int. J. Food Microbiol. 103, 271-284. 

Munro, N.J., Hiihmer, A.F.R., Landers, J.P., Robust polymeric microchannel coating for microchip-based analysis of neat PCR products. Anal. Chem. 2001, 73, 1784-1794. 

Zhang, Q.T., Wang, W.H., Zhang, H.S., Wang, Y.L., Temperature analysis of continuous-flow micro-PCR based on FEA. Sensors Actuators B 2002, 82, 75-81. 

Genomic tools 31 This method takes advantage of select genomic (microarray-or PCR-based approaches) and proteomic (antibody array analysis) tools to identify the receptors for growth factors, hormones, cytokines, and other components of cell signaling pathways expressed by a culture of interest. 

---