Polymerase chain reaction conditions

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. 

Fig. 9.4 Establishment of the quantitative methylation-specific polymerase chain reaction (MSP) analytical procedure. The ABI PRISM 7900 HT Sequence Detector system was used to perform real-time polymerase chain reaction (PCR) using MSP primers and bisulfite-modified template DNA. Upper panels Setting up the conditions to obtain the standard curves with 50% (A) or 25% (B) sequential dilution of the template. Lower panels The amplification curves on the left represent P-actin, unmethylated, and methylated MSP products, respectively, for reelin (RELN) (C). Amplification curves were compared at the set threshold before 40 cycles. Amplification curves from various samples are shown in the lower panel right (D)...

Recently, another interesting application of nitrilases has been demonstrated for the synthesis of pregabalin-the API of the neurophatic pain drug Lyrica. In this approach, the key step is the resolution of racemic isobutylsuccinonitrile (Scheme 10.8) [18], the process takes place with total regio- and stereoselectivity, and the (S)-acid is obtained and the (R)-substrate can be recycled under basic conditions. To improve the biocatalytic step, directed evolution was applied using the electronic polymerase chain reaction and in the first round of evolution a single C236S mutation led to a mutant with 3-fold increase in activity [19]. 

As the NNRTIs are structurally diverse and yet bind to RT at a common site, the similar occurrence of resistance-conferring mutations is not surprising. As a consequence, the effectiveness of other NNRTIs may be compromised by the emergence of HIV-1 variants caused by a previous NNRTI therapy (Sardana et ah, 1992). Experiments were performed in which HIV-1 strains (JR-CSF or ME) are cultured in human lymphocytes in the presence of partially inhibitory concentrations of delavirdine (Dueweke et al., 1993b). These conditions yield mutants that are 100-fold resistant. In order to determine what mutation(s) occurs, PCR (polymerase chain reaction) amplification and DNA sequence analysis of the RT coding region were applied and indicated that mutation P236L had occurred. Mutations at amino acids 181 or 183, which have been associated with resistance to other NNRTIs, are not detected. 

Polymerase chain reaction (PCR) is a method for amplifying DNA from a small amount of DNA catalyzed by thermostable DNA polymerase under appropriate reaction conditions with a pair of primers (oligonucleotides) that are complementary to DNA. K. Mullis, who invented the technique in the 1980s, was awarded a Nobel prize in 1994. Since its invention, various refinements and modifications have been described, and several review articles and books have been written on the subject [17-20]. 

The techniques that have proven most valuable in toxicology include those of molecular cloning, the polymerase chain reaction, and the production of genetically modified mice. Microarrays, used to evaluate gene expression under various conditions, including exposure to toxicants, are becoming more important and, in concert with other molecular techniques, are being considered as potentially useful in such applied areas as hazard assessment and risk analysis. 

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