Many of the common problems with PCR and RT-PCR are identified during 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 below.

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