Extracted from Nucleic Acid Sample Preparation for Downstream Analyses, GE Healthcare, 2007

Many of the common problems with PCR and RT-PCR are identified following agarose gel electrophoresis of the reaction products. These include the absence of the expected amplification product, the presence of nonspecific products, excessive smearing, and the presence of a “primer dimer” band. A summary of the possible causes and solutions for these problems is provided in Table 7.4.

Table 7.4.Possible causes and solutions for problems with PCR and RT-PCR amplification.
Materials
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